\n

\n \n 2023\n \n \n (1)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n A NuRD for all seasons.\n \n \n \n \n\n\n \n Reid, X.; Low, J.; and Mackay, J.\n\n\n \n\n\n\n Trends in Biochemical Sciences, 48(1): 11-25. 2023.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 6 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Reid202311,\nauthor={Reid, X.J. and Low, J.K.K. and Mackay, J.P.},\ntitle={A NuRD for all seasons},\njournal={Trends in Biochemical Sciences},\nyear={2023},\nvolume={48},\nnumber={1},\npages={11-25},\ndoi={10.1016/j.tibs.2022.06.002},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85133708937&doi=10.1016%2fj.tibs.2022.06.002&partnerID=40&md5=3370cc24e29c98a39f84ce5af7e56ead},\naffiliation={School of Life and Environmental Sciences, University of SydneyNSW  2006, Australia},\nabstract={The nucleosome-remodeling and deacetylase (NuRD) complex is an essential transcriptional regulator in all complex animals. All seven core subunits of the complex exist as multiple paralogs, raising the question of whether the complex might utilize paralog switching to achieve cell type-specific functions. We examine the evidence for this idea, making use of published quantitative proteomic data to dissect NuRD composition in 20 different tissues, as well as a large-scale CRISPR knockout screen carried out in >1000 human cancer cell lines. These data, together with recent reports, provide strong support for the idea that distinct permutations of the NuRD complex with tailored functions might regulate tissue-specific gene expression programs. © 2022 Elsevier Ltd},\nauthor_keywords={chromatin remodeling;  NuRD complex;  paralog switching;  transcriptional regulation},\nkeywords={nucleosome remodeling and deacetylase;  regulator protein;  unclassified drug;  histone deacetylase, cancer cell line;  case study;  cell specificity;  cells by body anatomy;  clustered regularly interspaced short palindromic repeat;  data analysis;  enzyme binding;  enzyme specificity;  gene expression regulation;  gene mutation;  genetic conservation;  human;  nonhuman;  paralogy;  protein assembly;  protein content;  protein processing;  proteomics;  quantitative analysis;  Review;  tissue specificity;  animal;  cell line;  genetics;  nucleosome;  proteomics, Animals;  Cell Line;  Humans;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Nucleosomes;  Proteomics},\ncorrespondence_address1={Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Elsevier Ltd},\nissn={09680004},\ncoden={TBSCD},\npubmed_id={35798615},\nlanguage={English},\nabbrev_source_title={Trends Biochem. Sci.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2022\n \n \n (8)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families.\n \n \n \n \n\n\n \n Zhong, Y.; Moghaddas Sani, H.; Paudel, B.; Low, J.; Silva, A.; Mueller, S.; Deshpande, C.; Panjikar, S.; Reid, X.; Bedward, M.; van Oijen, A.; and Mackay, J.\n\n\n \n\n\n\n Nature Communications, 13(1). 2022.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Zhong2022,\nauthor={Zhong, Y. and Moghaddas Sani, H. and Paudel, B.P. and Low, J.K.K. and Silva, A.P.G. and Mueller, S. and Deshpande, C. and Panjikar, S. and Reid, X.J. and Bedward, M.J. and van Oijen, A.M. and Mackay, J.P.},\ntitle={The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families},\njournal={Nature Communications},\nyear={2022},\nvolume={13},\nnumber={1},\ndoi={10.1038/s41467-022-35002-0},\nart_number={7524},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85143508092&doi=10.1038%2fs41467-022-35002-0&partnerID=40&md5=bd607e05153470df634725d1ba19b8ec},\naffiliation={School of Life and Environmental Sciences, University of SydneyNSW  2006, Australia; Molecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW  2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW  2522, Australia; Australian Synchrotron, Clayton, VIC  3168, Australia; Department of Molecular Biology and Biochemistry, Monash University, Clayton, VIC  3800, Australia},\nabstract={CHD4 is an essential, widely conserved ATP-dependent translocase that is also a broad tumour dependency. In common with other SF2-family chromatin remodelling enzymes, it alters chromatin accessibility by repositioning histone octamers. Besides the helicase and adjacent tandem chromodomains and PHD domains, CHD4 features 1000 residues of N- and C-terminal sequence with unknown structure and function. We demonstrate that these regions regulate CHD4 activity through different mechanisms. An N-terminal intrinsically disordered region (IDR) promotes remodelling integrity in a manner that depends on the composition but not sequence of the IDR. The C-terminal region harbours an auto-inhibitory region that contacts the helicase domain. Auto-inhibition is relieved by a previously unrecognized C-terminal SANT-SLIDE domain split by ~150 residues of disordered sequence, most likely by binding of this domain to substrate DNA. Our data shed light on CHD4 regulation and reveal strong mechanistic commonality between CHD family members, as well as with ISWI-family remodellers. © 2022, The Author(s).},\nkeywords={enzyme activity;  inhibition;  pigment;  tumor, family, Family},\ncorrespondence_address1={Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au; van Oijen, A.M.; Molecular Horizons, Australia; email: vanoijen@uow.edu.au},\npublisher={Nature Research},\nissn={20411723},\npubmed_id={36473839},\nlanguage={English},\nabbrev_source_title={Nat. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Mucosal TLR2-activating protein-based vaccination induces potent pulmonary immunity and protection against SARS-CoV-2 in mice.\n \n \n \n \n\n\n \n Ashhurst, A.; Johansen, M.; Maxwell, J.; Stockdale, S.; Ashley, C.; Aggarwal, A.; Siddiquee, R.; Miemczyk, S.; Nguyen, D.; Mackay, J.; Counoupas, C.; Byrne, S.; Turville, S.; Steain, M.; Triccas, J.; Hansbro, P.; Payne, R.; and Britton, W.\n\n\n \n\n\n\n Nature Communications, 13(1). 2022.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Mucosal$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Ashhurst2022,\nauthor={Ashhurst, A.S. and Johansen, M.D. and Maxwell, J.W.C. and Stockdale, S. and Ashley, C.L. and Aggarwal, A. and Siddiquee, R. and Miemczyk, S. and Nguyen, D.H. and Mackay, J.P. and Counoupas, C. and Byrne, S.N. and Turville, S. and Steain, M. and Triccas, J.A. and Hansbro, P.M. and Payne, R.J. and Britton, W.J.},\ntitle={Mucosal TLR2-activating protein-based vaccination induces potent pulmonary immunity and protection against SARS-CoV-2 in mice},\njournal={Nature Communications},\nyear={2022},\nvolume={13},\nnumber={1},\ndoi={10.1038/s41467-022-34297-3},\nart_number={6972},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85141834495&doi=10.1038%2fs41467-022-34297-3&partnerID=40&md5=b09a7df739b18ae623d85f1eaf7fe6b4},\naffiliation={School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW  2006, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW  2006, Australia; School of Chemistry, The University of Sydney, Sydney, NSW  2006, Australia; The University of Sydney Institute for Infectious Diseases, Sydney, NSW  2006, Australia; Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, NSW  2006, Australia; Centre for Inflammation, Centenary Institute and Faculty of Science, School of Life Sciences, University of Technology, Sydney, NSW  2007, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW  2006, Australia; Kirby Institute, Sydney, NSW  2052, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW  2006, Australia; Westmead Institute for Medical Research, Centre for Immunology and Allergy Research, Westmead, NSW  2145, Australia; Department of Clinical Immunology, Royal Prince Alfred Hospital, Camperdown, NSW  2050, Australia},\nabstract={Current vaccines against SARS-CoV-2 substantially reduce mortality, but protection against infection is less effective. Enhancing immunity in the respiratory tract, via mucosal vaccination, may provide protection against infection and minimise viral spread. Here, we report testing of a subunit vaccine in mice, consisting of SARS-CoV-2 Spike protein with a TLR2-stimulating adjuvant (Pam2Cys), delivered to mice parenterally or mucosally. Both routes of vaccination induce substantial neutralising antibody (nAb) titres, however, mucosal vaccination uniquely generates anti-Spike IgA, increases nAb in the serum and airways, and increases lung CD4+ T-cell responses. TLR2 is expressed by respiratory epithelia and immune cells. Using TLR2 deficient chimeric mice, we determine that TLR2 expression in either compartment facilitates early innate responses to mucosal vaccination. By contrast, TLR2 on hematopoietic cells is essential for optimal lung-localised, antigen-specific responses. In K18-hACE2 mice, vaccination provides complete protection against disease and sterilising lung immunity against SARS-CoV-2, with a short-term non-specific protective effect from mucosal Pam2Cys alone. These data support mucosal vaccination as a strategy to improve protection in the respiratory tract against SARS-CoV-2 and other respiratory viruses. © 2022, The Author(s).},\nkeywords={antibody;  immunity;  infectious disease;  severe acute respiratory syndrome;  vaccination, coronavirus spike glycoprotein;  neutralizing antibody;  spike protein, SARS-CoV-2;  TLR2 protein, human;  Tlr2 protein, mouse;  toll like receptor 2;  virus antibody;  virus vaccine, animal;  human;  lung;  mouse;  mucosal immunity;  prevention and control;  vaccination, Animals;  Antibodies, Neutralizing;  Antibodies, Viral;  COVID-19;  COVID-19 Vaccines;  Humans;  Immunity, Mucosal;  Lung;  Mice;  SARS-CoV-2;  Spike Glycoprotein, Coronavirus;  Toll-Like Receptor 2;  Vaccination;  Viral Vaccines},\ncorrespondence_address1={Payne, R.J.; School of Chemistry, Australia; email: richard.payne@sydney.edu; Britton, W.J.; Tuberculosis Research Program Centenary Institute, Australia; email: w.britton@centenary.org.au},\npublisher={Nature Research},\nissn={20411723},\npubmed_id={36379950},\nlanguage={English},\nabbrev_source_title={Nat. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine.\n \n \n \n \n\n\n \n Dowman, L.; Kulkarni, S.; Alegre-Requena, J.; Giltrap, A.; Norman, A.; Sharma, A.; Gallegos, L.; Mackay, A.; Welegedara, A.; Watson, E.; van Raad, D.; Niederacher, G.; Huhmann, S.; Proschogo, N.; Patel, K.; Larance, M.; Becker, C.; Mackay, J.; Lakhwani, G.; Huber, T.; Paton, R.; and Payne, R.\n\n\n \n\n\n\n Nature Communications, 13(1). 2022.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Site-selective$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Dowman2022,\nauthor={Dowman, L.J. and Kulkarni, S.S. and Alegre-Requena, J.V. and Giltrap, A.M. and Norman, A.R. and Sharma, A. and Gallegos, L.C. and Mackay, A.S. and Welegedara, A.P. and Watson, E.E. and van Raad, D. and Niederacher, G. and Huhmann, S. and Proschogo, N. and Patel, K. and Larance, M. and Becker, C.F.W. and Mackay, J.P. and Lakhwani, G. and Huber, T. and Paton, R.S. and Payne, R.J.},\ntitle={Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine},\njournal={Nature Communications},\nyear={2022},\nvolume={13},\nnumber={1},\ndoi={10.1038/s41467-022-34530-z},\nart_number={6885},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85141656405&doi=10.1038%2fs41467-022-34530-z&partnerID=40&md5=a53827926678d88d70ffa43b849e121f},\naffiliation={School of Chemistry, The University of Sydney, Sydney, NSW  2006, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW  2006, Australia; Department of Chemistry, Colorado State University, Fort Collins, CO  80523-1872, United States; Australian Research Council Centre of Excellence in Exciton Science, The University of Sydney, Sydney, NSW  2006, Australia; Research School of Chemistry, Australian National University, Canberra, ACT  2601, Australia; Institute of Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria; School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW  2006, Australia; Charles Perkins Centre and School of Medical Sciences, The University of Sydney, Sydney, NSW  2006, Australia},\nabstract={The importance of modified peptides and proteins for applications in drug discovery, and for illuminating biological processes at the molecular level, is fueling a demand for efficient methods that facilitate the precise modification of these biomolecules. Herein, we describe the development of a photocatalytic method for the rapid and efficient dimerization and site-specific functionalization of peptide and protein diselenides. This methodology, dubbed the photocatalytic diselenide contraction, involves irradiation at 450 nm in the presence of an iridium photocatalyst and a phosphine and results in rapid and clean conversion of diselenides to reductively stable selenoethers. A mechanism for this photocatalytic transformation is proposed, which is supported by photoluminescence spectroscopy and density functional theory calculations. The utility of the photocatalytic diselenide contraction transformation is highlighted through the dimerization of selenopeptides, and by the generation of two families of protein conjugates via the site-selective modification of calmodulin containing the 21st amino acid selenocysteine, and the C-terminal modification of a ubiquitin diselenide. © 2022, The Author(s).},\nkeywords={calmodulin;  iridium;  peptides and proteins;  phosphine;  selenocysteine;  selenoprotein;  amino acid;  peptide;  protein, amino acid;  biological processes;  drug;  irradiation;  molecular analysis;  peptide;  photodegradation;  protein, Article;  conjugate;  cyclic voltammetry;  density functional theory;  dimerization;  irradiation;  photocatalysis;  photoluminescence, Amino Acids;  Peptides;  Proteins;  Selenocysteine},\ncorrespondence_address1={Payne, R.J.; School of Chemistry, Australia; email: richard.payne@sydney.edu.au},\npublisher={Nature Research},\nissn={20411723},\npubmed_id={36371402},\nlanguage={English},\nabbrev_source_title={Nat. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n TNP Analogues Inhibit the Virulence Promoting IP3-4 Kinase Arg1 in the Fungal Pathogen Cryptococcus neoformans.\n \n \n \n \n\n\n \n Desmarini, D.; Truong, D.; Wilkinson-White, L.; Desphande, C.; Torrado, M.; Mackay, J.; Matthews, J.; Sorrell, T.; Lev, S.; Thompson, P.; and Djordjevic, J.\n\n\n \n\n\n\n Biomolecules, 12(10). 2022.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"TNP$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Desmarini2022,\nauthor={Desmarini, D. and Truong, D. and Wilkinson-White, L. and Desphande, C. and Torrado, M. and Mackay, J.P. and Matthews, J.M. and Sorrell, T.C. and Lev, S. and Thompson, P.E. and Djordjevic, J.T.},\ntitle={TNP Analogues Inhibit the Virulence Promoting IP3-4 Kinase Arg1 in the Fungal Pathogen Cryptococcus neoformans},\njournal={Biomolecules},\nyear={2022},\nvolume={12},\nnumber={10},\ndoi={10.3390/biom12101526},\nart_number={1526},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85140613596&doi=10.3390%2fbiom12101526&partnerID=40&md5=53c18264ecfbe3dee94f6c83a5a414c0},\naffiliation={Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, WestmeadNSW  2145, Australia; Sydney Institute for Infectious Diseases, Faculty of Medicine and Health, University of Sydney, Sydney, NSW  2006, Australia; Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC  3052, Australia; Sydney Analytical, Core Research Facilities, The University of Sydney, Sydney, NSW  2006, Australia; School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW  2006, Australia; Western Sydney Local Health District, WestmeadNSW  2145, Australia},\nabstract={New antifungals with unique modes of action are urgently needed to treat the increasing global burden of invasive fungal infections. The fungal inositol polyphosphate kinase (IPK) pathway, comprised of IPKs that convert IP3 to IP8, provides a promising new target due to its impact on multiple, critical cellular functions and, unlike in mammalian cells, its lack of redundancy. Nearly all IPKs in the fungal pathway are essential for virulence, with IP3-4 kinase (IP3-4K) the most critical. The dibenzylaminopurine compound, N2-(m-trifluorobenzylamino)-N6-(p-nitrobenzylamino)purine (TNP), is a commercially available inhibitor of mammalian IPKs. The ability of TNP to be adapted as an inhibitor of fungal IP3-4K has not been investigated. We purified IP3-4K from the human pathogens, Cryptococcus neoformans and Candida albicans, and optimised enzyme and surface plasmon resonance (SPR) assays to determine the half inhibitory concentration (IC50) and binding affinity (KD), respectively, of TNP and 38 analogues. A novel chemical route was developed to efficiently prepare TNP analogues. TNP and its analogues demonstrated inhibition of recombinant IP3-4K from C. neoformans (CnArg1) at low µM IC50s, but not IP3-4K from C. albicans (CaIpk2) and many analogues exhibited selectivity for CnArg1 over the human equivalent, HsIPMK. Our results provide a foundation for improving potency and selectivity of the TNP series for fungal IP3-4K. © 2022 by the authors.},\nauthor_keywords={antifungal drug discovery;  Cryptococcus neoformans;  dibenzylaminopurine;  enzyme assay;  fungal pathogens;  inositol polyphosphate kinase;  IP3-4K;  structure activity relationship;  surface plasmon resonance;  TNP},\nkeywords={antifungal agent;  complementary DNA;  complete;  glutathione;  inositol polyphosphate;  N2 (m trifluorobenzylamino) N6 (p nitrobenzylamino)purine;  proteinase inhibitor;  purine;  RNA directed DNA polymerase;  sepharose;  unclassified drug;  inositol;  purine derivative, Article;  bacterial strain;  binding affinity;  Candida albicans;  carbon nuclear magnetic resonance;  cell function;  Cryptococcus neoformans;  electrospray;  enzyme activity;  enzyme inhibition assay;  Escherichia coli;  fast protein liquid chromatography;  fungal virulence;  high performance liquid chromatography;  IC50;  luminescence;  mammal cell;  Moloney murine leukemia virus;  mycosis;  nonhuman;  nucleophilicity;  polyacrylamide gel electrophoresis;  protein expression;  proton nuclear magnetic resonance;  qualitative analysis;  RNA extraction;  size exclusion chromatography;  surface plasmon resonance;  time of flight mass spectrometry;  animal;  chemistry;  cryptococcosis;  human;  mammal;  metabolism;  microbiology;  virulence, Animals;  Antifungal Agents;  Candida albicans;  Cryptococcosis;  Cryptococcus neoformans;  Humans;  Inositol;  Mammals;  Purines;  Virulence},\ncorrespondence_address1={Djordjevic, J.T.; Centre for Infectious Diseases and Microbiology, Westmead, Australia; email: julianne.djordjevic@sydney.edu.au; Thompson, P.E.; Medicinal Chemistry, 381 Royal Parade, Australia; email: philip.thompson@monash.edu},\npublisher={MDPI},\nissn={2218273X},\npubmed_id={36291735},\nlanguage={English},\nabbrev_source_title={Biomolecules},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination.\n \n \n \n \n\n\n \n Arvindekar, S.; Jackman, M.; Low, J.; Landsberg, M.; Mackay, J.; and Viswanath, S.\n\n\n \n\n\n\n Protein Science, 31(9). 2022.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Molecular$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Arvindekar2022,\nauthor={Arvindekar, S. and Jackman, M.J. and Low, J.K.K. and Landsberg, M.J. and Mackay, J.P. and Viswanath, S.},\ntitle={Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination},\njournal={Protein Science},\nyear={2022},\nvolume={31},\nnumber={9},\ndoi={10.1002/pro.4387},\nart_number={e4387},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85137125219&doi=10.1002%2fpro.4387&partnerID=40&md5=2fd97ad8f2f39e441357f338a2e3100b},\naffiliation={National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia},\nabstract={The nucleosome remodeling and deacetylase (NuRD) complex is a chromatin-modifying assembly that regulates gene expression and DNA damage repair. Despite its importance, limited structural information describing the complete NuRD complex is available and a detailed understanding of its mechanism is therefore lacking. Drawing on information from SEC-MALLS, DIA-MS, XLMS, negative-stain EM, X-ray crystallography, NMR spectroscopy, secondary structure predictions, and homology models, we applied Bayesian integrative structure determination to investigate the molecular architecture of three NuRD sub-complexes: MTA1-HDAC1-RBBP4, MTA1N-HDAC1-MBD3GATAD2CC, and MTA1-HDAC1-RBBP4-MBD3-GATAD2A [nucleosome deacetylase (NuDe)]. The integrative structures were corroborated by examining independent crosslinks, cryo-EM maps, biochemical assays, known cancer-associated mutations, and structure predictions from AlphaFold. The robustness of the models was assessed by jack-knifing. Localization of the full-length MBD3, which connects the deacetylase and chromatin remodeling modules in NuRD, has not previously been possible; our models indicate two different locations for MBD3, suggesting a mechanism by which MBD3 in the presence of GATAD2A asymmetrically bridges the two modules in NuRD. Further, our models uncovered three previously unrecognized subunit interfaces in NuDe: HDAC1C-MTA1BAH, MTA1BAH-MBD3MBD, and HDAC160–100-MBD3MBD. Our approach also allowed us to localize regions of unknown structure, such as HDAC1C and MBD3IDR, thereby resulting in the most complete and robustly cross-validated structural characterization of these NuRD sub-complexes so far. © 2022 The Protein Society.},\nauthor_keywords={Bayesian integrative structure determination;  chromatin remodeling complexes;  cryo-EM;  histone modification;  integrative modeling;  nucleosome remodeling and deacetylase complex;  XLMS},\nkeywords={acyltransferase;  deacetylase;  DNA binding protein;  gata type zinc finger protein D2A;  histone deacetylase 1;  metastasis associated protein 1;  methyl CpG DNA binding protein;  peptides and proteins;  unclassified drug;  zinc finger protein;  histone deacetylase, Article;  chromatin assembly and disassembly;  cross linking;  cryoelectron microscopy;  DNA repair;  enzyme structure;  histone modification;  nuclear magnetic resonance spectroscopy;  nucleosome;  protein secondary structure;  structure analysis;  X ray crystallography;  Bayes theorem;  chemistry;  genetics;  metabolism, Bayes Theorem;  Chromatin Assembly and Disassembly;  Histone Deacetylases;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Nucleosomes},\ncorrespondence_address1={Viswanath, S.; National Centre for Biological Sciences, India; email: shruthiv@ncbs.res.in; Landsberg, M.J.; School of Chemistry and Molecular Biosciences, Australia; email: m.landsberg@uq.edu.au; Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={John Wiley and Sons Inc},\nissn={09618368},\ncoden={PRCIE},\npubmed_id={36040254},\nlanguage={English},\nabbrev_source_title={Protein Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n RNA inhibits dMi-2/CHD4 chromatin binding and nucleosome remodeling.\n \n \n \n \n\n\n \n Ullah, I.; Thölken, C.; Zhong, Y.; John, M.; Rossbach, O.; Lenz, J.; Gößringer, M.; Nist, A.; Albert, L.; Stiewe, T.; Hartmann, R.; Vázquez, O.; Chung, H.; Mackay, J.; and Brehm, A.\n\n\n \n\n\n\n Cell Reports, 39(9). 2022.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"RNA$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Ullah2022,\nauthor={Ullah, I. and Thölken, C. and Zhong, Y. and John, M. and Rossbach, O. and Lenz, J. and Gößringer, M. and Nist, A. and Albert, L. and Stiewe, T. and Hartmann, R. and Vázquez, O. and Chung, H.-R. and Mackay, J.P. and Brehm, A.},\ntitle={RNA inhibits dMi-2/CHD4 chromatin binding and nucleosome remodeling},\njournal={Cell Reports},\nyear={2022},\nvolume={39},\nnumber={9},\ndoi={10.1016/j.celrep.2022.110895},\nart_number={110895},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85131137236&doi=10.1016%2fj.celrep.2022.110895&partnerID=40&md5=81ba4ad302b294e56d6284ed93e82cb5},\naffiliation={Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Marburg, Germany; Institute for Medical Bioinformatics and Biostatistic, Philipps-University, Marburg, Germany; School of Life and Environmental Sciences, University of SydneyNSW  2006, Australia; Institute of Biochemistry, Department of Biology and Chemistry, Justus Liebig University Giessen, Giessen, Germany; Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany; Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, Marburg, Germany; Faculty of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, Marburg, 35043, Germany},\nabstract={The ATP-dependent nucleosome remodeler Mi-2/CHD4 broadly modulates chromatin landscapes to repress transcription and to maintain genome integrity. Here we use individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) to show that Drosophila Mi-2 associates with thousands of mRNA molecules in vivo. Biochemical data reveal that recombinant dMi-2 preferentially binds to G-rich RNA molecules using two intrinsically disordered regions of unclear function. Pharmacological inhibition of transcription and RNase digestion approaches establish that RNA inhibits the association of dMi-2 with chromatin. We also show that RNA inhibits dMi-2-mediated nucleosome mobilization by competing with the nucleosome substrate. Importantly, this activity is shared by CHD4, the human homolog of dMi-2, strongly suggesting that RNA-mediated regulation of remodeler activity is an evolutionary conserved mechanism. Our data support a model in which RNA serves to protect actively transcribed regions of the genome from dMi-2/CHD4-mediated establishment of repressive chromatin structures. © 2022 The Author(s)},\nauthor_keywords={ATP-dependent chromatin remodeling;  chromatin;  CP: Molecular biology;  gene regulation;  iCLIP;  NuRD;  RNA},\nkeywords={CHD4 protein;  dMi 2 protein;  guanine;  messenger RNA;  RNA;  RNA binding protein;  RNA polymerase II;  unclassified drug;  adenosine triphosphatase;  autoantigen;  Drosophila protein;  Mi-2 protein, Drosophila;  RNA, animal cell;  Article;  biochemistry;  bioinformatics;  chromatin;  chromatin immunoprecipitation;  chromatin structure;  controlled study;  crosslinking immunoprecipitation;  Drosophila;  genetic conservation;  genetic regulation;  human;  human cell;  in vivo study;  inhibition kinetics;  nonhuman;  nucleosome;  protein binding;  protein transport;  RNA transcription;  animal;  chromatin;  genetics;  metabolism, Adenosine Triphosphatases;  Animals;  Autoantigens;  Chromatin;  Drosophila;  Drosophila Proteins;  Nucleosomes;  RNA},\ncorrespondence_address1={Brehm, A.; Institute of Molecular Biology and Tumor Research, Germany; email: brehm@imt.uni-marburg.de},\npublisher={Elsevier B.V.},\nissn={22111247},\npubmed_id={35649367},\nlanguage={English},\nabbrev_source_title={Cell Rep.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Mechanism of Bloom syndrome complex assembly required for double Holliday junction dissolution and genome stability.\n \n \n \n \n\n\n \n Hodson, C.; Low, J.; van Twest, S.; Jones, S.; Swuec, P.; Murphy, V.; Tsukada, K.; Fawkes, M.; Bythell-Douglas, R.; Davies, A.; Holien, J.; O'Rourke, J.; Parker, B.; Glaser, A.; Parker, M.; Mackay, J.; Blackford, A.; Costa, A.; and Deans, A.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 119(6). 2022.\n cited By 2\n\n\n\n
\n\n\n\n \n \n $\"Mechanism$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Hodson2022,\nauthor={Hodson, C. and Low, J.K.K. and van Twest, S. and Jones, S.E. and Swuec, P. and Murphy, V. and Tsukada, K. and Fawkes, M. and Bythell-Douglas, R. and Davies, A. and Holien, J.K. and O'Rourke, J.J. and Parker, B.L. and Glaser, A. and Parker, M.W. and Mackay, J.P. and Blackford, A.N. and Costa, A. and Deans, A.J.},\ntitle={Mechanism of Bloom syndrome complex assembly required for double Holliday junction dissolution and genome stability},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2022},\nvolume={119},\nnumber={6},\ndoi={10.1073/pnas.2109093119},\nart_number={e2109093119},\nnote={cited By 2},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85124061373&doi=10.1073%2fpnas.2109093119&partnerID=40&md5=6dd83964f65b06ed9d5a697fdcec069f},\naffiliation={Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC  3065, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW  2006, Australia; Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, United Kingdom; Francis Crick Institute, London, NW1 1AT, United Kingdom; Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, 152-8550, Japan; MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, United Kingdom; Department of Medicine (St. Vincent's), University of Melbourne, Fitzroy, VIC  3065, Australia; School of Science, RMIT University, Melbourne, VIC  3001, Australia; Structural Biology Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC  3065, Australia; Bio21 Institute, University of Melbourne, Parkville, VIC  3010, Australia},\nabstract={The RecQ-like helicase BLM cooperates with topoisomerase IIIα, RMI1, and RMI2 in a heterotetrameric complex (the “Bloom syndrome complex”) for dissolution of double Holliday junctions, key intermediates in homologous recombination. Mutations in any component of the Bloom syndrome complex can cause genome instability and a highly cancer-prone disorder called Bloom syndrome. Some heterozygous carriers are also predisposed to breast cancer. To understand how the activities of BLM helicase and topoisomerase IIIα are coupled, we purified the active four-subunit complex. Chemical cross-linking and mass spectrometry revealed a unique architecture that links the helicase and topoisomerase domains. Using biochemical experiments, we demonstrated dimerization mediated by the N terminus of BLM with a 2:2:2:2 stoichiometry within the Bloom syndrome complex. We identified mutations that independently abrogate dimerization or association of BLM with RMI1, and we show that both are dysfunctional for dissolution using in vitro assays and cause genome instability and synthetic lethal interactions with GEN1/MUS81 in cells. Truncated BLM can also inhibit the activity of full-length BLM in mixed dimers, suggesting a putative mechanism of dominant-negative action in carriers of BLM truncation alleles. Our results identify critical molecular determinants of Bloom syndrome complex assembly required for double Holliday junction dissolution and maintenance of genome stability. © This article is distributed under Creative Commons Attribution-NonCommercialNoDerivatives License 4.0 (CC BY-NC-ND).},\nauthor_keywords={Bloom's complex;  Cross-link mass spectrometry;  Genome stability;  Helicase;  Topoisomerase},\nkeywords={Bloom syndrome helicase;  DNA topoisomerase;  RecQ helicase;  topoisomerase III alpha;  unclassified drug;  carrier protein;  cruciform DNA;  DNA topoisomerase;  protein binding;  RecQ helicase, amino terminal sequence;  Article;  Bloom syndrome;  complex formation;  controlled study;  dimerization;  dissolution;  genomic instability;  Holliday junction;  hTERT-RPE1 cell line;  human;  human cell;  mass spectrometry;  protein cross linking;  protein domain;  protein protein interaction;  stoichiometry;  allele;  Bloom syndrome;  cell line;  genetic recombination;  genetics;  genomic instability;  mutation;  solubility, Alleles;  Bloom Syndrome;  Carrier Proteins;  Cell Line;  DNA Topoisomerases, Type I;  DNA, Cruciform;  Genomic Instability;  Humans;  Mutation;  Protein Binding;  Recombination, Genetic;  RecQ Helicases;  Solubility},\ncorrespondence_address1={Deans, A.J.; Genome Stability Unit, Australia; email: adeans@svi.edu.au},\npublisher={National Academy of Sciences},\nissn={00278424},\ncoden={PNASA},\npubmed_id={35115399},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Unique protein interaction networks define the chromatin remodelling module of the NuRD complex.\n \n \n \n \n\n\n \n Sharifi Tabar, M.; Giardina, C.; Feng, Y.; Francis, H.; Moghaddas Sani, H.; Low, J.; Mackay, J.; Bailey, C.; and Rasko, J.\n\n\n \n\n\n\n FEBS Journal, 289(1): 199-214. 2022.\n cited By 4\n\n\n\n
\n\n\n\n \n \n $\"Unique$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{SharifiTabar2022199,\nauthor={Sharifi Tabar, M. and Giardina, C. and Feng, Y. and Francis, H. and Moghaddas Sani, H. and Low, J.K.K. and Mackay, J.P. and Bailey, C.G. and Rasko, J.E.J.},\ntitle={Unique protein interaction networks define the chromatin remodelling module of the NuRD complex},\njournal={FEBS Journal},\nyear={2022},\nvolume={289},\nnumber={1},\npages={199-214},\ndoi={10.1111/febs.16112},\nnote={cited By 4},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85111693208&doi=10.1111%2ffebs.16112&partnerID=40&md5=95efbe86683f6cedadb9cbd8fae46545},\naffiliation={Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW, Australia; Faculty of Medicine & Health, The University of SydneyNSW, Australia; School of Life & Environmental Sciences, The University of SydneyNSW, Australia; Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW, Australia; Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW, Australia},\nabstract={The combination of four proteins and their paralogues including MBD2/3, GATAD2A/B, CDK2AP1 and CHD3/4/5, which we refer to as the MGCC module, form the chromatin remodelling module of the nucleosome remodelling and deacetylase (NuRD) complex. To date, mechanisms by which the MGCC module acquires paralogue-specific function and specificity have not been addressed. Understanding the protein–protein interaction (PPI) network of the MGCC subunits is essential for defining underlying mechanisms of gene regulation. Therefore, using pulldown followed by mass spectrometry analysis (PD-MS), we report a proteome-wide interaction network of the MGCC module in a paralogue-specific manner. Our data also demonstrate that the disordered C-terminal region of CHD3/4/5 is a gateway to incorporate remodelling activity into both ChAHP (CHD4, ADNP, HP1γ) and NuRD complexes in a mutually exclusive manner. We define a short aggregation-prone region (APR) within the C-terminal segment of GATAD2B that is essential for the interaction of CHD4 and CDK2AP1 with the NuRD complex. Finally, we also report an association of CDK2AP1 with the nuclear receptor co-repressor (NCOR) complex. Overall, this study provides insight into the possible mechanisms through which the MGCC module can achieve specificity and diverse biological functions. © 2021 The Authors. The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies},\nkeywords={isoprotein;  multiprotein complex;  nuclear receptor corepressor;  nucleosome remodeling and deacetylase complex;  unclassified drug;  CDK2AP1 protein, human;  CHD3 protein, human;  CHD4 protein, human;  DNA binding protein;  DNA helicase;  GATAD2A protein, human;  histone deacetylase;  multiprotein complex;  proteome;  repressor protein;  tumor suppressor protein, ADNP gene;  Article;  biological activity;  cancer genetics;  carboxy terminal sequence;  CDK2AP1 gene;  ChAHP gene;  CHD3 gene;  CHD4 gene;  CHD5 gene;  chromatin assembly and disassembly;  controlled study;  GATAD2B gene;  gene;  gene expression regulation;  human;  mass spectrometry;  MBD2 gene;  missense mutation;  promoter region;  protein aggregation;  protein protein interaction;  protein structure;  proteomics;  stoichiometry;  chromatin assembly and disassembly;  genetics;  nucleosome;  protein analysis;  ultrastructure, Chromatin Assembly and Disassembly;  DNA Helicases;  DNA-Binding Proteins;  Gene Expression Regulation;  Humans;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Multiprotein Complexes;  Nucleosomes;  Protein Interaction Maps;  Proteome;  Repressor Proteins;  Tumor Suppressor Proteins},\ncorrespondence_address1={Rasko, J.E.J.; Gene and Stem Cell Therapy Program Centenary Institute, Australia; email: j.rasko@centenary.org.au},\npublisher={John Wiley and Sons Inc},\nissn={1742464X},\ncoden={FJEOA},\npubmed_id={34231305},\nlanguage={English},\nabbrev_source_title={FEBS J.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2021\n \n \n (7)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n A single dose, BCG-adjuvanted COVID-19 vaccine provides sterilising immunity against SARS-CoV-2 infection.\n \n \n \n \n\n\n \n Counoupas, C.; Johansen, M.; Stella, A.; Nguyen, D.; Ferguson, A.; Aggarwal, A.; Bhattacharyya, N.; Grey, A.; Hutchings, O.; Patel, K.; Siddiquee, R.; Stewart, E.; Feng, C.; Hansbro, N.; Palendira, U.; Steain, M.; Saunders, B.; Low, J.; Mackay, J.; Kelleher, A.; Britton, W.; Turville, S.; Hansbro, P.; and Triccas, J.\n\n\n \n\n\n\n npj Vaccines, 6(1). 2021.\n cited By 20\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Counoupas2021,\nauthor={Counoupas, C. and Johansen, M.D. and Stella, A.O. and Nguyen, D.H. and Ferguson, A.L. and Aggarwal, A. and Bhattacharyya, N.D. and Grey, A. and Hutchings, O. and Patel, K. and Siddiquee, R. and Stewart, E.L. and Feng, C.G. and Hansbro, N.G. and Palendira, U. and Steain, M.C. and Saunders, B.M. and Low, J.K.K. and Mackay, J.P. and Kelleher, A.D. and Britton, W.J. and Turville, S.G. and Hansbro, P.M. and Triccas, J.A.},\ntitle={A single dose, BCG-adjuvanted COVID-19 vaccine provides sterilising immunity against SARS-CoV-2 infection},\njournal={npj Vaccines},\nyear={2021},\nvolume={6},\nnumber={1},\ndoi={10.1038/s41541-021-00406-4},\nart_number={143},\nnote={cited By 20},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85120166235&doi=10.1038%2fs41541-021-00406-4&partnerID=40&md5=2ca0ba283661efbaa183752b3a050e9f},\naffiliation={School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia; Tuberculosis Research Program at the Centenary Institute, The University of Sydney, Sydney, NSW, Australia; Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia; Kirby Institute, University of New South Wales, Sydney, NSW, Australia; Department of Clinical Immunology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; RPA Virtual Hospital, Sydney Local Health District, Sydney, NSW, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW  2006, Australia; Sydney Institute for Infectious Diseases and Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia},\nabstract={Global control of COVID-19 requires broadly accessible vaccines that are effective against SARS-CoV-2 variants. In this report, we exploit the immunostimulatory properties of bacille Calmette-Guérin (BCG), the existing tuberculosis vaccine, to deliver a vaccination regimen with potent SARS-CoV-2-specific protective immunity. Combination of BCG with a stabilised, trimeric form of SARS-CoV-2 spike antigen promoted rapid development of virus-specific IgG antibodies in the blood of vaccinated mice, that was further augmented by the addition of alum. This vaccine formulation, BCG:CoVac, induced high-titre SARS-CoV-2 neutralising antibodies (NAbs) and Th1-biased cytokine release by vaccine-specific T cells, which correlated with the early emergence of T follicular helper cells in local lymph nodes and heightened levels of antigen-specific plasma B cells after vaccination. Vaccination of K18-hACE2 mice with a single dose of BCG:CoVac almost completely abrogated disease after SARS-CoV-2 challenge, with minimal inflammation and no detectable virus in the lungs of infected animals. Boosting BCG:CoVac-primed mice with a heterologous vaccine further increased SARS-CoV-2-specific antibody responses, which effectively neutralised B.1.1.7 and B.1.351 SARS-CoV-2 variants of concern. These findings demonstrate the potential for BCG-based vaccination to protect against major SARS-CoV-2 variants circulating globally. © 2021, The Author(s).},\nkeywords={aluminum potassium sulfate;  bcg covac;  BCG vaccine;  coronavirus spike glycoprotein;  immunoglobulin G antibody;  neutralizing antibody;  SARS-CoV-2 antibody;  SARS-CoV-2 vaccine;  unclassified drug;  vaccine adjuvant;  virus antigen, adult;  animal cell;  animal experiment;  animal model;  animal tissue;  antibody response;  antigen specificity;  Article;  asymptomatic infection;  BCG vaccination;  controlled study;  coronavirus disease 2019;  cytokine release;  drug formulation;  experimental coronavirus disease 2019;  female;  human;  immunostimulation;  local lymph node assay;  male;  mouse;  Mycobacterium bovis BCG;  nonhuman;  nose smear;  popliteal lymph node;  single drug dose;  sterilizing immunity;  Tfh cell;  Th1 cell;  trimerization;  Vero C1008 cell line},\ncorrespondence_address1={Triccas, J.A.; School of Medical Sciences, Australia; email: jamie.triccas@sydney.edu.au; Hansbro, P.M.; Centre for Inflammation, Australia; email: Philip.Hansbro@uts.edu.au},\npublisher={Nature Research},\nissn={20590105},\nlanguage={English},\nabbrev_source_title={npj Vaccines},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Purification of an insect juvenile hormone receptor complex enables insights into its post-translational phosphorylation.\n \n \n \n \n\n\n \n Jindra, M.; McKinstry, W.; Nebl, T.; Bittova, L.; Ren, B.; Shaw, J.; Phan, T.; Lu, L.; Low, J.; Mackay, J.; Sparrow, L.; Lovrecz, G.; and Hill, R.\n\n\n \n\n\n\n Journal of Biological Chemistry, 297(6). 2021.\n cited By 5\n\n\n\n
\n\n\n\n \n \n $\"Purification$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Jindra2021,\nauthor={Jindra, M. and McKinstry, W.J. and Nebl, T. and Bittova, L. and Ren, B. and Shaw, J. and Phan, T. and Lu, L. and Low, J.K.K. and Mackay, J.P. and Sparrow, L.G. and Lovrecz, G.O. and Hill, R.J.},\ntitle={Purification of an insect juvenile hormone receptor complex enables insights into its post-translational phosphorylation},\njournal={Journal of Biological Chemistry},\nyear={2021},\nvolume={297},\nnumber={6},\ndoi={10.1016/j.jbc.2021.101387},\nart_number={101387},\nnote={cited By 5},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85111949580&doi=10.1016%2fj.jbc.2021.101387&partnerID=40&md5=0ab33a3532572b577725952237277577},\naffiliation={Biology Center, Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic; CSIRO Manufacturing, CSIRO, Parkville, VIC, Australia; CSIRO Health and Biosecurity, CSIRO, North Ryde, NSW, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia},\nabstract={Juvenile hormone (JH) plays vital roles in insect reproduction, development, and in many aspects of physiology. JH primarily acts at the gene-regulatory level through interaction with an intracellular receptor (JH receptor [JHR]), a ligand-activated complex of transcription factors consisting of the JH-binding protein methoprene-tolerant (MET) and its partner taiman (TAI). Initial studies indicated significance of post-transcriptional phosphorylation, subunit assembly, and nucleocytoplasmic transport of JHR in JH signaling. However, our knowledge of JHR regulation at the protein level remains rudimentary, partly because of the difficulty of obtaining purified and functional JHR proteins. Here, we present a method for high-yield expression and purification of JHR complexes from two insect species, the beetle T. castaneum and the mosquito Aedes aegypti. Recombinant JHR subunits from each species were coexpressed in an insect cell line using a baculovirus system. MET–TAI complexes were purified through affinity chromatography and anion exchange columns to yield proteins capable of binding both the hormonal ligand (JH III) and DNA bearing cognate JH-response elements. We further examined the beetle JHR complex in greater detail. Biochemical analyses and MS confirmed that T. castaneum JHR was a 1:1 heterodimer consisting of MET and Taiman proteins, stabilized by the JHR agonist ligand methoprene. Phosphoproteomics uncovered multiple phosphorylation sites in the MET protein, some of which were induced by methoprene treatment. Finally, we report a functional bipartite nuclear localization signal, straddled by phosphorylated residues, within the disordered C-terminal region of MET. Our present characterization of the recombinant JHR is an initial step toward understanding JHR structure and function. © 2021 THE AUTHORS. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology.},\nkeywords={Affinity chromatography;  Cell culture;  Cell proliferation;  Hormones;  Phosphorylation;  Proteins;  Purification;  Transcription, Activated complex;  Hormone binding;  Hormone receptors;  Hormone-receptor complex;  Intracellular receptors;  Juvenile hormone;  Methoprene;  Receptor complex;  Regulatory level;  T. castaneum, Ligands, alkaline phosphatase;  DNA polymerase;  juvenile hormone;  ligand;  methoprene;  phosphoserine;  phosphothreonine;  transcription factor;  cell surface receptor;  insect protein;  juvenile hormone, Aedes aegypti;  affinity chromatography;  anion exchange;  Article;  Baculoviridae;  controlled study;  Drosophila melanogaster;  liquid chromatography;  mass spectrometry;  nonhuman;  nucleocytoplasmic transport;  phosphoproteomics;  protein binding;  protein expression;  protein function;  protein phosphorylation;  protein processing;  protein protein interaction;  protein purification;  protein structure;  site directed mutagenesis;  size exclusion chromatography;  Tribolium castaneum;  Aedes;  animal;  genetics;  metabolism;  phosphorylation;  Sf9 cell line;  Spodoptera;  Tribolium, Aedes;  Animals;  Insect Proteins;  Juvenile Hormones;  Phosphorylation;  Protein Processing, Post-Translational;  Receptors, Cell Surface;  Sf9 Cells;  Spodoptera;  Tribolium},\ncorrespondence_address1={Jindra, M.; Biology Center, Czech Republic; email: jindra@entu.cas.cz; Hill, R.J.; CSIRO Health and Biosecurity, Australia; email: ronald.hill@sydney.edu.au},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={34758356},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The characterization of protein interactions-what, how and how much?.\n \n \n \n \n\n\n \n Walport, L.; Low, J.; Matthews, J.; and MacKay, J.\n\n\n \n\n\n\n Chemical Society Reviews, 50(22): 12292-12307. 2021.\n cited By 10\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Walport202112292,\nauthor={Walport, L.J. and Low, J.K.K. and Matthews, J.M. and MacKay, J.P.},\ntitle={The characterization of protein interactions-what, how and how much?},\njournal={Chemical Society Reviews},\nyear={2021},\nvolume={50},\nnumber={22},\npages={12292-12307},\ndoi={10.1039/d1cs00548k},\nnote={cited By 10},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85120047522&doi=10.1039%2fd1cs00548k&partnerID=40&md5=0c8f631567b78902ac959e00f6541448},\naffiliation={The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, United Kingdom; Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, United Kingdom; School of Life and Environmental Sciences, University of SydneyNSW  2006, Australia},\nabstract={Protein interactions underlie most molecular events in biology. Many methods have been developed to identify protein partners, to measure the affinity with which these biomolecules interact and to characterise the structures of the complexes. Each approach has its own advantages and limitations, and it can be difficult for the newcomer to determine which methodology would best suit their system. This review provides an overview of many of the techniques most widely used to identify protein partners, assess stoichiometry and binding affinity, and determine low-resolution models for complexes. Key methods covered include: yeast two-hybrid analysis, affinity purification mass spectrometry and proximity labelling to identify partners; size-exclusion chromatography, scattering methods, native mass spectrometry and analytical ultracentrifugation to estimate stoichiometry; isothermal titration calorimetry, biosensors and fluorometric methods (including microscale thermophoresis, anisotropy/polarisation, resonance energy transfer, AlphaScreen, and differential scanning fluorimetry) to measure binding affinity; and crosslinking and hydrogen-deuterium exchange mass spectrometry to probe the structure of complexes. This journal is © The Royal Society of Chemistry.},\nkeywords={Binding energy;  Energy transfer;  Mass spectrometry;  Molecular biology;  Proteins;  Size exclusion chromatography, Affinity purification;  Binding affinities;  Labelings;  Lower resolution;  Molecular events;  Protein interaction;  Resolution modeling;  Size-exclusion chromatography;  Two-hybrid analysis;  Yeast two hybrid, Stoichiometry, protein, affinity chromatography;  mass spectrometry, Chromatography, Affinity;  Mass Spectrometry;  Proteins},\ncorrespondence_address1={Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Royal Society of Chemistry},\nissn={03060012},\ncoden={CSRVB},\npubmed_id={34581717},\nlanguage={English},\nabbrev_source_title={Chem. Soc. Rev.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Late-stage modification of peptides and proteins at cysteine with diaryliodonium salts.\n \n \n \n \n\n\n \n Byrne, S.; Bedding, M.; Corcilius, L.; Ford, D.; Zhong, Y.; Franck, C.; Larance, M.; Mackay, J.; and Payne, R.\n\n\n \n\n\n\n Chemical Science, 12(42): 14159-14166. 2021.\n cited By 3\n\n\n\n
\n\n\n\n \n \n $\"Late-stage$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Byrne202114159,\nauthor={Byrne, S.A. and Bedding, M.J. and Corcilius, L. and Ford, D.J. and Zhong, Y. and Franck, C. and Larance, M. and Mackay, J.P. and Payne, R.J.},\ntitle={Late-stage modification of peptides and proteins at cysteine with diaryliodonium salts},\njournal={Chemical Science},\nyear={2021},\nvolume={12},\nnumber={42},\npages={14159-14166},\ndoi={10.1039/d1sc03127a},\nnote={cited By 3},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85118686045&doi=10.1039%2fd1sc03127a&partnerID=40&md5=94c2178c112a034e4f85a6e585d33294},\naffiliation={School of Chemistry, University of Sydney, Sydney, NSW  2006, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Sydney, NSW  2006, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW  2006, Australia; Charles Perkins Centre, University of SydneyNSW  2006, Australia},\nabstract={The modification of peptides and proteins has emerged as a powerful means to efficiently prepare high value bioconjugates for a range of applications in chemical biology and for the development of next-generation therapeutics. Herein, we report a novel method for the chemoselective late-stage modification of peptides and proteins at cysteine in aqueous buffer with suitably functionalised diaryliodonium salts, furnishing stable thioether-linked synthetic conjugates. The power of this new platform is showcased through the late-stage modification of the affibody zEGFR and the histone protein H2A. © The Royal Society of Chemistry 2021.},\nkeywords={Amino acids;  Chemical modification;  Salts, Aqueous buffer;  Bioconjugates;  Chemical biology;  Chemoselective;  Diaryliodonium salts;  Functionalized;  Late stage;  Novel methods;  Power;  Thioethers, Peptides},\ncorrespondence_address1={Payne, R.J.; School of Chemistry, Australia; email: richard.payne@sydney.edu.au},\npublisher={Royal Society of Chemistry},\nissn={20416520},\ncoden={CSHCC},\nlanguage={English},\nabbrev_source_title={Chem. Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Discovery of Cyclic Peptide Ligands to the SARS-CoV-2 Spike Protein Using mRNA Display.\n \n \n \n \n\n\n \n Norman, A.; Franck, C.; Christie, M.; Hawkins, P.; Patel, K.; Ashhurst, A.; Aggarwal, A.; Low, J.; Siddiquee, R.; Ashley, C.; Steain, M.; Triccas, J.; Turville, S.; MacKay, J.; Passioura, T.; and Payne, R.\n\n\n \n\n\n\n ACS Central Science, 7(6): 1001-1008. 2021.\n cited By 14\n\n\n\n
\n\n\n\n \n \n $\"Discovery$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Norman20211001,\nauthor={Norman, A. and Franck, C. and Christie, M. and Hawkins, P.M.E. and Patel, K. and Ashhurst, A.S. and Aggarwal, A. and Low, J.K.K. and Siddiquee, R. and Ashley, C.L. and Steain, M. and Triccas, J.A. and Turville, S. and MacKay, J.P. and Passioura, T. and Payne, R.J.},\ntitle={Discovery of Cyclic Peptide Ligands to the SARS-CoV-2 Spike Protein Using mRNA Display},\njournal={ACS Central Science},\nyear={2021},\nvolume={7},\nnumber={6},\npages={1001-1008},\ndoi={10.1021/acscentsci.0c01708},\nnote={cited By 14},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108408365&doi=10.1021%2facscentsci.0c01708&partnerID=40&md5=2b5198825f7083293fb010a94ac2ca0f},\naffiliation={School of Chemistry, University of Sydney, Sydney, NSW  2006, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Sydney, NSW  2006, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW  2006, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW  2006, Australia; Kirby Institute, Sydney, NSW  2052, Australia; Sydney Analytical, University of Sydney, Sydney, NSW  2006, Australia},\nabstract={The COVID-19 pandemic, caused by SARS-CoV-2, has led to substantial morbidity, mortality, and disruption globally. Cellular entry of SARS-CoV-2 is mediated by the viral spike protein, and affinity ligands to this surface protein have the potential for applications as antivirals and diagnostic reagents. Here, we describe the affinity selection of cyclic peptide ligands to the SARS-CoV-2 spike protein receptor binding domain (RBD) from three distinct libraries (in excess of a trillion molecules each) by mRNA display. We identified six high affinity molecules with dissociation constants (KD) in the nanomolar range (15-550 nM) to the RBD. The highest affinity ligand could be used as an affinity reagent to detect the spike protein in solution by ELISA, and the cocrystal structure of this molecule bound to the RBD demonstrated that it binds to a cryptic binding site, displacing a β-strand near the C-terminus. Our findings provide key mechanistic insight into the binding of peptide ligands to the SARS-CoV-2 spike RBD, and the ligands discovered in this work may find future use as reagents for diagnostic applications. © 2021 The Authors. Published by American Chemical Society.},\nkeywords={Diseases;  Dissociation;  Molecules;  Peptides;  Reagents, Affinity ligands;  Affinity reagents;  Affinity selection;  Cocrystal structure;  Diagnostic applications;  Dissociation constant;  Nanomolar range;  Surface proteins, Ligands},\ncorrespondence_address1={Passioura, T.; School of Chemistry, Australia; email: toby.passioura@sydney.edu.au; Payne, R.J.; School of Chemistry, Australia; email: richard.payne@sydney.edu.au; Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={American Chemical Society},\nissn={23747943},\nlanguage={English},\nabbrev_source_title={ACS Cent. Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n BET-Family Bromodomains Can Recognize Diacetylated Sequences from Transcription Factors Using a Conserved Mechanism.\n \n \n \n \n\n\n \n Patel, K.; Solomon, P.; Walshe, J.; Ford, D.; Wilkinson-White, L.; Payne, R.; Low, J.; and Mackay, J.\n\n\n \n\n\n\n Biochemistry, 60(9): 648-662. 2021.\n cited By 5\n\n\n\n
\n\n\n\n \n \n $\"BET-Family$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Patel2021648,\nauthor={Patel, K. and Solomon, P.D. and Walshe, J.L. and Ford, D.J. and Wilkinson-White, L. and Payne, R.J. and Low, J.K.K. and Mackay, J.P.},\ntitle={BET-Family Bromodomains Can Recognize Diacetylated Sequences from Transcription Factors Using a Conserved Mechanism},\njournal={Biochemistry},\nyear={2021},\nvolume={60},\nnumber={9},\npages={648-662},\ndoi={10.1021/acs.biochem.0c00816},\nnote={cited By 5},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85101870748&doi=10.1021%2facs.biochem.0c00816&partnerID=40&md5=2b52d0089dfc5a9217ca703298cbe837},\naffiliation={School of Life and Environmental Sciences, University of Sydney, Sydney, NSW  2006, Australia; School of Chemistry, University of Sydney, Sydney, NSW  2006, Australia; Sydney Analytical Core Facility, University of Sydney, Sydney, NSW  2006, Australia},\nabstract={Almost all eukaryotic proteins receive diverse post-translational modifications (PTMs) that modulate protein activity. Many histone PTMs are well characterized, heavily influence gene regulation, and are often predictors of distinct transcriptional programs. Although our understanding of the histone PTM network has matured, much is yet to be understood about the roles of transcription factor (TF) PTMs, which might well represent a similarly complex and dynamic network of functional regulation. Members of the bromodomain and extra-terminal domain (BET) family of proteins recognize acetyllysine residues and relay the signals encoded by these modifications. Here, we have investigated the acetylation dependence of several functionally relevant BET-TF interactions in vitro using surface plasmon resonance, nuclear magnetic resonance, and X-ray crystallography. We show that motifs known to be acetylated in TFs E2F1 and MyoD1 can interact with all bromodomains of BRD2, BRD3, and BRD4. The interactions are dependent on diacetylation of the motifs and show a preference for the first BET bromodomain. Structural mapping of the interactions confirms a conserved mode of binding for the two TFs to the acetyllysine binding pocket of the BET bromodomains, mimicking that of other already established functionally important histone- and TF-BET interactions. We also examined a motif from the TF RelA that is known to be acetylated but were unable to observe any interaction, regardless of the acetylation state of the sequence. Our findings overall advance our understanding of BET-TF interactions and suggest a physical link between the important diacetylated motifs found in E2F1 and MyoD1 and the BET-family proteins. ©},\nkeywords={Acetylation;  Plasmons;  Proteins;  Surface plasmon resonance;  Transcription;  Transcription factors, Dynamic network;  Eukaryotic proteins;  Functional regulation;  Mode of binding;  Post-translational modifications;  Protein activity;  Structural mapping;  Transcriptional program, X ray crystallography, binding protein;  brd 2 protein;  brd 3 protein;  brd 4 protein;  bromodomain and extra terminal domain family protein;  histone;  histone H4;  lysine;  MyoD1 protein;  transcription factor;  transcription factor E2F1;  transcription factor GATA 1;  transcription factor RelA;  Twist related protein 1;  unclassified drug;  BRD2 protein, human;  BRD3 protein, human;  BRD4 protein, human;  cell cycle protein;  E2F1 protein, human;  histone;  lysine;  MyoD protein;  MyoD1 myogenic differentiation protein;  transcription factor;  transcription factor E2F1, amino acid sequence;  Article;  binding site;  gene control;  genetic transcription;  human;  in vitro study;  molecular recognition;  nuclear magnetic resonance spectroscopy;  prediction;  priority journal;  protein acetylation;  protein binding;  protein expression;  protein family;  protein interaction;  protein motif;  protein processing;  protein purification;  protein structure;  surface plasmon resonance;  X ray crystallography;  acetylation;  chemistry;  metabolism;  molecular model;  protein conformation;  protein domain, Acetylation;  Cell Cycle Proteins;  Crystallography, X-Ray;  E2F1 Transcription Factor;  Histones;  Humans;  Lysine;  Models, Molecular;  MyoD Protein;  Protein Conformation;  Protein Domains;  Protein Processing, Post-Translational;  Transcription Factors},\ncorrespondence_address1={Low, J.K.K.; School of Life and Environmental Sciences, Australia; email: jason.low@sydney.edu.au; Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={American Chemical Society},\nissn={00062960},\ncoden={BICHA},\npubmed_id={33620209},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The bromodomains of BET family proteins can recognize diacetylated histone H2A.Z.\n \n \n \n \n\n\n \n Patel, K.; Solomon, P.; Walshe, J.; Low, J.; and Mackay, J.\n\n\n \n\n\n\n Protein Science, 30(2): 464-476. 2021.\n cited By 4\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Patel2021464,\nauthor={Patel, K. and Solomon, P.D. and Walshe, J.L. and Low, J.K.K. and Mackay, J.P.},\ntitle={The bromodomains of BET family proteins can recognize diacetylated histone H2A.Z},\njournal={Protein Science},\nyear={2021},\nvolume={30},\nnumber={2},\npages={464-476},\ndoi={10.1002/pro.4006},\nnote={cited By 4},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85097269890&doi=10.1002%2fpro.4006&partnerID=40&md5=a036ae17056a77200df9ea479a4abfef},\naffiliation={School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia; Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia},\nabstract={Chemical modifications of histone tails influence genome accessibility and the transcriptional state of eukaryotic cells. Lysine acetylation is one of the most common modifications and acetyllysine-binding bromodomains (BDs) provide a means for acetyllysine marks to be translated into meaningful cellular responses. Here, we have investigated the mechanism underlying the reported association between the Bromodomain and Extra Terminal (BET) family of BD proteins and the essential histone variant H2A.Z. We use NMR spectroscopy to demonstrate a physical interaction between the N-terminal tail of H2A.Z and the BDs of BRD2, BRD3, and BRD4, and show that the interaction is dependent on lysine acetylation in H2A.Z. The BDs preferentially engage a diacetylated H2A.Z-K4acK7ac motif that is reminiscent of sequences found in other biologically important BET BD target proteins, including histones and transcription factors. A H2A.Z-K7acK11ac motif can also bind BET BDs—with a preference for the second BD of each protein. Chemical shift perturbation mapping of the interactions, together with an X-ray crystal structure of BRD2-BD1 bound to H2A.Z-K4acK7ac, shows that H2A.Z binds the canonical AcK binding pocket of the BDs. This mechanism mirrors the conserved binding mode that is unique to the BET BDs, in which two acetylation marks are read simultaneously by a single BD. Our findings provide structural corroboration of biochemical and cell biological data that link H2A.Z and BET-family proteins, suggesting that the function of H2A.Z is enacted through interactions with these chromatin readers. © 2020 The Protein Society},\nauthor_keywords={acetylation;  BET family proteins;  BRD2;  BRD3;  BRD4;  epigenetics;  H2A.Z;  histone},\nkeywords={brd2 protien;  brd3 protein;  brd4 protein;  bromodomain and extra terminal protein;  histone H2AZ;  k4ack7ac protein;  k7ack11ac protein;  lysine;  protein;  transcription factor;  transcription factor GATA 1;  unclassified drug;  BRD2 protein, human;  BRD3 protein, human;  BRD4 protein, human;  cell cycle protein;  histone;  histone H2A.F-Z;  protein binding, acetylation;  animal experiment;  Article;  chromatin;  controlled study;  crystal structure;  epigenetics;  histone acetylation;  human;  nonhuman;  nuclear magnetic resonance spectroscopy;  priority journal;  protein analysis;  protein expression;  protein interaction;  protein motif;  proton nuclear magnetic resonance;  rat;  regulatory mechanism;  X ray;  X ray crystallography;  chemistry;  protein domain;  structure activity relation, Acetylation;  Cell Cycle Proteins;  Crystallography, X-Ray;  Histones;  Humans;  Protein Binding;  Protein Domains;  Structure-Activity Relationship;  Transcription Factors},\ncorrespondence_address1={Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Blackwell Publishing Ltd},\nissn={09618368},\ncoden={PRCIE},\npubmed_id={33247496},\nlanguage={English},\nabbrev_source_title={Protein Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2020\n \n \n (12)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n The Nucleosome Remodeling and Deacetylase Complex Has an Asymmetric, Dynamic, and Modular Architecture.\n \n \n \n \n\n\n \n Low, J.; Silva, A.; Sharifi Tabar, M.; Torrado, M.; Webb, S.; Parker, B.; Sana, M.; Smits, C.; Schmidberger, J.; Brillault, L.; Jackman, M.; Williams, D.; Blobel, G.; Hake, S.; Shepherd, N.; Landsberg, M.; and Mackay, J.\n\n\n \n\n\n\n Cell Reports, 33(9). 2020.\n cited By 16\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Low2020,\nauthor={Low, J.K.K. and Silva, A.P.G. and Sharifi Tabar, M. and Torrado, M. and Webb, S.R. and Parker, B.L. and Sana, M. and Smits, C. and Schmidberger, J.W. and Brillault, L. and Jackman, M.J. and Williams, D.C., Jr. and Blobel, G.A. and Hake, S.B. and Shepherd, N.E. and Landsberg, M.J. and Mackay, J.P.},\ntitle={The Nucleosome Remodeling and Deacetylase Complex Has an Asymmetric, Dynamic, and Modular Architecture},\njournal={Cell Reports},\nyear={2020},\nvolume={33},\nnumber={9},\ndoi={10.1016/j.celrep.2020.108450},\nart_number={108450},\nnote={cited By 16},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85097050261&doi=10.1016%2fj.celrep.2020.108450&partnerID=40&md5=0101beb6878ed842b4b95162002921c3},\naffiliation={School of Life and Environmental Sciences, University of SydneyNSW, Australia; School of Chemistry and Molecular Biosciences, University of QueenslandQLD, Australia; Dept of Pathology and Laboratory Medicine, University of North Carolina at Chapel HillNC, United States; The Division of Hematology, Children's Hospital of Philadelphia, and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA  19104, United States; Institute for Genetics, FB08 Biology, Justus-Liebig-University Giessen, Giessen, Germany; Sydney, NSW, Australia},\nabstract={Low et al. examine the architecture of the nucleosome remodeling and deacetylase complex. They define its stoichiometry, use cross-linking mass spectrometry to define subunit locations, and use electron microscopy to reveal large-scale dynamics. They also demonstrate that PWWP2A competes with MBD3 to sequester the HDAC-MTA-RBBP module from NuRD. © 2020 The Authors\nThe nucleosome remodeling and deacetylase (NuRD) complex is essential for metazoan development but has been refractory to biochemical analysis. We present an integrated analysis of the native mammalian NuRD complex, combining quantitative mass spectrometry, cross-linking, protein biochemistry, and electron microscopy to define the architecture of the complex. NuRD is built from a 2:2:4 (MTA, HDAC, and RBBP) deacetylase module and a 1:1:1 (MBD, GATAD2, and Chromodomain-Helicase-DNA-binding [CHD]) remodeling module, and the complex displays considerable structural dynamics. The enigmatic GATAD2 controls the asymmetry of the complex and directly recruits the CHD remodeler. The MTA-MBD interaction acts as a point of functional switching, with the transcriptional regulator PWWP2A competing with MBD for binding to the MTA-HDAC-RBBP subcomplex. Overall, our data address the long-running controversy over NuRD stoichiometry, provide imaging of the mammalian NuRD complex, and establish the biochemical mechanism by which PWWP2A can regulate NuRD composition. © 2020 The Authors},\nauthor_keywords={cross-linking MS;  DIA-MS;  electron microscopy;  EM;  gene regulation;  nucleosome remodeling;  NuRD;  PWWP2A},\nkeywords={binding protein;  cell protein;  chromatin binding protein PWWP2A;  DNA;  enzyme;  GATAD2 protein;  helicase;  histone deacetylase;  methyl CpG binding protein;  MTA protein;  nucleosome remodeling and deacetylase complex;  retinoblastoma binding protein;  unclassified drug;  histone deacetylase, animal cell;  Article;  biochemistry;  catalysis;  chromodomain helicase DNA binding;  controlled study;  dynamics;  electron microscopy;  enzyme structure;  mass spectrometry;  mouse;  nonhuman;  priority journal;  protein conformation;  protein cross linking;  protein DNA binding;  protein protein interaction;  regulatory mechanism;  stoichiometry;  gene expression regulation;  genetics;  human;  metabolism;  molecular model;  nucleosome, Gene Expression Regulation;  Histone Deacetylases;  Humans;  Models, Molecular;  Nucleosomes},\ncorrespondence_address1={Low, J.K.K.; School of Life and Environmental Sciences, Australia; email: jason.low@sydney.edu.au; Landsberg, M.J.; School of Chemistry and Molecular Biosciences, Australia; email: m.landsberg@uq.edu.au; Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Elsevier B.V.},\nissn={22111247},\npubmed_id={33264611},\nlanguage={English},\nabbrev_source_title={Cell Rep.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation.\n \n \n \n \n\n\n \n Zhong, Y.; Paudel, B.; Ryan, D.; Low, J.; Franck, C.; Patel, K.; Bedward, M.; Torrado, M.; Payne, R.; van Oijen, A.; and Mackay, J.\n\n\n \n\n\n\n Nature Communications, 11(1). 2020.\n cited By 15\n\n\n\n
\n\n\n\n \n \n $\"CHD4$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Zhong2020,\nauthor={Zhong, Y. and Paudel, B.P. and Ryan, D.P. and Low, J.K.K. and Franck, C. and Patel, K. and Bedward, M.J. and Torrado, M. and Payne, R.J. and van Oijen, A.M. and Mackay, J.P.},\ntitle={CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation},\njournal={Nature Communications},\nyear={2020},\nvolume={11},\nnumber={1},\ndoi={10.1038/s41467-020-15183-2},\nart_number={1519},\nnote={cited By 15},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85082508825&doi=10.1038%2fs41467-020-15183-2&partnerID=40&md5=675dd2848264da5c83141ef36dc14c80},\naffiliation={School of Life and Environmental Sciences, University of Sydney, Sydney, NSW  2006, Australia; Molecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW  2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW  2522, Australia; Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT  2601, Australia; School of Chemistry, The University of Sydney, Sydney, NSW  2006, Australia},\nabstract={Chromatin remodellers hydrolyse ATP to move nucleosomal DNA against histone octamers. The mechanism, however, is only partially resolved, and it is unclear if it is conserved among the four remodeller families. Here we use single-molecule assays to examine the mechanism of action of CHD4, which is part of the least well understood family. We demonstrate that the binding energy for CHD4-nucleosome complex formation—even in the absence of nucleotide—triggers significant conformational changes in DNA at the entry side, effectively priming the system for remodelling. During remodelling, flanking DNA enters the nucleosome in a continuous, gradual manner but exits in concerted 4–6 base-pair steps. This decoupling of entry- and exit-side translocation suggests that ATP-driven movement of entry-side DNA builds up strain inside the nucleosome that is subsequently released at the exit side by DNA expulsion. Based on our work and previous studies, we propose a mechanism for nucleosome sliding. © 2020, The Author(s).},\nkeywords={adenosine triphosphate;  chd4 protein;  DNA;  histone;  nucleotide;  protein;  unclassified drug;  CHD1 protein, S cerevisiae;  CHD4 protein, human;  DNA binding protein;  histone deacetylase;  recombinant protein;  Saccharomyces cerevisiae protein, DNA;  enzyme;  enzyme activity;  protein;  translocation, Article;  chromatin;  complex formation;  conformational transition;  control;  controlled study;  gene translocation;  hydrolysis;  nucleosome;  protein binding;  chromatin assembly and disassembly;  fluorescence microscopy;  genetics;  HEK293 cell line;  human;  intravital microscopy;  metabolism;  nucleosome;  protein domain;  single molecule imaging, Chromatin Assembly and Disassembly;  DNA-Binding Proteins;  HEK293 Cells;  Histones;  Humans;  Intravital Microscopy;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Microscopy, Fluorescence;  Nucleosomes;  Protein Domains;  Recombinant Proteins;  Saccharomyces cerevisiae Proteins;  Single Molecule Imaging;  Translocation, Genetic},\ncorrespondence_address1={Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Nature Research},\nissn={20411723},\npubmed_id={32251276},\nlanguage={English},\nabbrev_source_title={Nat. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n A Novel Purification Procedure for Active Recombinant Human DPP4 and the Inability of DPP4 to Bind SARS-CoV-2.\n \n \n \n \n\n\n \n Xi, C.; Di Fazio, A.; Nadvi, N.; Patel, K.; Xiang, M.; Zhang, H.; Deshpande, C.; Low, J.; Wang, X.; Chen, Y.; McMillan, C.; Isaacs, A.; Osborne, B.; de Ribeiro, A.; McCaughan, G.; Mackay, J.; Church, W.; and Gorrell, M.\n\n\n \n\n\n\n Molecules, 25(22). 2020.\n cited By 21\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Xi2020,\nauthor={Xi, C.R. and Di Fazio, A. and Nadvi, N.A. and Patel, K. and Xiang, M.S.W. and Zhang, H.E. and Deshpande, C. and Low, J.K.K. and Wang, X.T. and Chen, Y. and McMillan, C.L.D. and Isaacs, A. and Osborne, B. and de Ribeiro, A.J.V. and McCaughan, G.W. and Mackay, J.P. and Church, W.B. and Gorrell, M.D.},\ntitle={A Novel Purification Procedure for Active Recombinant Human DPP4 and the Inability of DPP4 to Bind SARS-CoV-2},\njournal={Molecules},\nyear={2020},\nvolume={25},\nnumber={22},\ndoi={10.3390/MOLECULES25225392},\nart_number={5392},\nnote={cited By 21},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096814881&doi=10.3390%2fMOLECULES25225392&partnerID=40&md5=fb61e407106a0397653efc1298eb268a},\naffiliation={Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW  2006, Australia; Research Portfolio Core Research Facilities, The University of Sydney, Sydney, NSW  2006, Australia; Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW  2006, Australia; Drug Discovery, Sydney Analytical, Core Research Facilities, The University of Sydney, Sydney, NSW  2006, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD  4072, Australia; AW Morrow GE & Liver Centre, Royal Prince Alfred Hospital, Camperdown, NSW  2050, Australia; Faculty of Medicine and Health, School of Pharmacy, The University of Sydney, Sydney, NSW  2006, Australia},\nabstract={Proteases catalyse irreversible posttranslational modifications that often alter a biological function of the substrate. The protease dipeptidyl peptidase 4 (DPP4) is a pharmacological target in type 2 diabetes therapy primarily because it inactivates glucagon-like protein-1. DPP4 also has roles in steatosis, insulin resistance, cancers and inflammatory and fibrotic diseases. In addition, DPP4 binds to the spike protein of the MERS virus, causing it to be the human cell surface receptor for that virus. DPP4 has been identified as a potential binding target of SARS-CoV-2 spike protein, so this question requires experimental investigation. Understanding protein structure and function requires reliable protocols for production and purification. We developed such strategies for baculovirus generated soluble recombinant human DPP4 (residues 29–766) produced in insect cells. Purification used differential ammonium sulphate precipitation, hydrophobic interaction chromatography, dye affinity chromatography in series with immobilised metal affinity chromatography, and ion-exchange chromatography. The binding affinities of DPP4 to the SARS-CoV-2 full-length spike protein and its receptor-binding domain (RBD) were measured using surface plasmon resonance and ELISA. This optimised DPP4 purification procedure yielded 1 to 1.8 mg of pure fully active soluble DPP4 protein per litre of insect cell culture with specific activity >30 U/mg, indicative of high purity. No specific binding between DPP4 and CoV-2 spike protein was detected by surface plasmon resonance or ELISA. In summary, a procedure for high purity high yield soluble human DPP4 was achieved and used to show that, unlike MERS, SARS-CoV-2 does not bind human DPP4. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},\nauthor_keywords={Covid-19;  DPP4;  protease;  recombinant protein},\nkeywords={ACE2 protein, human;  coronavirus spike glycoprotein;  dipeptidyl peptidase IV;  DPP4 protein, human;  recombinant protein;  spike protein, SARS-CoV-2, animal;  Baculoviridae;  biosynthesis;  chemistry;  enzyme linked immunosorbent assay;  gene expression;  genetics;  human;  isolation and purification;  kinetics;  metabolism;  molecular cloning;  molecular model;  plasmid;  protein domain;  protein secondary structure;  Sf9 cell line;  Spodoptera;  surface plasmon resonance, Angiotensin-Converting Enzyme 2;  Animals;  Baculoviridae;  Cloning, Molecular;  Dipeptidyl Peptidase 4;  Enzyme-Linked Immunosorbent Assay;  Gene Expression;  Humans;  Kinetics;  Models, Molecular;  Plasmids;  Protein Interaction Domains and Motifs;  Protein Structure, Secondary;  Recombinant Proteins;  Sf9 Cells;  Spike Glycoprotein, Coronavirus;  Spodoptera;  Surface Plasmon Resonance},\ncorrespondence_address1={Gorrell, M.D.; Centenary Institute, Australia; email: m.gorrell@centenary.org.au},\npublisher={MDPI},\nissn={14203049},\ncoden={MOLEF},\npubmed_id={33218025},\nlanguage={English},\nabbrev_source_title={Molecules},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Cyclic peptides can engage a single binding pocket through highly divergent modes.\n \n \n \n \n\n\n \n Patel, K.; Walport, L.; Walshe, J.; Solomon, P.; Low, J.; Tran, D.; Mouradian, K.; Silva, A.; Wilkinson-White, L.; Norman, A.; Franck, C.; Matthews, J.; Mitchell Guss, J.; Payne, R.; Passioura, T.; Suga, H.; and Mackay, J.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 117(43): 26728-26738. 2020.\n cited By 6\n\n\n\n
\n\n\n\n \n \n $\"Cyclic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Patel202026728,\nauthor={Patel, K. and Walport, L.J. and Walshe, J.L. and Solomon, P.D. and Low, J.K.K. and Tran, D.H. and Mouradian, K.S. and Silva, A.P.G. and Wilkinson-White, L. and Norman, A. and Franck, C. and Matthews, J.M. and Mitchell Guss, J. and Payne, R.J. and Passioura, T. and Suga, H. and Mackay, J.P.},\ntitle={Cyclic peptides can engage a single binding pocket through highly divergent modes},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2020},\nvolume={117},\nnumber={43},\npages={26728-26738},\ndoi={10.1073/pnas.2003086117},\nnote={cited By 6},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85094858446&doi=10.1073%2fpnas.2003086117&partnerID=40&md5=a7ce18f21ffb64f058f201de78e963ed},\naffiliation={School of Life and Environmental Sciences, University of Sydney, Sydney, NSW  2006, Australia; Protein–Protein Interaction Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom; Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, W12 0BZ, United Kingdom; Department of Chemistry, Graduate School of Science, University of Tokyo, Tokyo, 113-0033, Japan; School of Chemistry, University of Sydney, Sydney, NSW  2006, Australia; Sydney Analytical Core Research Facility, University of SydneyNSW  2006, Australia},\nabstract={Cyclic peptide library screening technologies show immense promise for identifying drug leads and chemical probes for challenging targets. However, the structural and functional diversity encoded within such libraries is largely undefined. We have systematically profiled the affinity, selectivity, and structural features of library-derived cyclic peptides selected to recognize three closely related targets: the acetyllysine-binding bromodomain proteins BRD2, -3, and -4. We report affinities as low as 100 pM and specificities of up to 106-fold. Crystal structures of 13 peptide–bromodomain complexes reveal remarkable diversity in both structure and binding mode, including both α-helical and β-sheet structures as well as bivalent binding modes. The peptides can also exhibit a high degree of structural preorganization. Our data demonstrate the enormous potential within these libraries to provide diverse binding modes against a single target, which underpins their capacity to yield highly potent and selective ligands. © 2020 National Academy of Sciences. All rights reserved.},\nauthor_keywords={BET bromodomain inhibition;  BRD3;  BRD4;  De novo cyclic peptides;  Structural biology},\nkeywords={bromodomain protein 2;  bromodomain protein 3;  bromodomain protein 4;  cyclopeptide;  transcription factor;  unclassified drug;  BRD2 protein, human;  BRD3 protein, human;  cyclopeptide;  protein binding, alpha helix;  Article;  beta sheet;  binding affinity;  binding kinetics;  binding site;  controlled study;  crystal structure;  drug identification;  drug protein binding;  drug screening;  drug selectivity;  drug targeting;  priority journal;  protein domain;  chemistry;  drug development;  human;  metabolism;  peptide library, Binding Sites;  Drug Discovery;  Humans;  Peptide Library;  Peptides, Cyclic;  Protein Binding;  Protein Domains;  Transcription Factors},\ncorrespondence_address1={Walport, L.J.; Protein–Protein Interaction Laboratory, United Kingdom; email: louise.walport@crick.ac.uk; Suga, H.; Department of Chemistry, Japan; email: hsuga@chem.s.u-tokyo.ac.jp; Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={National Academy of Sciences},\nissn={00278424},\ncoden={PNASA},\npubmed_id={33046654},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Thermostable small-molecule inhibitor of angiogenesis and vascular permeability that suppresses a pERK-FosB/ΔFosB-VCAM-1 axis.\n \n \n \n \n\n\n \n Li, Y.; Alhendi, A.; Yeh, M.; Elahy, M.; Santiago, F.; Deshpande, N.; Wu, B.; Chan, E.; Inam, S.; Prado-Lourenco, L.; Marchand, J.; Joyce, R.; Wilkinson-White, L.; Raftery, M.; Zhu, M.; Adamson, S.; Barnat, F.; Viaud-Quentric, K.; Sockler, J.; Mackay, J.; Chang, A.; Mitchell, P.; Marcuccio, S.; and Khachigian, L.\n\n\n \n\n\n\n Science Advances, 6(31). 2020.\n cited By 9\n\n\n\n
\n\n\n\n \n \n $\"Thermostable$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Li2020,\nauthor={Li, Y. and Alhendi, A.M.N. and Yeh, M.-C. and Elahy, M. and Santiago, F.S. and Deshpande, N.P. and Wu, B. and Chan, E. and Inam, S. and Prado-Lourenco, L. and Marchand, J. and Joyce, R.D. and Wilkinson-White, L.E. and Raftery, M.J. and Zhu, M. and Adamson, S.J. and Barnat, F. and Viaud-Quentric, K. and Sockler, J. and Mackay, J.P. and Chang, A. and Mitchell, P. and Marcuccio, S.M. and Khachigian, L.M.},\ntitle={Thermostable small-molecule inhibitor of angiogenesis and vascular permeability that suppresses a pERK-FosB/ΔFosB-VCAM-1 axis},\njournal={Science Advances},\nyear={2020},\nvolume={6},\nnumber={31},\ndoi={10.1126/sciadv.aaz7815},\nart_number={aaz7815},\nnote={cited By 9},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85090873217&doi=10.1126%2fsciadv.aaz7815&partnerID=40&md5=abf727ee07197389effb3ee377cd26bb},\naffiliation={Vascular Biology and Translational Research, School of Medical Sciences and UNSW Medicine, University of New South Wales, Sydney, NSW  2052, Australia; Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW  2052, Australia; Advanced Molecular Technologies Pty Ltd, Scoresby, VIC  3179, Australia; Sydney Analytical Core Facility, University of SydneyNSW  2006, Australia; Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW  2052, Australia; New South Wales Tissue Bank, New South Wales Organ and Tissue Donation Service, South Eastern Sydney Local Health District, Kogarah, NSW  2217, Australia; Save Sight Institute, Discipline of Clinical Ophthalmology and Eye Health, University of SydneyNSW  2006, Australia; GreenLight Clinical Pty. Ltd., Woolloomooloo, NSW  2011, Australia; Iris Pharma, La Gaude, 06610, France; Statistical Operations and Programming, Datapharm Australia Pty. Ltd., Drummoyne, NSW  2047, Australia; School of Life and Environmental Sciences, University of SydneyNSW  2006, Australia; Sydney Eye Hospital, Sydney, NSW  2000, Australia; Centre for Vision Research, Department of Ophthalmology, Westmead Institute for Medical Research, Westmead Hospital, University of Sydney, Westmead, NSW  2145, Australia; La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC  3086, Australia},\nabstract={Vascular permeability and angiogenesis underpin neovascular age-related macular degeneration and diabetic retinopathy. While anti-VEGF therapies are widely used clinically, many patients do not respond optimally, or at all, and small-molecule therapies are lacking. Here, we identified a dibenzoxazepinone BT2 that inhibits endothelial cell proliferation, migration, wound repair in vitro, network formation, and angiogenesis in mice bearing Matrigel plugs. BT2 interacts with MEK1 and inhibits ERK phosphorylation and the expression of FosB/ΔFosB, VCAM-1, and many genes involved in proliferation, migration, angiogenesis, and inflammation. BT2 reduced retinal vascular leakage following rat choroidal laser trauma and rabbit intravitreal VEGF-A165 administration. BT2 suppressed retinal CD31, pERK, VCAM-1, and VEGF-A165 expression. BT2 reduced retinal leakage in rats at least as effectively as aflibercept, a first-line therapy for nAMD/DR. BT2 withstands boiling or autoclaving and several months' storage at 22°C. BT2 is a new small-molecule inhibitor of vascular permeability and angiogenesis. © 2020 The Authors.},\nkeywords={Cell proliferation;  Endothelial cells;  Eye protection;  Mammals;  Ophthalmology, Age-related macular degeneration;  Angiogenesis;  Diabetic retinopathy;  Network formation;  Small molecule inhibitor;  Small molecules;  Vascular permeability;  Wound repair, Molecules, angiogenesis inhibitor;  FOSB protein, human;  Fosb protein, mouse;  Fosb protein, rat;  protein c fos;  vascular cell adhesion molecule 1;  vasculotropin A, animal;  capillary permeability;  genetics;  human;  Leporidae;  metabolism;  mouse;  neovascularization (pathology);  rat, Angiogenesis Inhibitors;  Animals;  Capillary Permeability;  Humans;  Mice;  Neovascularization, Pathologic;  Proto-Oncogene Proteins c-fos;  Rabbits;  Rats;  Vascular Cell Adhesion Molecule-1;  Vascular Endothelial Growth Factor A},\ncorrespondence_address1={Khachigian, L.M.; Vascular Biology and Translational Research, Australia; email: l.khachigian@unsw.edu.au},\npublisher={American Association for the Advancement of Science},\nissn={23752548},\npubmed_id={32923607},\nlanguage={English},\nabbrev_source_title={Sci. Adv.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Semisynthesis of an evasin from tick saliva reveals a critical role of tyrosine sulfation for chemokine binding and inhibition.\n \n \n \n \n\n\n \n Franck, C.; Foster, S.; Johansen-Leete, J.; Chowdhury, S.; Cielesh, M.; Bhusal, R.; Mackay, J.; Larance, M.; Stone, M.; and Payne, R.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 117(23): 12657-12664. 2020.\n cited By 19\n\n\n\n
\n\n\n\n \n \n $\"Semisynthesis$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 4 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Franck202012657,\nauthor={Franck, C. and Foster, S.R. and Johansen-Leete, J. and Chowdhury, S. and Cielesh, M. and Bhusal, R.P. and Mackay, J.P. and Larance, M. and Stone, M.J. and Payne, R.J.},\ntitle={Semisynthesis of an evasin from tick saliva reveals a critical role of tyrosine sulfation for chemokine binding and inhibition},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2020},\nvolume={117},\nnumber={23},\npages={12657-12664},\ndoi={10.1073/pnas.2000605117},\nnote={cited By 19},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85086172342&doi=10.1073%2fpnas.2000605117&partnerID=40&md5=a437ad879cf88f80d61e6b4f11bfeef8},\naffiliation={School of Chemistry, University of Sydney, Sydney, NSW  2006, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of SydneyNSW  2006, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW  2006, Australia; Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC  3800, Australia; Cardiovascular Disease Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC  3800, Australia; Charles Perkins Centre, University of SydneyNSW  2006, Australia},\nabstract={Blood-feeding arthropods produce antiinflammatory salivary proteins called evasins that function through inhibition of chemokine-receptor signaling in the host. Herein, we show that the evasin ACA-01 from the Amblyomma cajennense tick can be posttranslationally sulfated at two tyrosine residues, albeit as a mixture of sulfated variants. Homogenously sulfated variants of the proteins were efficiently assembled via a semisynthetic native chemical ligation strategy. Sulfation significantly improved the binding affinity of ACA-01 for a range of proinflammatory chemokines and enhanced the ability of ACA-01 to inhibit chemokine signaling through cognate receptors. Comparisons of evasin sequences and structural data suggest that tyrosine sulfation serves as a receptor mimetic strategy for recognizing and suppressing the proinflammatory activity of a wide variety of mammalian chemokines. As such, the incorporation of this posttranslational modification (PTM) or mimics thereof into evasins may provide a strategy to optimize tick salivary proteins for antiinflammatory applications. © 2020 National Academy of Sciences. All rights reserved.},\nauthor_keywords={Antiinflammatory;  Chemokines;  Evasins;  Sulfation;  Ticks},\nkeywords={chemokine;  evasin;  natural product;  tyrosine;  unclassified drug;  arthropod protein;  chemokine;  protein binding;  sulfate;  tyrosine, Amblyomma cajennense;  Article;  binding affinity;  controlled study;  HEK293 cell line;  human;  human cell;  mass spectrometry;  nonhuman;  polyacrylamide gel electrophoresis;  priority journal;  protein binding;  protein function;  protein processing;  protein structure;  sequence analysis;  sulfation;  synthesis;  ultra performance liquid chromatography;  Acari;  animal;  chemistry;  metabolism;  protein processing;  saliva, Acari;  Animals;  Arthropod Proteins;  Chemokines;  HEK293 Cells;  Humans;  Protein Binding;  Protein Processing, Post-Translational;  Saliva;  Sulfates;  Tyrosine},\ncorrespondence_address1={Stone, M.J.; Infection and Immunity Program, Australia; email: martin.stone@monash.edu; Payne, R.J.; School of Chemistry, Australia; email: richard.payne@sydney.edu.au},\npublisher={National Academy of Sciences},\nissn={00278424},\ncoden={PNASA},\npubmed_id={32461364},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Correction: Comparative structure-function analysis of bromodomain and extraterminal motif (BET) proteins in a gene-complementation system.(Applied Optics(2020)295(1898–1914)Doi: 10.1074/jbc.RA119.010679).\n \n \n \n \n\n\n \n Werner, M.; Wang, H.; Hamagami, N.; Hsu, S.; Yano, J.; Stonestrom, A.; Behera, V.; Zhong, Y.; MacKay, J.; and Blobel, G.\n\n\n \n\n\n\n Journal of Biological Chemistry, 295(18): 6251. 2020.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Correction:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Werner20206251,\nauthor={Werner, M.T. and Wang, H. and Hamagami, N. and Hsu, S.C. and Yano, J.A. and Stonestrom, A.J. and Behera, V. and Zhong, Y. and MacKay, J.P. and Blobel, G.A.},\ntitle={Correction: Comparative structure-function analysis of bromodomain and extraterminal motif (BET) proteins in a gene-complementation system.(Applied Optics(2020)295(1898–1914)Doi: 10.1074/jbc.RA119.010679)},\njournal={Journal of Biological Chemistry},\nyear={2020},\nvolume={295},\nnumber={18},\npages={6251},\ndoi={10.1074/jbc.AAC120.013771},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85084817876&doi=10.1074%2fjbc.AAC120.013771&partnerID=40&md5=1d38b680d49136df67db596a6dc6725e},\nabstract={Yichen Zhong's name was misspelled. The correct spelling is shown above. © 2020 American Society for Biochemistry and Molecular Biology Inc.. All rights reserved.},\nkeywords={erratum},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={32358084},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Erratum},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder.\n \n \n \n \n\n\n \n Shieh, C.; Jones, N.; Vanle, B.; Au, M.; Huang, A.; Silva, A.; Lee, H.; Douine, E.; Otero, M.; Choi, A.; Grand, K.; Taff, I.; Delgado, M.; Hajianpour, M.; Seeley, A.; Rohena, L.; Vernon, H.; Gripp, K.; Vergano, S.; Mahida, S.; Naidu, S.; Sousa, A.; Wain, K.; Challman, T.; Beek, G.; Basel, D.; Ranells, J.; Smith, R.; Yusupov, R.; Freckmann, M.; Ohden, L.; Davis-Keppen, L.; Chitayat, D.; Dowling, J.; Finkel, R.; Dauber, A.; Spillmann, R.; Pena, L.; Metcalfe, K.; Splitt, M.; Lachlan, K.; McKee, S.; Hurst, J.; Fitzpatrick, D.; Morton, J.; Cox, H.; Venkateswaran, S.; Young, J.; Marsh, E.; Nelson, S.; Martinez, J.; Graham, J.; Kini, U.; Mackay, J.; Pierson, T.; and Network, T. U. D.\n\n\n \n\n\n\n Genetics in Medicine, 22(5): 878-888. 2020.\n cited By 12\n\n\n\n
\n\n\n\n \n \n $\"GATAD2B-associated$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Shieh2020878,\nauthor={Shieh, C. and Jones, N. and Vanle, B. and Au, M. and Huang, A.Y. and Silva, A.P.G. and Lee, H. and Douine, E.D. and Otero, M.G. and Choi, A. and Grand, K. and Taff, I.P. and Delgado, M.R. and Hajianpour, M.J. and Seeley, A. and Rohena, L. and Vernon, H. and Gripp, K.W. and Vergano, S.A. and Mahida, S. and Naidu, S. and Sousa, A.B. and Wain, K.E. and Challman, T.D. and Beek, G. and Basel, D. and Ranells, J. and Smith, R. and Yusupov, R. and Freckmann, M.-L. and Ohden, L. and Davis-Keppen, L. and Chitayat, D. and Dowling, J.J. and Finkel, R. and Dauber, A. and Spillmann, R. and Pena, L.D.M. and Metcalfe, K. and Splitt, M. and Lachlan, K. and McKee, S.A. and Hurst, J. and Fitzpatrick, D.R. and Morton, J.E.V. and Cox, H. and Venkateswaran, S. and Young, J.I. and Marsh, E.D. and Nelson, S.F. and Martinez, J.A. and Graham, J.M., Jr and Kini, U. and Mackay, J.P. and Pierson, T.M. and The Undiagnosed Diseases Network},\ntitle={GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder},\njournal={Genetics in Medicine},\nyear={2020},\nvolume={22},\nnumber={5},\npages={878-888},\ndoi={10.1038/s41436-019-0747-z},\nnote={cited By 12},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85078297373&doi=10.1038%2fs41436-019-0747-z&partnerID=40&md5=ab869b021c683e11f5de64f9d79420f7},\naffiliation={David Geffen School of Medicine at UCLA, Los Angeles, CA, United States; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia; Department of Psychiatry & Behavioral Neurosciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States; Medical College of Wisconsin–Central Wisconsin, Wausau, WI, United States; Department of Pediatrics Cedars-Sinai Medical Center, Los Angeles, CA, United States; Institute for Precision Health, David Geffen School ofMedicine, University of California–Los Angeles, Los Angeles, CA, United States; Department of Human Genetics and Pathology and Laboratory Medicine,David Geffen School of Medicine, University of California–Los Angeles, Los Angeles, CA, United States; Department of Human Genetics, David Geffen School ofMedicine, University of California–Los Angeles, Los Angeles, CA, United States; Board of Governor’s Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States; Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, United States; Department of Neurology, Hofstra School of Medicine, Great Neck, NY, United States; Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center and Texas Scottish RiteHospital for Children, Dallas, TX, United States; Department of Pediatrics, Division of Medical Genetics, East Tennessee State University, QuillenCollege of Medicine, Mountain Home, TN, United States; Geisinger Medical Center, Danville, PA, United States; Division of Genetics, Department of Pediatrics, Brooke Army Medical Center, Fort Sam Houston, TX, United States; Department of Pediatrics, UT Health San Antonio, Long School of Medicine, San Antonio, TX, United States; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Balitmore, MD, United States; Division of Medical Genetics, Al DuPont Hospital for Children, Wilmington, DE, United States; Division of Medical Genetics and Metabolism, Children’s Hospital of The King’s Daughters, Norfolk, VA, United States; Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, United States; Department of Neurology and Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, United States; Hugo Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD, United States; Serviço de Genética Médica, Hospital Santa Maria, CHULN, Lisboa, Portugal and Faculdade de Medicina de Lisboa, Universidadede Lisboa, Lisboa, Portugal; Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, United States; Children’s Hospitals and Clinics of Minnesota Department ofGenetics, Minneapolis, MN, United States; Department of Pediatrics, Division of Genetics; Children’s Hospital of Wisconsin, Milwaukee, WI, United States; Division of Genetics and Metabolism, Department ofPediatrics, University of South Florida, Tampa, FL, United States; Department of Pediatrics, Division of Genetics, Maine Medical Center, Portland, ME, United States; Division of Clinical Genetics, Joe DiMaggio Children’s Hospital, Hollywood, FL, United States; Royal North Shore Hospital, St Leonards, NSW, Australia; Department of Genetic Counseling, Sanford Children’s Specialty Clinic, Sioux Falls, SD, United States; Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, Sioux Falls, SD, United States; The Prenatal Diagnosis and Medical Genetics Program, Department ofObstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada; Division of Clinical and Metabolic Genetics, Department of Pediatrics,The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; Division of Neurology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada; Division of Pediatric Neurology, Department of Pediatrics, Nemours Children’s Hospital, Orlando, FL, United States; Division of Endocrinology, Children’s National Health System, Washington, DC, United States; Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, United States; Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Manchester Centre for Genomic Medicine, Manchester University NHS FT, Manchester, United Kingdom; Institute of Genetic Medicine, Northern Genetics Service, Newcastle uponTyne Hospitals Trust, Newcastle, United Kingdom; Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Human Development and Health Division, Wessex Clinical GeneticsService, University Hospitals of Southampton NHS Trust, Southampton, United Kingdom; Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, United Kingdom; Department of Clinical Genetics, NE Thames Genetics Service, Great Ormond Street Hospital, London, United Kingdom; Medical Research Council Human Genetics Unit, University of Edinburgh, Edinburgh, United Kingdom; West Midlands Regional Clinical Genetics Service and Birmingham HealthPartners, Birmingham, United Kingdom; Birmingham Women’s and Children’s Hospitals NHS Foundation Trust, Birmingham, United Kingdom; Birmingham Women’s Hospital, Edgbaston, Birmingham, United Kingdom; Division of Neurology, Department of Pediatrics, Children’s Hospital ofEastern Ontario, University of Ottawa, Ottawa, ON, Canada; John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States; Division of Neurology, Children’s Hospital of Philadelphia andDepartment of Neurology and Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States; Department of Human Genetics; Division of Medical Genetics, Departmentof Pediatrics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States; Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, CA, United States; Oxford Centre for Genomic Medicine, Oxford University Hospital NHS Foundation Trust, Oxford, United Kingdom; Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, United States; Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States},\nabstract={Purpose: Determination of genotypic/phenotypic features of GATAD2B-associated neurodevelopmental disorder(GAND). Methods: Fifty GAND subjects were evaluated to determine consistentgenotypic/phenotypic features. Immunoprecipitation assays utilizing in vitrotranscription–translation products were used to evaluate GATAD2B missensevariants’ ability to interact with binding partners within the nucleosomeremodeling and deacetylase (NuRD) complex. Results: Subjects had clinical findings that included macrocephaly,hypotonia, intellectual disability, neonatal feeding issues, polyhydramnios,apraxia of speech, epilepsy, and bicuspid aortic valves. Forty-one novelGATAD2B variants were identified withmultiple variant types (nonsense, truncating frameshift, splice-site variants,deletions, and missense). Seven subjects were identified with missense variantsthat localized within two conserved region domains (CR1 or CR2) of the GATAD2Bprotein. Immunoprecipitation assays revealed several of these missense variantsdisrupted GATAD2B interactions with its NuRD complex binding partners. Conclusions: A consistent GAND phenotype was caused by a range of geneticvariants in GATAD2B that includeloss-of-function and missense subtypes. Missense variants were present inconserved region domains that disrupted assembly of NuRD complex proteins.GAND’s clinical phenotype had substantial clinical overlap with other disordersassociated with the NuRD complex that involve CHD3 and CHD4, with clinicalfeatures of hypotonia, intellectual disability, cardiac defects, childhoodapraxia of speech, and macrocephaly. © 2020, American College of Medical Genetics and Genomics.},\nauthor_keywords={GATAD2B; NuRD complex; apraxia of speech; chromatin remodeling;macrocephaly},\nkeywords={DNA binding protein;  histone deacetylase;  protein CHD3;  protein CHD4;  unclassified drug;  GATAD2B protein, human;  repressor protein;  transcription factor GATA, anisocoria;  apraxia of speech;  Article;  astigmatism;  bicuspid aortic valve;  child;  clinical article;  cohort analysis;  controlled study;  epilepsy;  feeding disorder;  female;  GATAD2B gene;  gene;  gene disruption;  gene identification;  gene interaction;  gene location;  genetic analysis;  genetic association;  genetic transcription;  genetic variability;  genotype;  hearing impairment;  human;  hydramnios;  hypermetropia;  hypertelorism;  immunoprecipitation;  in vitro study;  infantile hypotonia;  intellectual impairment;  loss of function mutation;  macrocephaly;  male;  mental disease;  muscle hypotonia;  myopia;  nucleosome;  optic nerve hypoplasia;  phenotype;  preschool child;  protein domain;  retrospective study;  site directed mutagenesis;  strabismus;  Alexander disease;  genetics;  intellectual impairment;  nucleosome;  pregnancy, Child;  Female;  GATA Transcription Factors;  Humans;  Intellectual Disability;  Megalencephaly;  Neurodevelopmental Disorders;  Nucleosomes;  Phenotype;  Pregnancy;  Repressor Proteins},\ncorrespondence_address1={Pierson, T.M.; Department of Pediatrics, United States; email: Tyler.Pierson@cshs.org},\npublisher={Springer Nature},\nissn={10983600},\ncoden={GEMEF},\npubmed_id={31949314},\nlanguage={English},\nabbrev_source_title={Gen. Med.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Correction: GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder (Genetics in Medicine, (2020), 10.1038/s41436-019-0747-z).\n \n \n \n \n\n\n \n Shieh, C.; Jones, N.; Vanle, B.; Au, M.; Huang, A.; Silva, A.; Lee, H.; Douine, E.; Otero, M.; Choi, A.; Grand, K.; Taff, I.; Delgado, M.; Hajianpour, M.; Seeley, A.; Rohena, L.; Vernon, H.; Gripp, K.; Vergano, S.; Mahida, S.; Naidu, S.; Sousa, A.; Wain, K.; Challman, T.; Beek, G.; Basel, D.; Ranells, J.; Smith, R.; Yusupov, R.; Freckmann, M.; Ohden, L.; Davis-Keppen, L.; Chitayat, D.; Dowling, J.; Finkel, R.; Dauber, A.; Spillmann, R.; Pena, L.; Metcalfe, K.; Splitt, M.; Lachlan, K.; McKee, S.; Hurst, J.; Fitzpatrick, D.; Morton, J.; Cox, H.; Venkateswaran, S.; Young, J.; Marsh, E.; Nelson, S.; Martinez, J.; Graham, J.; Kini, U.; Mackay, J.; Pierson, T.; and Network, T. U. D.\n\n\n \n\n\n\n Genetics in Medicine, 22(4): 822. 2020.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Correction:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Shieh2020822,\nauthor={Shieh, C. and Jones, N. and Vanle, B. and Au, M. and Huang, A.Y. and Silva, A.P.G. and Lee, H. and Douine, E.D. and Otero, M.G. and Choi, A. and Grand, K. and Taff, I.P. and Delgado, M.R. and Hajianpour, M.J. and Seeley, A. and Rohena, L. and Vernon, H. and Gripp, K.W. and Vergano, S.A. and Mahida, S. and Naidu, S. and Sousa, A.B. and Wain, K.E. and Challman, T.D. and Beek, G. and Basel, D. and Ranells, J. and Smith, R. and Yusupov, R. and Freckmann, M.-L. and Ohden, L. and Davis-Keppen, L. and Chitayat, D. and Dowling, J.J. and Finkel, R. and Dauber, A. and Spillmann, R. and Pena, L.D.M. and Metcalfe, K. and Splitt, M. and Lachlan, K. and McKee, S.A. and Hurst, J. and Fitzpatrick, D.R. and Morton, J.E.V. and Cox, H. and Venkateswaran, S. and Young, J.I. and Marsh, E.D. and Nelson, S.F. and Martinez, J.A. and Graham, J.M., Jr. and Kini, U. and Mackay, J.P. and Pierson, T.M. and The Undiagnosed Diseases Network},\ntitle={Correction: GATAD2B-associated neurodevelopmental disorder (GAND): clinical and molecular insights into a NuRD-related disorder (Genetics in Medicine, (2020), 10.1038/s41436-019-0747-z)},\njournal={Genetics in Medicine},\nyear={2020},\nvolume={22},\nnumber={4},\npages={822},\ndoi={10.1038/s41436-020-0760-2},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079441963&doi=10.1038%2fs41436-020-0760-2&partnerID=40&md5=0c610d08824c10fa3e027ae94beb65da},\naffiliation={David Geffen School of Medicine at UCLA, Los Angeles, CA, United States; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia; Department of Psychiatry & Behavioral Neurosciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States; Medical College of Wisconsin–Central Wisconsin, Wausau, WI, United States; Department of Pediatrics Cedars-Sinai Medical Center, Los Angeles, CA, United States; Institute for Precision Health, David Geffen School of Medicine, University of California–Los Angeles, Los Angeles, CA, United States; Department of Human Genetics and Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California–Los Angeles, Los Angeles, CA, United States; Department of Human Genetics, David Geffen School of Medicine, University of California–Los Angeles, Los Angeles, CA, United States; Board of Governor’s Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States; Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, United States; Department of Neurology, Hofstra School of Medicine, Great Neck, NY, United States; Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center and Texas Scottish Rite Hospital for Children, Dallas, TX, United States; Department of Pediatrics, Division of Medical Genetics, East Tennessee State University, Quillen College of Medicine, Mountain Home, TN, United States; Geisinger Medical Center, Danville, PA, United States; Division of Genetics, Department of Pediatrics, Brooke Army Medical Center, Fort Sam Houston, TX, United States; Department of Pediatrics, UT Health San Antonio, Long School of Medicine, San Antonio, TX, United States; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Balitmore, MD, United States; Division of Medical Genetics, Al DuPont Hospital for Children, Wilmington, DE, United States; Division of Medical Genetics and Metabolism, Children’s Hospital of The King’s Daughters, Norfolk, VA, United States; Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, United States; Department of Neurology and Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, United States; Hugo Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD, United States; Serviço de Genética Médica, Hospital Santa Maria, CHULN, Lisboa, Portugal and Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisboa, Portugal; Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, United States; Children’s Hospitals and Clinics of Minnesota Department of Genetics, Minneapolis, MN, United States; Department of Pediatrics, Division of Genetics, Children’s Hospital of Wisconsin, Milwaukee, WI, United States; Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, FL, United States; Department of Pediatrics, Division of Genetics, Maine Medical Center, Portland, ME, United States; Division of Clinical Genetics, Joe DiMaggio Children’s Hospital, Hollywood, FlL, United States; Royal North Shore Hospital, St Leonards, NSW, Australia; Department of Genetic Counseling, Sanford Children’s Specialty Clinic, Sioux Falls, SD, United States; Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, Sioux Falls, SD, United States; The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada; Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; Division of Neurology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada; Division of Pediatric Neurology, Department of Pediatrics, Nemours Children’s Hospital, Orlando, FL, United States; Division of Endocrinology, Children’s National Health System, Washington, DC, United States; Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, United States; Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Manchester Centre for Genomic Medicine, Manchester University NHS FT, Manchester, United Kingdom; Institute of Genetic Medicine, Northern Genetics Service, Newcastle upon Tyne Hospitals Trust, Newcastle, United Kingdom; Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Human Development and Health Division, Wessex Clinical Genetics Service, University Hospitals of Southampton NHS Trust, Southampton, United Kingdom; Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, United Kingdom; Department of Clinical Genetics, NE Thames Genetics Service, Great Ormond Street Hospital, London, United Kingdom; Medical Research Council Human Genetics Unit, University of Edinburgh, Edinburgh, United Kingdom; West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham, United Kingdom; Birmingham Women’s and Children’s Hospitals NHS Foundation Trust, Birmingham, United Kingdom; Birmingham Women’s Hospital, Edgbaston, Birmingham, United Kingdom; Division of Neurology, Department of Pediatrics, Children’s Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada; John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States; Division of Neurology, Children’s Hospital of Philadelphia and Department of Neurology and Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States; Department of Human Genetics; Division of Medical Genetics, Department of Pediatrics; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States; Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, CA, United States; Oxford Centre for Genomic Medicine, Oxford University Hospital NHS Foundation Trust, Oxford, United Kingdom; Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, United States; Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States},\nabstract={An amendment to this paper has been published and can be accessed via a link at the top of the paper. © 2020, American College of Medical Genetics and Genomics.},\nkeywords={erratum},\ncorrespondence_address1={Pierson, T.M.; Department of Pediatrics, United States; email: Tyler.Pierson@cshs.org},\npublisher={Springer Nature},\nissn={10983600},\ncoden={GEMEF},\npubmed_id={32047287},\nlanguage={English},\nabbrev_source_title={Gen. Med.},\ndocument_type={Erratum},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n A heme-binding protein produced by Haemophilus haemolyticus inhibits non-typeable Haemophilus influenzae.\n \n \n \n \n\n\n \n Latham, R.; Torrado, M.; Atto, B.; Walshe, J.; Wilson, R.; Guss, J.; Mackay, J.; Tristram, S.; and Gell, D.\n\n\n \n\n\n\n Molecular Microbiology, 113(2): 381-398. 2020.\n cited By 9\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 4 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Latham2020381,\nauthor={Latham, R.D. and Torrado, M. and Atto, B. and Walshe, J.L. and Wilson, R. and Guss, J.M. and Mackay, J.P. and Tristram, S. and Gell, D.A.},\ntitle={A heme-binding protein produced by Haemophilus haemolyticus inhibits non-typeable Haemophilus influenzae},\njournal={Molecular Microbiology},\nyear={2020},\nvolume={113},\nnumber={2},\npages={381-398},\ndoi={10.1111/mmi.14426},\nnote={cited By 9},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85076090830&doi=10.1111%2fmmi.14426&partnerID=40&md5=a902681f54cf60719ad21723608097b9},\naffiliation={School of Medicine, University of Tasmania, Hobart, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, Australia; School of Health Sciences, University of Tasmania, Launceston, Australia; Central Science Laboratory, University of Tasmania, Hobart, Australia},\nabstract={Commensal bacteria serve as an important line of defense against colonisation by opportunisitic pathogens, but the underlying molecular mechanisms remain poorly explored. Here, we show that strains of a commensal bacterium, Haemophilus haemolyticus, make hemophilin, a heme-binding protein that inhibits growth of the opportunistic pathogen, non-typeable Haemophilus influenzae (NTHi) in culture. We purified the NTHi-inhibitory protein from H. haemolyticus and identified the hemophilin gene using proteomics and a gene knockout. An x-ray crystal structure of recombinant hemophilin shows that the protein does not belong to any of the known heme-binding protein folds, suggesting that it evolved independently. Biochemical characterisation shows that heme can be captured in the ferrous or ferric state, and with a variety of small heme-ligands bound, suggesting that hemophilin could function under a range of physiological conditions. Hemophilin knockout bacteria show a limited capacity to utilise free heme for growth. Our data suggest that hemophilin is a hemophore and that inhibition of NTHi occurs by heme starvation, raising the possibility that competition from hemophilin-producing H. haemolyticus could antagonise NTHi colonisation in the respiratory tract. © 2019 John Wiley & Sons Ltd},\nauthor_keywords={Haemophilus haemolyticus;  hemophilin;  hemophore;  non-typeable Haemophilus influenzae (NTHi)},\nkeywords={heme;  heme binding protein;  hemophilin;  recombinant protein;  unclassified drug;  bacterial protein;  heme, agar diffusion;  Article;  bacterial growth;  bacterial strain;  bacterium culture;  bacterium isolate;  circular dichroism;  controlled study;  crystal structure;  crystallography;  gene identification;  gene knockout;  Haemophilus;  Haemophilus haemolyticus;  Haemophilus influenzae;  mass spectrometry;  nonhuman;  priority journal;  protein function;  protein purification;  proteomics;  reversed phase high performance liquid chromatography;  starvation;  ultraviolet visible spectrophotometry;  chemistry;  drug effect;  growth, development and aging;  Haemophilus;  Haemophilus infection;  Haemophilus influenzae;  human;  isolation and purification;  metabolism;  microbiology;  pharmacology, Bacterial Proteins;  Haemophilus;  Haemophilus Infections;  Haemophilus influenzae;  Heme;  Heme-Binding Proteins;  Humans},\ncorrespondence_address1={Tristram, S.; School of Health Sciences, Australia; email: stephen.tristram@utas.edu.au},\npublisher={Blackwell Publishing Ltd},\nissn={0950382X},\ncoden={MOMIE},\npubmed_id={31742788},\nlanguage={English},\nabbrev_source_title={Mol. Microbiol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Comparative structure-function analysis of bromodomain and extraterminal motif (BET) proteins in a gene-complementation system.\n \n \n \n \n\n\n \n Werner, M.; Wang, H.; Hamagami, N.; Hsu, S.; Yano, J.; Stonestrom, A.; Behera, V.; Zong, Y.; Mackay, J.; and Blobel, G.\n\n\n \n\n\n\n Journal of Biological Chemistry, 295(7): 1898-1914. 2020.\n cited By 8\n\n\n\n
\n\n\n\n \n \n $\"Comparative$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Werner20201898,\nauthor={Werner, M.T. and Wang, H. and Hamagami, N. and Hsu, S.C. and Yano, J.A. and Stonestrom, A.J. and Behera, V. and Zong, Y. and Mackay, J.P. and Blobel, G.A.},\ntitle={Comparative structure-function analysis of bromodomain and extraterminal motif (BET) proteins in a gene-complementation system},\njournal={Journal of Biological Chemistry},\nyear={2020},\nvolume={295},\nnumber={7},\npages={1898-1914},\ndoi={10.1074/jbc.RA119.010679},\nnote={cited By 8},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079473376&doi=10.1074%2fjbc.RA119.010679&partnerID=40&md5=79f955437bc67e462f539e1baf5b367d},\naffiliation={Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA  19104, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA  19104, United States; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW  2006, Australia; Division of Hematology, Children's Hospital of Philadelphia, 316 H Abramson Research Center, 3615 Civic Center Blvd, Philadelphia, PA  19104, United States},\nabstract={The widely expressed bromodomain and extraterminal motif (BET) proteins bromodomain-containing protein 2 (BRD2), BRD3, and BRD4 are multifunctional transcriptional regulators that bind acetylated chromatin via their conserved tandem bromodomains. Small molecules that target BET bromodomains are being tested for various diseases but typically do not discern between BET family members. Genomic distributions and protein partners of BET proteins have been described, but the basis for differences in BET protein function within a given lineage remains unclear. By establishing a gene knockout-rescue system in a Brd2-null erythroblast cell line, here we compared a series of mutant and chimeric BET proteins for their ability to modulate cell growth, differentiation, and gene expression. We found that the BET N-terminal halves bearing the bromodomains convey marked differences in protein stability but do not account for specificity in BET protein function. Instead, when BET proteins were expressed at comparable levels, their specificity was largely determined by the C-terminal half. Remarkably, a chimeric BET protein comprising the N-terminal half of the structurally similar short BRD4 isoform (BRD4S) and the C-terminal half of BRD2 functioned similarly to intact BRD2. We traced part of the BRD2-specific activity to a previously uncharacterized short segment predicted to harbor a coiled-coil (CC) domain. Deleting the CC segment impaired BRD2's ability to restore growth and differentiation, and the CC region functioned in conjunction with the adjacent ET domain to impart BRD2-like activity onto BRD4S. In summary, our results identify distinct BET protein domains that regulate protein turnover and biological activities. © 2020 Werner et al. Published under exclusive license by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Cell culture;  Cell proliferation;  Gene expression, Genomic distribution;  Protein functions;  Protein stability;  Protein turnovers;  Small molecules;  Specific activity;  Structure-function analysis;  Transcriptional regulator, Proteins, amino acid;  bromodomain containing protein 2;  bromodomain containing protein 3;  bromodomain containing protein 4;  fusion protein;  protein;  RNA;  transcription factor GATA 1;  unclassified drug;  BRD2 protein, human;  BRD3 protein, human;  BRD4 protein, human;  cell cycle protein;  isoprotein;  transcription factor, acetylation;  amino acid sequence;  Article;  biological activity;  carboxy terminal sequence;  cell differentiation;  cell growth;  comparative study;  controlled study;  erythroblast;  erythroid cell;  gene expression;  genetic complementation;  human;  mass spectrometry;  mouse;  nonhuman;  point mutation;  priority journal;  protein analysis;  protein domain;  protein function;  protein metabolism;  protein motif;  protein protein interaction;  protein stability;  protein structure;  protein targeting;  RNA sequence;  cell line;  cell proliferation;  chemistry;  chromatin;  gene expression regulation;  genetics;  metabolism;  molecular library;  protein motif;  structure activity relation;  ultrastructure, Acetylation;  Amino Acid Motifs;  Cell Cycle Proteins;  Cell Differentiation;  Cell Line;  Cell Proliferation;  Chromatin;  Erythroblasts;  Gene Expression Regulation;  Humans;  Protein Domains;  Protein Isoforms;  Small Molecule Libraries;  Structure-Activity Relationship;  Transcription Factors},\ncorrespondence_address1={Werner, M.T.; Perelman School of Medicine, United States; email: miwerner@pennmedicine.upenn.edu},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={31792058},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Peppy: A virtual reality environment for exploring the principles of polypeptide structure.\n \n \n \n \n\n\n \n Doak, D.; Denyer, G.; Gerrard, J.; Mackay, J.; and Allison, J.\n\n\n \n\n\n\n Protein Science, 29(1): 157-168. 2020.\n cited By 15\n\n\n\n
\n\n\n\n \n \n $\"Peppy:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Doak2020157,\nauthor={Doak, D.G. and Denyer, G.S. and Gerrard, J.A. and Mackay, J.P. and Allison, J.R.},\ntitle={Peppy: A virtual reality environment for exploring the principles of polypeptide structure},\njournal={Protein Science},\nyear={2020},\nvolume={29},\nnumber={1},\npages={157-168},\ndoi={10.1002/pro.3752},\nnote={cited By 15},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85075195261&doi=10.1002%2fpro.3752&partnerID=40&md5=496836126f38f0a580937fad9f1bfa65},\naffiliation={Games Art and Design, Norwich University of the Arts, Norwich, United Kingdom; School of Life and Environmental Sciences, University of SydneyNSW, Australia; School of Biological Sciences, University of Auckland, Auckland, New Zealand; School of Chemical Sciences, University of Auckland, Auckland, New Zealand},\nabstract={A key learning outcome for undergraduate biochemistry classes is a thorough understanding of the principles of protein structure. Traditional approaches to teaching this material, which include two-dimensional (2D) images on paper, physical molecular modeling kits, and projections of 3D structures into 2D, are unable to fully capture the dynamic 3D nature of proteins. We have built a virtual reality application, Peppy, aimed at facilitating teaching of the principles of protein secondary structure. Rather than attempt to model molecules with the same fidelity to the underlying physical chemistry as existing, research-oriented molecular modelling approaches, we took the more straightforward approach of harnessing the Unity video game physics engine. Indeed, the simplicity and limitations of our model are strengths in a teaching context, provoking questions and thus deeper understanding. Peppy allows exploration of the relative effects of hydrogen bonding (and electrostatic interactions more generally), backbone φ/ψ angles, basic chemical structure, and steric effects on a polypeptide structure in an accessible format that is novel, dynamic, and fun to use. Apart from describing the implementation and use of Peppy, we discuss the outcomes of deploying Peppy in undergraduate biochemistry courses. © 2019 The Protein Society},\nauthor_keywords={polypeptide;  protein;  secondary structure;  teaching;  undergraduate;  virtual reality},\nkeywords={article;  biochemistry;  conformation;  hydrogen bond;  learning;  molecular model;  physical chemistry;  physics;  protein secondary structure;  static electricity;  structure activity relation;  teaching;  video game;  virtual reality;  chemistry;  computer interface;  education;  human;  protein secondary structure;  virtual reality, peptide, Biochemistry;  Humans;  Hydrogen Bonding;  Models, Molecular;  Peptides;  Protein Structure, Secondary;  User-Computer Interface;  Video Games;  Virtual Reality},\ncorrespondence_address1={Doak, D.G.; Games Art and Design, United Kingdom; email: david@ddoak.com},\npublisher={Blackwell Publishing Ltd},\nissn={09618368},\ncoden={PRCIE},\npubmed_id={31622516},\nlanguage={English},\nabbrev_source_title={Protein Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2019\n \n \n (4)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n The NuRD complex and macrocephaly associated neurodevelopmental disorders.\n \n \n \n \n\n\n \n Pierson, T.; Otero, M.; Grand, K.; Choi, A.; Graham, J.; Young, J.; and Mackay, J.\n\n\n \n\n\n\n American Journal of Medical Genetics, Part C: Seminars in Medical Genetics, 181(4): 548-556. 2019.\n cited By 15\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Pierson2019548,\nauthor={Pierson, T.M. and Otero, M.G. and Grand, K. and Choi, A. and Graham, J.M., Jr. and Young, J.I. and Mackay, J.P.},\ntitle={The NuRD complex and macrocephaly associated neurodevelopmental disorders},\njournal={American Journal of Medical Genetics, Part C: Seminars in Medical Genetics},\nyear={2019},\nvolume={181},\nnumber={4},\npages={548-556},\ndoi={10.1002/ajmg.c.31752},\nnote={cited By 15},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85075278859&doi=10.1002%2fajmg.c.31752&partnerID=40&md5=d7025caae0e93a87de39dcc2a1f6355d},\naffiliation={Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, United States; Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, United States; Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States; Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, CA, United States; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, United States; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia},\nabstract={The nucleosome remodeling and deacetylase (NuRD) complex is a major regulator of gene expression involved in pluripotency, lineage commitment, and corticogenesis. This important complex is composed of seven different proteins, with mutations in CHD3, CHD4, and GATAD2B being associated with neurodevelopmental disorders presenting with macrocephaly and intellectual disability similar to other overgrowth and intellectual disability (OGID) syndromes. Pathogenic variants in CHD3 and CHD4 primarily involve disruption of enzymatic function. GATAD2B variants include loss-of-function mutations that alter protein dosage and missense variants that involve either of two conserved domains (CR1 and CR2) known to interact with other NuRD proteins. In addition to macrocephaly and intellectual disability, CHD3 variants are associated with inguinal hernias and apraxia of speech; whereas CHD4 variants are associated with skeletal anomalies, deafness, and cardiac defects. GATAD2B-associated neurodevelopmental disorder (GAND) has phenotypic overlap with both of these disorders. Of note, structural models of NuRD indicate that CHD3 and CHD4 require direct contact with the GATAD2B-CR2 domain to interact with the rest of the complex. Therefore, the phenotypic overlaps of CHD3- and CHD4-related disorders with GAND are consistent with a loss in the ability of GATAD2B to recruit CHD3 or CHD4 to the complex. The shared features of these neurodevelopmental disorders may represent a new class of OGID syndrome: the NuRDopathies. © 2019 Wiley Periodicals, Inc.},\nauthor_keywords={CHD3;  CHD4;  GATAD2B;  macrocephaly;  NuRD complex},\nkeywords={hydrolase;  nucleosome remodeling and deacetylase complex;  unclassified drug;  DNA binding protein;  histone deacetylase, apraxia of speech;  Article;  CHD3 gene;  CHD4 gene;  GATAD2B gene;  gene;  gene mutation;  genetic variability;  human;  inguinal hernia;  intellectual impairment;  loss of function mutation;  macrocephaly;  mental disease;  missense mutation;  priority journal;  Sifrim Hitz Weiss syndrome;  Snijders Blok Campeau syndrome;  Alexander disease;  genetics;  mental disease;  metabolism;  physiology;  syndrome, DNA-Binding Proteins;  Humans;  Megalencephaly;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Neurodevelopmental Disorders;  Syndrome},\ncorrespondence_address1={Pierson, T.M.; Department of Pediatrics, United States; email: tyler.pierson@cshs.org},\npublisher={Blackwell Publishing Inc.},\nissn={15524868},\ncoden={AMSGF},\npubmed_id={31737996},\nlanguage={English},\nabbrev_source_title={Am. J. Med. Genet. Part C Semin. Med. Genet.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Exploring the suitability of RanBP2-type Zinc Fingers for RNA-binding protein design.\n \n \n \n \n\n\n \n De Franco, S.; Vandenameele, J.; Brans, A.; Verlaine, O.; Bendak, K.; Damblon, C.; Matagne, A.; Segal, D.; Galleni, M.; Mackay, J.; and Vandevenne, M.\n\n\n \n\n\n\n Scientific Reports, 9(1). 2019.\n cited By 4\n\n\n\n
\n\n\n\n \n \n $\"Exploring$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 6 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{DeFranco2019,\nauthor={De Franco, S. and Vandenameele, J. and Brans, A. and Verlaine, O. and Bendak, K. and Damblon, C. and Matagne, A. and Segal, D.J. and Galleni, M. and Mackay, J.P. and Vandevenne, M.},\ntitle={Exploring the suitability of RanBP2-type Zinc Fingers for RNA-binding protein design},\njournal={Scientific Reports},\nyear={2019},\nvolume={9},\nnumber={1},\ndoi={10.1038/s41598-019-38655-y},\nart_number={2484},\nnote={cited By 4},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85061971393&doi=10.1038%2fs41598-019-38655-y&partnerID=40&md5=bf0e317ed376e6fa82a237ed574264dc},\naffiliation={InBioS-Centre d’Ingénierie des Protéines (CIP), Université de Liège, Liège, 4000, Belgium; Children’s Cancer Institute Lowy Cancer Research, Kensington, 2033, Australia; Laboratoire de Chimie Biologique Structurale (CBS), Département de Chimie, Université de Liège, Liège, 4000, Belgium; Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA  95616, United States; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW  2006, Australia},\nabstract={Transcriptomes consist of several classes of RNA that have wide-ranging but often poorly described functions and the deregulation of which leads to numerous diseases. Engineering of functionalized RNA-binding proteins (RBPs) could therefore have many applications. Our previous studies suggested that the RanBP2-type Zinc Finger (ZF) domain is a suitable scaffold to investigate the design of single-stranded RBPs. In the present work, we have analyzed the natural sequence specificity of various members of the RanBP2-type ZF family and characterized the interaction with their target RNA. Surprisingly, our data showed that natural RanBP2-type ZFs with different RNA-binding residues exhibit a similar sequence specificity and therefore no simple recognition code can be established. Despite this finding, different discriminative abilities were observed within the family. In addition, in order to target a long RNA sequence and therefore gain in specificity, we generated a 6-ZF array by combining ZFs from the RanBP2-type family but also from different families, in an effort to achieve a wider target sequence repertoire. We showed that this chimeric protein recognizes its target sequence (20 nucleotides), both in vitro and in living cells. Altogether, our results indicate that the use of ZFs in RBP design remains attractive even though engineering of specificity changes is challenging. © 2019, The Author(s).},\nkeywords={protein binding;  RNA;  RNA binding protein;  zinc finger protein;  ZRANB2 protein, human, binding site;  chemistry;  drug design;  genetics;  human;  metabolism;  molecular model;  nucleotide sequence;  procedures;  protein conformation;  protein engineering;  structure activity relation;  systematic evolution of ligands by exponential enrichment aptamer technique, Base Sequence;  Binding Sites;  Drug Design;  Humans;  Models, Molecular;  Protein Binding;  Protein Conformation;  Protein Engineering;  RNA;  RNA-Binding Proteins;  SELEX Aptamer Technique;  Structure-Activity Relationship;  Zinc Fingers},\ncorrespondence_address1={Galleni, M.; InBioS-Centre d’Ingénierie des Protéines (CIP), Belgium; email: mgalleni@uliege.be},\npublisher={Nature Publishing Group},\nissn={20452322},\npubmed_id={30792407},\nlanguage={English},\nabbrev_source_title={Sci. Rep.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The uncharacterized bacterial protein YejG has the same architecture as domain III of elongation factor G.\n \n \n \n \n\n\n \n Mohanty, B.; Hanson-Manful, P.; Finn, T.; Chambers, C.; McKellar, J.; Macindoe, I.; Helder, S.; Setiyaputra, S.; Zhong, Y.; Mackay, J.; and Patrick, W.\n\n\n \n\n\n\n Proteins: Structure, Function and Bioinformatics, 87(8): 699-705. 2019.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mohanty2019699,\nauthor={Mohanty, B. and Hanson-Manful, P. and Finn, T.J. and Chambers, C.R. and McKellar, J.L.O. and Macindoe, I. and Helder, S. and Setiyaputra, S. and Zhong, Y. and Mackay, J.P. and Patrick, W.M.},\ntitle={The uncharacterized bacterial protein YejG has the same architecture as domain III of elongation factor G},\njournal={Proteins: Structure, Function and Bioinformatics},\nyear={2019},\nvolume={87},\nnumber={8},\npages={699-705},\ndoi={10.1002/prot.25687},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064682096&doi=10.1002%2fprot.25687&partnerID=40&md5=c754ab7922a60498496e97b94bf9cf3e},\naffiliation={Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia; Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand; Department of Biochemistry, University of Otago, Dunedin, New Zealand; School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia; School of Biological Sciences, Victoria University, Wellington, New Zealand},\nabstract={InterPro family IPR020489 comprises ~1000 uncharacterized bacterial proteins. Previously we showed that overexpressing the Escherichia coli representative of this family, EcYejG, conferred low-level resistance to aminoglycoside antibiotics. In an attempt to shed light on the biochemical function of EcYejG, we have solved its structure using multinuclear solution NMR spectroscopy. The structure most closely resembles that of domain III from elongation factor G (EF-G). EF-G catalyzes ribosomal translocation and mutations in EF-G have also been associated with aminoglycoside resistance. While we were unable to demonstrate a direct interaction between EcYejG and the ribosome, the protein might play a role in translation. © 2019 Wiley Periodicals, Inc.},\nauthor_keywords={aminoglycoside;  elongation factor;  IPR020489;  NMR;  PF13989;  RNA recognition motif},\nkeywords={aminoglycoside;  bacterial protein;  elongation factor G;  unclassified drug;  YejG protein;  elongation factor G, aminoglycoside resistance;  Article;  controlled study;  mutation;  nonhuman;  nuclear magnetic resonance spectroscopy;  priority journal;  protein analysis;  protein domain;  protein function;  protein structure;  RNA recognition motif;  chemistry;  Escherichia coli;  molecular model;  nuclear magnetic resonance;  protein conformation;  protein domain;  protein synthesis;  ribosome, Escherichia coli;  Models, Molecular;  Nuclear Magnetic Resonance, Biomolecular;  Peptide Elongation Factor G;  Protein Biosynthesis;  Protein Conformation;  Protein Domains;  Ribosomes},\ncorrespondence_address1={Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={John Wiley and Sons Inc.},\nissn={08873585},\npubmed_id={30958578},\nlanguage={English},\nabbrev_source_title={Proteins Struct. Funct. Bioinformatics},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The stoichiometry and interactome of the Nucleosome Remodeling and Deacetylase (NuRD) complex are conserved across multiple cell lines.\n \n \n \n \n\n\n \n Sharifi Tabar, M.; Mackay, J.; and Low, J.\n\n\n \n\n\n\n FEBS Journal, 286(11): 2043-2061. 2019.\n cited By 13\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{SharifiTabar20192043,\nauthor={Sharifi Tabar, M. and Mackay, J.P. and Low, J.K.K.},\ntitle={The stoichiometry and interactome of the Nucleosome Remodeling and Deacetylase (NuRD) complex are conserved across multiple cell lines},\njournal={FEBS Journal},\nyear={2019},\nvolume={286},\nnumber={11},\npages={2043-2061},\ndoi={10.1111/febs.14800},\nnote={cited By 13},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85063166416&doi=10.1111%2ffebs.14800&partnerID=40&md5=7adbaf425e6b2de40eb9c607524ce7af},\naffiliation={School of Life and Environmental Sciences, University of Sydney, Australia},\nabstract={The nucleosome remodelling and deacetylase complex (NuRD) is a widely conserved regulator of gene expression. The determination of the subunit composition of the complex and identification of its binding partners are important steps towards understanding its architecture and function. The question of how these properties of the complex vary across different cell types has not been addressed in detail to date. Here, we set up a two-step purification protocol coupled to liquid chromatography-tandem mass spectrometry to assess NuRD composition and interaction partners in three different cancer cell lines, using label-free intensity-based absolute quantification (iBAQ). Our data indicate that the stoichiometry of the NuRD complex is preserved across our three different cancer cell lines. In addition, our interactome data suggest ZNF219 and SLC25A5 as possible interaction partners of the complex. To corroborate this latter finding, in vitro and cell-based pull-down experiments were carried out. These experiments indicated that ZNF219 can interact with RBBP4, GATAD2A/B and chromodomain helicase DNA binding 4, whereas SLC25A5 might interact with MTA2 and GATAD2A. © 2019 Federation of European Biochemical Societies},\nauthor_keywords={iBAQ stoichiometry;  NuRD;  protein-protein interactions;  SLC25A5;  ZNF219},\nkeywords={chromodomain helicase DNA binding 4;  DNA binding protein;  hydrolase;  membrane protein;  membrane protein SLC25A5;  nucleosome remodeling and deacetylase complex;  protein;  protein GATAD2A;  protein GATAD2B;  protein MTA2;  retinoblastoma binding protein 4;  unclassified drug;  zinc finger protein;  zinc finger protein ZNF219;  adenine nucleotide translocase;  DNA binding protein;  histone deacetylase;  messenger RNA;  recombinant protein;  RNA;  tumor protein;  zinc finger protein;  ZNF219 protein, human, Article;  cancer cell;  controlled study;  enzyme activity;  enzyme analysis;  enzyme purification;  enzyme structure;  human;  human cell;  in vitro study;  intensity based absolute quantification;  liquid chromatography-mass spectrometry;  male;  MCF-7 cell line;  molecular interaction;  NTERA-2 cell line;  PC-3 [Human prostate carcinoma] cell line;  priority journal;  protein protein interaction;  quantitative analysis;  stoichiometry;  affinity chromatography;  biosynthesis;  chemistry;  comparative study;  density gradient centrifugation;  gene expression profiling;  genetics;  liquid chromatography;  metabolism;  neoplasm;  pathology;  procedures;  protein analysis;  protein subunit;  tandem mass spectrometry;  tumor cell line, Adenine Nucleotide Translocator 2;  Cell Line, Tumor;  Centrifugation, Density Gradient;  Chromatography, Affinity;  Chromatography, Liquid;  DNA-Binding Proteins;  Gene Expression Profiling;  Humans;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Neoplasm Proteins;  Neoplasms;  Protein Interaction Mapping;  Protein Interaction Maps;  Protein Subunits;  Recombinant Proteins;  RNA, Messenger;  RNA, Neoplasm;  Tandem Mass Spectrometry;  Zinc Fingers},\ncorrespondence_address1={Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Blackwell Publishing Ltd},\nissn={1742464X},\ncoden={FJEOA},\npubmed_id={30828972},\nlanguage={English},\nabbrev_source_title={FEBS J.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2018\n \n \n (7)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence.\n \n \n \n \n\n\n \n Lu, B.; Klingbeil, O.; Tarumoto, Y.; Somerville, T.; Huang, Y.; Wei, Y.; Wai, D.; Low, J.; Milazzo, J.; Wu, X.; Cao, Z.; Yan, X.; Demerdash, O.; Huang, G.; Mackay, J.; Kinney, J.; Shi, J.; and Vakoc, C.\n\n\n \n\n\n\n Cancer Cell, 34(6): 970-981.e8. 2018.\n cited By 26\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Lu2018970,\nauthor={Lu, B. and Klingbeil, O. and Tarumoto, Y. and Somerville, T.D.D. and Huang, Y.-H. and Wei, Y. and Wai, D.C. and Low, J.K.K. and Milazzo, J.P. and Wu, X.S. and Cao, Z. and Yan, X. and Demerdash, O.E. and Huang, G. and Mackay, J.P. and Kinney, J.B. and Shi, J. and Vakoc, C.R.},\ntitle={A Transcription Factor Addiction in Leukemia Imposed by the MLL Promoter Sequence},\njournal={Cancer Cell},\nyear={2018},\nvolume={34},\nnumber={6},\npages={970-981.e8},\ndoi={10.1016/j.ccell.2018.10.015},\nnote={cited By 26},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85058593248&doi=10.1016%2fj.ccell.2018.10.015&partnerID=40&md5=94952285920daee3b271e70dbe9b4aa8},\naffiliation={Cold Spring Harbor Laboratory, Cold Spring Harbor, NY  11724, United States; School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW  2006, Australia; Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH  45229, United States; Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA  19104, United States},\nabstract={The Mixed Lineage Leukemia gene (MLL) is altered in leukemia by chromosomal translocations to produce oncoproteins composed of the MLL N-terminus fused to the C-terminus of a partner protein. Here, we used domain-focused CRISPR screening to identify ZFP64 as an essential transcription factor in MLL-rearranged leukemia. We show that the critical function of ZFP64 in leukemia is to maintain MLL expression via binding to the MLL promoter, which is the most enriched location of ZFP64 occupancy in the human genome. The specificity of ZFP64 for MLL is accounted for by an exceptional density of ZFP64 motifs embedded within the MLL promoter. These findings demonstrate how a sequence anomaly of an oncogene promoter can impose a transcriptional addiction in cancer. © 2018 Elsevier Inc.\nLu et al. show that MLL-rearranged leukemia is addicted to the transcription factor ZFP64 due to direct regulation of MLL by ZFP64. The MLL promoter has an unusually high number of ZFP64 binding motifs and is the most enriched location of ZFP64 occupancy in the human genome. © 2018 Elsevier Inc.},\nauthor_keywords={addiction;  CRISPR screen;  leukemia;  MLL;  motif;  oncogene;  promoter;  ZFP64},\nkeywords={transcription factor;  transcription factor ZFP64;  unclassified drug, amino terminal sequence;  animal cell;  animal experiment;  animal model;  animal tissue;  Article;  carboxy terminal sequence;  chromosome translocation;  controlled study;  gene;  gene expression;  leukemia;  mixed lineage leukemia gene;  mouse;  nonhuman;  priority journal;  promoter region},\ncorrespondence_address1={Shi, J.; Department of Cancer Biology, United States; email: jushi@upenn.edu},\npublisher={Cell Press},\nissn={15356108},\ncoden={CCAEC},\npubmed_id={30503706},\nlanguage={English},\nabbrev_source_title={Cancer Cell},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex.\n \n \n \n \n\n\n \n Link, S.; Spitzer, R.; Sana, M.; Torrado, M.; Völker-Albert, M.; Keilhauer, E.; Burgold, T.; Pünzeler, S.; Low, J.; Lindström, I.; Nist, A.; Regnard, C.; Stiewe, T.; Hendrich, B.; Imhof, A.; Mann, M.; Mackay, J.; Bartkuhn, M.; and Hake, S.\n\n\n \n\n\n\n Nature Communications, 9(1). 2018.\n cited By 28\n\n\n\n
\n\n\n\n \n \n $\"PWWP2A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Link2018,\nauthor={Link, S. and Spitzer, R.M.M. and Sana, M. and Torrado, M. and Völker-Albert, M.C. and Keilhauer, E.C. and Burgold, T. and Pünzeler, S. and Low, J.K.K. and Lindström, I. and Nist, A. and Regnard, C. and Stiewe, T. and Hendrich, B. and Imhof, A. and Mann, M. and Mackay, J.P. and Bartkuhn, M. and Hake, S.B.},\ntitle={PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex},\njournal={Nature Communications},\nyear={2018},\nvolume={9},\nnumber={1},\ndoi={10.1038/s41467-018-06665-5},\nart_number={4300},\nnote={cited By 28},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85055075794&doi=10.1038%2fs41467-018-06665-5&partnerID=40&md5=0091e9513d65502a71ba3ee0aa0b5829},\naffiliation={Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, Planegg-Martinsried, 82152, Germany; Institute for Genetics, Justus-Liebig University Giessen, Giessen, 35392, Germany; School of Life and Environmental Sciences, University of SydneyNSW  2006, Australia; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany; Wellcome Trust – MRC Stem Cell Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, United Kingdom; Genomics Core Facility, Philipps-University Marburg, Marburg, 35043, Germany; Institute for Molecular Oncology, Philipps-University Marburg, Marburg, 35043, Germany; Center for Integrated Protein Science Munich (CIPSM), Munich, 81377, Germany; Coriolis Pharma, Fraunhoferstr. 18B, Planegg, 82152, Germany; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton  CB10 1SA, United Kingdom; Coparion GmbH & Co. KG, Charles-de-Gaulle-Platz 1d, Cologne, 50679, Germany},\nabstract={Chromatin structure and function is regulated by reader proteins recognizing histone modifications and/or histone variants. We recently identified that PWWP2A tightly binds to H2A.Z-containing nucleosomes and is involved in mitotic progression and cranial–facial development. Here, using in vitro assays, we show that distinct domains of PWWP2A mediate binding to free linker DNA as well as H3K36me3 nucleosomes. In vivo, PWWP2A strongly recognizes H2A.Z-containing regulatory regions and weakly binds H3K36me3-containing gene bodies. Further, PWWP2A binds to an MTA1-specific subcomplex of the NuRD complex (M1HR), which consists solely of MTA1, HDAC1, and RBBP4/7, and excludes CHD, GATAD2 and MBD proteins. Depletion of PWWP2A leads to an increase of acetylation levels on H3K27 as well as H2A.Z, presumably by impaired chromatin recruitment of M1HR. Thus, this study identifies PWWP2A as a complex chromatin-binding protein that serves to direct the deacetylase complex M1HR to H2A.Z-containing chromatin, thereby promoting changes in histone acetylation levels. © 2018, The Author(s).},\nkeywords={histone;  histone deacetylase;  histone H2A.F-Z;  lysine;  Mta1 protein, human;  nonhistone protein;  PWWP2A protein, human;  repressor protein;  small interfering RNA, acetylation;  animal;  chromatin;  genetics;  HEK293 cell line;  human;  metabolism;  methylation;  mouse;  nucleosome, Acetylation;  Animals;  Chromatin;  Chromosomal Proteins, Non-Histone;  HEK293 Cells;  Histone Deacetylases;  Histones;  Humans;  Lysine;  Methylation;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Mice;  Nucleosomes;  Repressor Proteins;  RNA, Small Interfering},\ncorrespondence_address1={Bartkuhn, M.; Institute for Genetics, Germany; email: marek.bartkuhn@gen.bio.uni-giessen},\npublisher={Nature Publishing Group},\nissn={20411723},\npubmed_id={30327463},\nlanguage={English},\nabbrev_source_title={Nat. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n NMR spectroscopy in the analysis of protein-protein interactions.\n \n \n \n \n\n\n \n Gell, D.; Kwan, A.; and Mackay, J.\n\n\n \n\n\n\n Springer International Publishing, 2018.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"NMR$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@BOOK{Gell20182099,\nauthor={Gell, D.A. and Kwan, A.H. and Mackay, J.P.},\ntitle={NMR spectroscopy in the analysis of protein-protein interactions},\njournal={Modern Magnetic Resonance},\nyear={2018},\npages={2099-2132},\ndoi={10.1007/978-3-319-28388-3_121},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054381005&doi=10.1007%2f978-3-319-28388-3_121&partnerID=40&md5=de16992134050e970ff7e240eed7ada4},\naffiliation={School of Medicine, University of Tasmania, Hobart, TAS, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia},\nabstract={Protein-protein interactions are a central aspect of biology and NMR spectroscopy is one of the most powerful and versatile methods available to characterize their structure, dynamics, kinetics and thermodynamics. In this article, we give an overview of the suite of approaches available to the researcher who wishes to understand their favourite protein-protein interaction in more detail. We begin with an outline of two fundamental concepts that are important for understanding the strengths and limitations of NMR spectroscopy - nuclear spin relaxation and chemical exchange. We then present a range of methods including chemical shift perturbation analysis, nuclear Overhauser effects (and its derivatives), residual dipolar couplings, paramagnetic approaches, solid-state NMR and the analysis of low-abundance species. Each method is accompanied by recen texamples from the literature. Together, these techniques can allow both broad and deep insight into the mechanistic underpinnings of protein-protein interactions. © Springer International Publishing AG, part of Springer Nature 2018.},\nauthor_keywords={Chemical exchange;  Chemical shift perturbation;  Cross-saturation;  Dark states;  Macromolecular NMR spectroscopy;  Methyl-TROSY;  Protein complexes;  Protein-protein interactions},\nkeywords={Chemical analysis;  Chemical shift;  Nuclear magnetic resonance spectroscopy;  Spectrum analysis;  Thermodynamics, Chemical exchange;  Chemical shift perturbations;  Cross saturation;  Dark state;  Methyl-TROSY;  Protein complexes;  Protein-protein interactions, Proteins},\ncorrespondence_address1={Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Springer International Publishing},\nisbn={9783319283883; 9783319283876},\nlanguage={English},\nabbrev_source_title={Mod. Magn. Reson.},\ndocument_type={Book Chapter},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators.\n \n \n \n \n\n\n \n Wai, D.; Szyszka, T.; Campbell, A.; Kwong, C.; Lorna, E.; Silva, A.; Low, J.; Kwan, A.; Gamsjaeger, R.; Chalmers, J.; Patrick, W.; Lu, B.; Vakoc, C.; Blobel, G.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 293(19): 7160-7175. 2018.\n cited By 22\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Wai20187160,\nauthor={Wai, D.C.C. and Szyszka, T.N. and Campbell, A.E. and Kwong, C. and Lorna, E.W.-W. and Silva, A.P.G. and Low, J.K.K. and Kwan, A.H. and Gamsjaeger, R. and Chalmers, J.D. and Patrick, W.M. and Lu, B. and Vakoc, C.R. and Blobel, G.A. and Mackay, J.P.},\ntitle={The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators},\njournal={Journal of Biological Chemistry},\nyear={2018},\nvolume={293},\nnumber={19},\npages={7160-7175},\ndoi={10.1074/jbc.RA117.000678},\nnote={cited By 22},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85047097831&doi=10.1074%2fjbc.RA117.000678&partnerID=40&md5=5341db36fef79b3f4d2dbbd19e0aa4da},\naffiliation={School of Life and Environmental Sciences, University of SydneyNSW  2006, Australia; Division of Hematology, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA  19104, United States; Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY  11724, United States},\nabstract={Members of the bromodomain and extra-terminal domain (BET) family of proteins (bromodomain-containing (BRD) 2, 3, 4, and T) are widely expressed and highly conserved regulators of gene expression in eukaryotes. These proteins have been intimately linked to human disease, and more than a dozen clinical trials are currently underway to test BET-protein inhibitors as modulators of cancer. However, although it is clear that these proteins use their bromodomains to bind both histones and transcription factors bearing acetylated lysine residues, the molecular mechanisms by which BET family proteins regulate gene expression are not well defined. In particular, the functions of the other domains such as the ET domain have been less extensively studied. Here, we examine the properties of the ET domain of BRD3 as a protein/protein interaction module. Using a combination of pulldown and biophysical assays, we demonstrate that BRD3 binds to a range of chromatin-remodeling complexes, including the NuRD, BAF, and INO80 complexes, via a short linear “KIKL” motif in one of the complex subunits. NMR-based structural analysis revealed that, surprisingly, this mode of interaction is shared by the AF9 and ENL transcriptional coregulators that contain an acetyl-lysine-binding YEATS domain and regulate transcriptional elongation. This observation establishes a functional commonality between these two families of cancer-related transcriptional regulators. In summary, our data provide insight into the mechanisms by which BET family proteins might link chromatin acetylation to transcriptional outcomes and uncover an unexpected functional similarity between BET and YEATS family proteins. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Acetylation;  Amino acids;  Diseases;  Transcription, Chromatin remodeling complex;  Functional similarity;  Interaction modules;  Molecular mechanism;  Protein inhibitors;  Transcriptional coregulators;  Transcriptional elongations;  Transcriptional regulator, Proteins, barrier to autointegration factor;  bromodomain containing 3 protein;  regulator protein;  unclassified drug;  BANF1 protein, human;  BRD3 protein, human;  CHD4 protein, human;  DNA binding protein;  DNA helicase;  histone deacetylase;  INO80 protein, human;  nuclear protein;  peptide;  protein binding;  RNA binding protein;  transactivator protein, amino acid substitution;  amino terminal sequence;  Article;  binding affinity;  carboxy terminal sequence;  conserved sequence;  controlled study;  embryo;  human;  human cell;  hydrophobicity;  molecular recognition;  mutant;  nonhuman;  nuclear magnetic resonance;  nucleotide motif;  priority journal;  protein domain;  protein protein interaction;  sequence analysis;  sequence homology;  surface plasmon resonance;  wild type;  acetylation;  amino acid sequence;  biophysics;  chemistry;  chromatin assembly and disassembly;  gene expression regulation;  gene regulatory network;  HEK293 cell line;  metabolism;  physiology;  protein domain;  protein motif, Acetylation;  Amino Acid Motifs;  Amino Acid Sequence;  Biophysical Phenomena;  Chromatin Assembly and Disassembly;  DNA Helicases;  DNA-Binding Proteins;  Gene Expression Regulation;  Gene Regulatory Networks;  HEK293 Cells;  Humans;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Nuclear Proteins;  Peptides;  Protein Binding;  Protein Domains;  RNA-Binding Proteins;  Sequence Homology, Amino Acid;  Trans-Activators},\ncorrespondence_address1={Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={29567837},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Crystal structure of the Melampsora lini effector AvrP reveals insights into a possible nuclear function and recognition by the flax disease resistance protein P.\n \n \n \n \n\n\n \n Zhang, X.; Farah, N.; Rolston, L.; Ericsson, D.; Catanzariti, A.; Bernoux, M.; Ve, T.; Bendak, K.; Chen, C.; Mackay, J.; Lawrence, G.; Hardham, A.; Ellis, J.; Williams, S.; Dodds, P.; Jones, D.; and Kobe, B.\n\n\n \n\n\n\n Molecular Plant Pathology, 19(5): 1196-1209. 2018.\n cited By 13\n\n\n\n
\n\n\n\n \n \n $\"Crystal$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Zhang20181196,\nauthor={Zhang, X. and Farah, N. and Rolston, L. and Ericsson, D.J. and Catanzariti, A.-M. and Bernoux, M. and Ve, T. and Bendak, K. and Chen, C. and Mackay, J.P. and Lawrence, G.J. and Hardham, A. and Ellis, J.G. and Williams, S.J. and Dodds, P.N. and Jones, D.A. and Kobe, B.},\ntitle={Crystal structure of the Melampsora lini effector AvrP reveals insights into a possible nuclear function and recognition by the flax disease resistance protein P},\njournal={Molecular Plant Pathology},\nyear={2018},\nvolume={19},\nnumber={5},\npages={1196-1209},\ndoi={10.1111/mpp.12597},\nnote={cited By 13},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85034222061&doi=10.1111%2fmpp.12597&partnerID=40&md5=c9ad59e0267ade0a2b3bda6b6ad11132},\naffiliation={School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre and Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD  4072, Australia; Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, ACT  2601, Australia; Division of Plant Sciences, Research School of Biology, Australian National University, Acton, ACT  2601, Australia; Australian Synchrotron, Macromolecular crystallography, Clayton, VIC  3168, Australia; Institute for Glycomics, Griffith University, Southport, QLD  4222, Australia; School of Molecular Bioscience, University of Sydney, Sydney, NSW  2006, Australia},\nabstract={The effector protein AvrP is secreted by the flax rust fungal pathogen (Melampsora lini) and recognized specifically by the flax (Linum usitatissimum) P disease resistance protein, leading to effector-triggered immunity. To investigate the biological function of this effector and the mechanisms of specific recognition by the P resistance protein, we determined the crystal structure of AvrP. The structure reveals an elongated zinc-finger-like structure with a novel interleaved zinc-binding topology. The residues responsible for zinc binding are conserved in AvrP effector variants and mutations of these motifs result in a loss of P-mediated recognition. The first zinc-coordinating region of the structure displays a positively charged surface and shows some limited similarities to nucleic acid-binding and chromatin-associated proteins. We show that the majority of the AvrP protein accumulates in the plant nucleus when transiently expressed in Nicotiana benthamiana cells, suggesting a nuclear pathogenic function. Polymorphic residues in AvrP and its allelic variants map to the protein surface and could be associated with differences in recognition specificity. Several point mutations of residues on the non-conserved surface patch result in a loss of recognition by P, suggesting that these residues are required for recognition. © 2017 BSPP AND JOHN WILEY & SONS LTD},\nauthor_keywords={crystal structure;  effector-triggered immunity;  flax rust (Melampsora lini) effector;  NLR [nucleotide-binding and oligomerization domain (NOD)-like receptor;  nuclear localization;  nucleotide-binding/leucine-rich repeat receptor];  plant disease resistance;  zinc finger},\nkeywords={fungal protein;  plant protein;  protein binding;  zinc, Agrobacterium;  amino acid sequence;  Basidiomycetes;  cell nucleus;  chemistry;  conserved sequence;  disease resistance;  flax;  genetics;  metabolism;  microbiology;  molecular model;  plant cell;  plant disease;  protein domain;  protein motif;  Saccharomyces cerevisiae;  structural homology;  tobacco;  X ray crystallography, Agrobacterium;  Amino Acid Motifs;  Amino Acid Sequence;  Basidiomycota;  Cell Nucleus;  Conserved Sequence;  Crystallography, X-Ray;  Disease Resistance;  Flax;  Fungal Proteins;  Models, Molecular;  Plant Cells;  Plant Diseases;  Plant Proteins;  Protein Binding;  Protein Domains;  Saccharomyces cerevisiae;  Structural Homology, Protein;  Tobacco;  Zinc},\ncorrespondence_address1={Zhang, X.; School of Chemistry and Molecular Biosciences, Australia; email: xiaoxiao.zhang@csiro.au},\npublisher={Blackwell Publishing Ltd},\nissn={14646722},\ncoden={MPPAF},\npubmed_id={28817232},\nlanguage={English},\nabbrev_source_title={Mol. Plant Pathol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Expression, purification and DNA-binding properties of zinc finger domains of DOF proteins from Arabidopsis thaliana.\n \n \n \n \n\n\n \n Sani, H.; Hamzeh-Mivehroud, M.; Silva, A.; Walshe, J.; Abolghasem Mohammadi, S.; Rahbar-Shahrouziasl, M.; Abbasi, M.; Jamshidi, O.; Low, J.; Dastmalchi, S.; and Mackay, J.\n\n\n \n\n\n\n BioImpacts, 8(3): 167-176. 2018.\n cited By 8\n\n\n\n
\n\n\n\n \n \n $\"Expression,$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Sani2018167,\nauthor={Sani, H.M. and Hamzeh-Mivehroud, M. and Silva, A.P. and Walshe, J.L. and Abolghasem Mohammadi, S. and Rahbar-Shahrouziasl, M. and Abbasi, M. and Jamshidi, O. and Low, J.K.K. and Dastmalchi, S. and Mackay, J.P.},\ntitle={Expression, purification and DNA-binding properties of zinc finger domains of DOF proteins from Arabidopsis thaliana},\njournal={BioImpacts},\nyear={2018},\nvolume={8},\nnumber={3},\npages={167-176},\ndoi={10.15171/bi.2018.19},\nnote={cited By 8},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85050667095&doi=10.15171%2fbi.2018.19&partnerID=40&md5=118d06b4b5c86f61e981d401560d0397},\naffiliation={Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; School of Life and Environmental Sciences, The University of SydneyNSW  2006, Australia; School of Agriculture, University of Tabriz, Tabriz, Iran; Faculty of Pharmacy, Near East University, POBOX:99138, Nicosia, Mersin 10, Cyprus},\nabstract={Introduction: DOF proteins are a family of plant-specific transcription factors with a conserved zinc finger (ZF) DNA-binding domain. Although several studies have demonstrated their specific DNA binding, quantitative affinity data is not available for the binding of DOF domains to their binding sites. Methods: ZF domains of DOF2.1, DOF3.4, and DOF5.8 from Arabidopsis thaliana were expressed and purified. Their DNA binding affinities were assessed using gel retardation assays and microscale thermophoresis with two different oligonucleotide probes containing one and two copies of recognition sequence AAAG. Results: DOF zinc finger domains (DOF-ZFs) were shown to form independently folded structures. Assessments using microscale thermophoresis demonstrated that DOF-ZFs interact more tightly (~100 fold) with double-motif probe than the single-motif probe. The overall Kd values for the DOF3.4-ZF and DOF5.8-ZF to the double-motif probe were ~2.3±1 and 2.5±1 μM, respectively. Conclusion: Studied DOF-ZF domains formed stable complexes with the double-motif probe. Although DOF3.4-ZF and DOF5.8-ZF do not dimerize with an appreciable affinity in the absence of DNA (judging from size-exclusion and multiangle laser light scattering data), it is possible that these ZFs form protein-protein contacts when bound to this oligonucleotide, consistent with previous reports that DOF proteins can homo- and hetero-dimerize. © 2018 The Author(s).},\nauthor_keywords={DNA binding affinity;  DOF zinc finger domain;  Gel retardation assay;  Microscale thermophoresis},\nkeywords={DNA binding protein;  DNA binding protein with one finger;  recombinant protein;  unclassified drug, Arabidopsis thaliana;  Article;  atomic absorption spectrometry;  binding affinity;  binding site;  expression vector;  nonhuman;  oligonucleotide probe;  protein DNA binding;  protein expression;  protein folding;  protein interaction;  protein purification;  protein structure;  zinc finger motif},\ncorrespondence_address1={Dastmalchi, S.; Biotechnology Research Center, Iran; email: dastmalchi.s@tbzmed.ac.ir},\npublisher={Tabriz University of Medical Sciences},\nissn={22285652},\nlanguage={English},\nabbrev_source_title={BioImpacts},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Receptor homodimerization plays a critical role in a novel dominant negative P2RY12 variant identified in a family with severe bleeding.\n \n \n \n \n\n\n \n Mundell, S.; Rabbolini, D.; Gabrielli, S.; Chen, Q.; Aungraheeta, R.; Hutchinson, J.; Kilo, T.; Mackay, J.; Ward, C.; Stevenson, W.; and Morel-Kopp, M.\n\n\n \n\n\n\n Journal of Thrombosis and Haemostasis, 16(1): 44-53. 2018.\n cited By 18\n\n\n\n
\n\n\n\n \n \n $\"Receptor$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mundell201844,\nauthor={Mundell, S.J. and Rabbolini, D. and Gabrielli, S. and Chen, Q. and Aungraheeta, R. and Hutchinson, J.L. and Kilo, T. and Mackay, J. and Ward, C.M. and Stevenson, W. and Morel-Kopp, M.-C.},\ntitle={Receptor homodimerization plays a critical role in a novel dominant negative P2RY12 variant identified in a family with severe bleeding},\njournal={Journal of Thrombosis and Haemostasis},\nyear={2018},\nvolume={16},\nnumber={1},\npages={44-53},\ndoi={10.1111/jth.13900},\nnote={cited By 18},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85036559062&doi=10.1111%2fjth.13900&partnerID=40&md5=140cf7fd0af7b9e7e835729fc1eba234},\naffiliation={School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom; Department of Haematology and Transfusion Medicine, Royal North Shore Hospital, Sydney, Australia; Northern Blood Research Centre, Kolling Institute, The University of Sydney, Sydney, Australia; Haematology Department, Westmead Children's Hospital, Sydney, Australia; School of Molecular Biosciences, The University of Sydney, Sydney, Australia},\nabstract={Essentials Three dominant variants for the autosomal recessive bleeding disorder type-8 have been described. To date, there has been no phenotype/genotype correlation explaining their dominant transmission. Proline plays an important role in P2Y12R ligand binding and signaling defects. P2Y12R homodimer formation is critical for the receptor function and signaling. Summary: Background Although inherited platelet disorders are still underdiagnosed worldwide, advances in molecular techniques are improving disease diagnosis and patient management. Objective To identify and characterize the mechanism underlying the bleeding phenotype in a Caucasian family with an autosomal dominant P2RY12 variant. Methods Full blood counts, platelet aggregometry, flow cytometry and western blotting were performed before next-generation sequencing (NGS). Detailed molecular analysis of the identified variant of the P2Y12 receptor (P2Y12R) was subsequently performed in mammalian cells overexpressing receptor constructs. Results All three referred individuals had markedly impaired ADP-induced platelet aggregation with primary wave only, despite normal total and surface P2Y12R expression. By NGS, a single P2RY12:c.G794C substitution (p.R265P) was identified in all affected individuals, and this was confirmed by Sanger sequencing. Mammalian cell experiments with the R265P-P2Y12R variant showed normal receptor surface expression versus wild-type (WT) P2Y12R. Agonist-stimulated R265P-P2Y12R function (both signaling and surface receptor loss) was reduced versus WT P2Y12R. Critically, R265P-P2Y12R acted in a dominant negative manner, with agonist-stimulated WT P2Y12R activity being reduced by variant coexpression, suggesting dramatic loss of WT homodimers. Importantly, platelet P2RY12 cDNA cloning and sequencing in two affected individuals also revealed three-fold mutant mRNA overexpression, decreasing even further the likelihood of WT homodimer formation. R265 located within extracellular loop 3 (EL3) is one of four residues that are important for receptor functional integrity, maintaining the binding pocket conformation and allowing rotation following ligand binding. Conclusion This novel dominant negative variant confirms the important role of R265 in EL3 in the functional integrity of P2Y12R, and suggests that pathologic heterodimer formation may underlie this family bleeding phenotype. © 2017 International Society on Thrombosis and Haemostasis},\nauthor_keywords={blood platelet disorder;  human;  inherited;  P2RY12;  platelet dysfunction},\nkeywords={arginine;  blood clotting factor 8;  complementary DNA;  homodimer;  messenger RNA;  proline;  purinergic P2Y12 receptor;  von Willebrand factor;  P2RY12 protein, human;  proline;  purinergic P2Y12 receptor, amino acid substitution;  Article;  autosomal dominant inheritance;  bleeding;  bleeding disorder;  case report;  Caucasian;  clinical article;  disease severity;  epistaxis;  flow cytometry;  gene expression;  gene mutation;  gene overexpression;  genetic variability;  human;  human cell;  ligand binding;  male;  molecular cloning;  next generation sequencing;  phenotype;  priority journal;  protein conformation;  Sanger sequencing;  thrombocyte aggregation;  Western blotting;  adolescent;  bleeding;  blood;  blood clotting parameters;  chemistry;  dna mutational analysis;  female;  genetic predisposition;  genetics;  HEK293 cell line;  heredity;  high throughput sequencing;  middle aged;  molecular model;  mutation;  pedigree;  procedures;  protein multimerization;  protein quaternary structure;  severity of illness index;  structure activity relation;  thrombocyte disorder;  young adult, Adolescent;  Blood Platelet Disorders;  DNA Mutational Analysis;  European Continental Ancestry Group;  Female;  Genetic Predisposition to Disease;  HEK293 Cells;  Hemorrhage;  Heredity;  High-Throughput Nucleotide Sequencing;  Humans;  Male;  Middle Aged;  Models, Molecular;  Mutation;  Pedigree;  Phenotype;  Platelet Aggregation;  Platelet Function Tests;  Proline;  Protein Multimerization;  Protein Structure, Quaternary;  Receptors, Purinergic P2Y12;  Severity of Illness Index;  Structure-Activity Relationship;  Young Adult},\ncorrespondence_address1={Morel-Kopp, M.-C.; Department of Haematology and Transfusion Medicine, Australia; email: marie-christine.kopp@sydney.edu.au},\npublisher={Blackwell Publishing Ltd},\nissn={15387933},\ncoden={JTHOA},\npubmed_id={29117459},\nlanguage={English},\nabbrev_source_title={J. Thromb. Haemost.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n

\n Essentials Three dominant variants for the autosomal recessive bleeding disorder type-8 have been described. To date, there has been no phenotype/genotype correlation explaining their dominant transmission. Proline plays an important role in P2Y12R ligand binding and signaling defects. P2Y12R homodimer formation is critical for the receptor function and signaling. Summary: Background Although inherited platelet disorders are still underdiagnosed worldwide, advances in molecular techniques are improving disease diagnosis and patient management. Objective To identify and characterize the mechanism underlying the bleeding phenotype in a Caucasian family with an autosomal dominant P2RY12 variant. Methods Full blood counts, platelet aggregometry, flow cytometry and western blotting were performed before next-generation sequencing (NGS). Detailed molecular analysis of the identified variant of the P2Y12 receptor (P2Y12R) was subsequently performed in mammalian cells overexpressing receptor constructs. Results All three referred individuals had markedly impaired ADP-induced platelet aggregation with primary wave only, despite normal total and surface P2Y12R expression. By NGS, a single P2RY12:c.G794C substitution (p.R265P) was identified in all affected individuals, and this was confirmed by Sanger sequencing. Mammalian cell experiments with the R265P-P2Y12R variant showed normal receptor surface expression versus wild-type (WT) P2Y12R. Agonist-stimulated R265P-P2Y12R function (both signaling and surface receptor loss) was reduced versus WT P2Y12R. Critically, R265P-P2Y12R acted in a dominant negative manner, with agonist-stimulated WT P2Y12R activity being reduced by variant coexpression, suggesting dramatic loss of WT homodimers. Importantly, platelet P2RY12 cDNA cloning and sequencing in two affected individuals also revealed three-fold mutant mRNA overexpression, decreasing even further the likelihood of WT homodimer formation. R265 located within extracellular loop 3 (EL3) is one of four residues that are important for receptor functional integrity, maintaining the binding pocket conformation and allowing rotation following ligand binding. Conclusion This novel dominant negative variant confirms the important role of R265 in EL3 in the functional integrity of P2Y12R, and suggests that pathologic heterodimer formation may underlie this family bleeding phenotype. © 2017 International Society on Thrombosis and Haemostasis\n

\n\n\n

\n\n\n\n\n\n

\n

\n \n 2017\n \n \n (5)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Refinement of the subunit interaction network within the nucleosome remodelling and deacetylase (NuRD) complex.\n \n \n \n \n\n\n \n Torrado, M.; Low, J.; Silva, A.; Schmidberger, J.; Sana, M.; Sharifi Tabar, M.; Isilak, M.; Winning, C.; Kwong, C.; Bedward, M.; Sperlazza, M.; Williams, D.; Shepherd, N.; and Mackay, J.\n\n\n \n\n\n\n FEBS Journal, 284(24): 4216-4232. 2017.\n cited By 34\n\n\n\n
\n\n\n\n \n \n $\"Refinement$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Torrado20174216,\nauthor={Torrado, M. and Low, J.K.K. and Silva, A.P.G. and Schmidberger, J.W. and Sana, M. and Sharifi Tabar, M. and Isilak, M.E. and Winning, C.S. and Kwong, C. and Bedward, M.J. and Sperlazza, M.J. and Williams, D.C., Jr. and Shepherd, N.E. and Mackay, J.P.},\ntitle={Refinement of the subunit interaction network within the nucleosome remodelling and deacetylase (NuRD) complex},\njournal={FEBS Journal},\nyear={2017},\nvolume={284},\nnumber={24},\npages={4216-4232},\ndoi={10.1111/febs.14301},\nnote={cited By 34},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85033719610&doi=10.1111%2ffebs.14301&partnerID=40&md5=a28e03cfd99d6e9cc54ffd31863f9683},\naffiliation={School of Life and Environmental Sciences, University of Sydney, Australia; Department of Pathology and Laboratory Medicine, The University of North Carolina – Chapel HillNC, United States; Institute for Molecular Biosciences, The University of Queensland, St Lucia, Australia},\nabstract={The nucleosome remodelling and deacetylase (NuRD) complex is essential for the development of complex animals. NuRD has roles in regulating gene expression and repairing damaged DNA. The complex comprises at least six proteins with two or more paralogues of each protein routinely identified when the complex is purified from cell extracts. To understand the structure and function of NuRD, a map of direct subunit interactions is needed. Dozens of published studies have attempted to define direct inter-subunit connectivities. We propose that conclusions reported in many such studies are in fact ambiguous for one of several reasons. First, the expression of many NuRD subunits in bacteria is unlikely to lead to folded, active protein. Second, interaction studies carried out in cells that contain endogenous NuRD complex can lead to false positives through bridging of target proteins by endogenous components. Combining existing information on NuRD structure with a protocol designed to minimize false positives, we report a conservative and robust interaction map for the NuRD complex. We also suggest a 3D model of the complex that brings together the existing data on the complex. The issues and strategies discussed herein are also applicable to the analysis of a wide range of multi-subunit complexes. Enzymes: Micrococcal nuclease (MNase), EC 3.1.31.1; histone deacetylase (HDAC), EC 3.5.1.98. © 2017 Federation of European Biochemical Societies},\nauthor_keywords={chromatin remodelling;  co-immunoprecipitations;  nucleosome remodelling and deacetylase (NuRD) complex;  protein structure;  protein–protein interactions},\nkeywords={histone deacetylase;  histone deacetylase 1;  HDAC1 protein, human;  histone deacetylase;  histone deacetylase 1;  hybrid protein, Article;  in vitro study;  molecular interaction;  nonhuman;  nucleosome;  priority journal;  protein expression;  protein folding;  protein processing;  protein protein interaction;  protein subunit;  protein targeting;  structure activity relation;  animal;  artifact;  chemistry;  Escherichia coli;  HEK293 cell line;  HeLa cell line;  human;  Leporidae;  molecular model;  mouse;  nucleosome;  procedures;  protein analysis;  protein conformation;  reticulocyte;  Western blotting, Animals;  Artifacts;  Blotting, Western;  Escherichia coli;  HEK293 Cells;  HeLa Cells;  Histone Deacetylase 1;  Humans;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Mice;  Models, Molecular;  Nucleosomes;  Protein Conformation;  Protein Folding;  Protein Interaction Mapping;  Protein Subunits;  Rabbits;  Recombinant Fusion Proteins;  Reticulocytes},\ncorrespondence_address1={Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Blackwell Publishing Ltd},\nissn={1742464X},\ncoden={FJEOA},\npubmed_id={29063705},\nlanguage={English},\nabbrev_source_title={FEBS J.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n IP3-4 kinase Arg1 regulates cell wall homeostasis and surface architecture to promote clearance of Cryptococcus neoformans infection in a mouse model.\n \n \n \n \n\n\n \n Li, C.; Lev, S.; Desmarini, D.; Kaufman-Francis, K.; Saiardi, A.; Silva, A.; Mackay, J.; Thompson, P.; Sorrell, T.; and Djordjevic, J.\n\n\n \n\n\n\n Virulence, 8(8): 1833-1848. 2017.\n cited By 8\n\n\n\n
\n\n\n\n \n \n $\"IP3-4$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Li20171833,\nauthor={Li, C. and Lev, S. and Desmarini, D. and Kaufman-Francis, K. and Saiardi, A. and Silva, A.P.G. and Mackay, J.P. and Thompson, P.E. and Sorrell, T.C. and Djordjevic, J.T.},\ntitle={IP3-4 kinase Arg1 regulates cell wall homeostasis and surface architecture to promote clearance of Cryptococcus neoformans infection in a mouse model},\njournal={Virulence},\nyear={2017},\nvolume={8},\nnumber={8},\npages={1833-1848},\ndoi={10.1080/21505594.2017.1385692},\nnote={cited By 8},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85040535275&doi=10.1080%2f21505594.2017.1385692&partnerID=40&md5=42fcc3e18ff51e829b88d17bafb9841c},\naffiliation={Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, 176 Hawkesbury road, Westmead, NSW  2145, Australia; Sydney Medical School-Westmead, The University of Sydney, Westmead, NSW  2145, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, University of SydneyNSW, Australia; Medical Research Council Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, United Kingdom; School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW  2006, Australia; Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC  3052, Australia; Westmead Hospital, Westmead, NSW  2145, Australia},\nabstract={We previously identified a series of inositol polyphosphate kinases (IPKs), Arg1, Ipk1, Kcs1 and Asp1, in the opportunistic fungal pathogen Cryptococcus neoformans. Using gene deletion analysis, we characterized Arg1, Ipk1 and Kcs1 and showed that they act sequentially to convert IP3 to PP-IP5 (IP7), a key metabolite promoting stress tolerance, metabolic adaptation and fungal dissemination to the brain. We have now directly characterized the enzymatic activity of Arg1, demonstrating that it is a dual specificity (IP3/IP4) kinase producing IP5. We showed previously that IP5 is further phosphorylated by Ipk1 to produce IP6, which is a substrate for the synthesis of PP-IP5 by Kcs1. Phenotypic comparison of the arg1Δ and kcs1Δ deletion mutants (both PP-IP5-deficient) reveals that arg1Δ has the most deleterious phenotype: while PP-IP5 is essential for metabolic and stress adaptation in both mutant strains, PP-IP5 is dispensable for virulence-associated functions such as capsule production, cell wall organization, and normal N-linked mannosylation of the virulence factor, phospholipase B1, as these phenotypes were defective only in arg1Δ. The more deleterious arg1Δ phenotype correlated with a higher rate of arg1Δ phagocytosis by human peripheral blood monocytes and rapid arg1Δ clearance from lung in a mouse model. This observation is in contrast to kcs1Δ, which we previously reported establishes a chronic, confined lung infection. In summary, we show that Arg1 is the most crucial IPK for cryptococcal virulence, conveying PP-IP5–dependent and novel PP-IP5–independent functions. © 2017 Taylor & Francis.},\nauthor_keywords={cell wall;  Cryptococcus neoformans;  inositol polyphosphate kinase;  inositol pyrophosphate;  IP7;  meningitis;  molecular fungal pathogenesis;  mouse model;  PP-IP5;  virulence},\nkeywords={glycan;  glycosylphosphatidylinositol;  inositol polyphosphate;  lysophospholipase;  virulence factor;  bacterial protein;  inositol phosphate;  inositol polyphosphate multikinase;  phosphotransferase, animal experiment;  animal model;  Article;  cell phagocytosis;  cell ultrastructure;  cell wall;  cryptococcosis;  Cryptococcus neoformans;  enzyme activity;  fungal cell wall;  fungal strain;  gene expression;  homeostasis;  lung infection;  microscopy;  monocyte;  mouse;  nonhuman;  parasite clearance;  phagocytosis;  phenotype;  protein-fragment complementation assay;  RNA extraction;  Saccharomyces cerevisiae;  sensitivity analysis;  stress;  survival;  thickness;  transmission electron microscopy;  Western blotting;  yeast;  animal;  Bagg albino mouse;  cell wall;  cryptococcosis;  disease model;  enzymology;  female;  genetics;  homeostasis;  human;  kinetics;  metabolism;  microbiology;  pathogenicity;  phosphorylation;  virulence, Animals;  Bacterial Proteins;  Cell Wall;  Cryptococcosis;  Cryptococcus neoformans;  Disease Models, Animal;  Female;  Homeostasis;  Humans;  Inositol Phosphates;  Kinetics;  Mice;  Mice, Inbred BALB C;  Phosphorylation;  Phosphotransferases (Alcohol Group Acceptor);  Virulence},\ncorrespondence_address1={Djordjevic, J.T.; Westmead Institute for Medical Research, 176 Hawkesbury Road, Australia; email: julianne.djordjevic@sydney.edu.au},\npublisher={Taylor and Francis Inc.},\nissn={21505594},\npubmed_id={28976803},\nlanguage={English},\nabbrev_source_title={Virulence},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Arabinosylation Modulates the Growth-Regulating Activity of the Peptide Hormone CLE40a from Soybean.\n \n \n \n \n\n\n \n Corcilius, L.; Hastwell, A.; Zhang, M.; Williams, J.; Mackay, J.; Gresshoff, P.; Ferguson, B.; and Payne, R.\n\n\n \n\n\n\n Cell Chemical Biology, 24(11): 1347-1355.e7. 2017.\n cited By 25\n\n\n\n
\n\n\n\n \n \n $\"Arabinosylation$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Corcilius20171347,\nauthor={Corcilius, L. and Hastwell, A.H. and Zhang, M. and Williams, J. and Mackay, J.P. and Gresshoff, P.M. and Ferguson, B.J. and Payne, R.J.},\ntitle={Arabinosylation Modulates the Growth-Regulating Activity of the Peptide Hormone CLE40a from Soybean},\njournal={Cell Chemical Biology},\nyear={2017},\nvolume={24},\nnumber={11},\npages={1347-1355.e7},\ndoi={10.1016/j.chembiol.2017.08.014},\nnote={cited By 25},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85029680585&doi=10.1016%2fj.chembiol.2017.08.014&partnerID=40&md5=81f6bfeda051932e688e3f0511c7347b},\naffiliation={School of Chemistry, The University of Sydney, Sydney, NSW  2006, Australia; Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD  4072, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW  2006, Australia},\nabstract={Small post-translationally modified peptide hormones mediate crucial developmental and regulatory processes in plants. CLAVATA/ENDOSPERM-SURROUNDING REGION (CLE) genes are found throughout the plant kingdom and encode for 12–13 amino acid peptides that must often undergo post-translational proline hydroxylation and glycosylation with O-β1,2-triarabinose moieties before they become functional. Apart from a few recent examples, a detailed understanding of the structure and function of most CLE hormones is yet to be uncovered. This is mainly owing to difficulties in isolating mature homogeneously modified CLE peptides from natural plant sources. In this study, we describe the efficient synthesis of a synthetic Araf 3 Hyp glycosylamino acid building block that was used to access a hitherto uninvestigated CLE hormone from soybean called GmCLE40a. Through the development and implementation of a novel in vivo root growth assay, we show that the synthetic triarabinosylated glycopeptide suppresses primary root growth in this important crop species. Herein Corcilius et al. describe an improved chemical synthesis of the β-O-tri-β1,2-arabinofuranosylated hydroxyproline post-translational modification present in plant glycopeptides and demonstrate its utility through the synthesis and biological evaluation of a novel root growth regulatory glycopeptide hormone, GmCLE40a, from soybean. The glycopeptide hormone displayed enhanced root growth suppressive activity in vivo compared with its unglycosylated isoform. © 2017 Elsevier Ltd},\nauthor_keywords={arabinosylation;  CLE;  CLE40;  glycopeptide;  glycosylation;  hormone;  IAD;  legume;  root apical meristem;  soybean},\nkeywords={peptide hormone;  arabinose;  peptide hormone;  plant protein, arabinosylation;  Article;  bioassay;  carbohydrate analysis;  chemical modification;  growth regulation;  nonhuman;  priority journal;  protein purification;  reporter gene;  root growth;  scale up;  soybean;  stereoselectivity;  synthesis;  amino acid sequence;  chemistry;  classification;  drug effect;  gene expression regulation;  genetics;  glycosylation;  growth, development and aging;  metabolism;  nuclear magnetic resonance;  phylogeny;  plant gene;  plant root;  sequence alignment;  soybean, Amino Acid Sequence;  Arabinose;  Gene Expression Regulation, Plant;  Genes, Plant;  Glycosylation;  Nuclear Magnetic Resonance, Biomolecular;  Peptide Hormones;  Phylogeny;  Plant Proteins;  Plant Roots;  Sequence Alignment;  Soybeans},\npublisher={Elsevier Ltd},\nissn={24519456},\npubmed_id={28943356},\nlanguage={English},\nabbrev_source_title={Cell Chem. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Promiscuous DNA-binding of a mutant zinc finger protein corrupts the transcriptome and diminishes cell viability.\n \n \n \n \n\n\n \n Gillinder, K.; Ilsley, M.; Nébor, D.; Sachidanandam, R.; Lajoie, M.; Magor, G.; Tallack, M.; Bailey, T.; Landsberg, M.; Mackay, J.; Parker, M.; Miles, L.; Graber, J.; Peters, L.; Bieker, J.; and Perkins, A.\n\n\n \n\n\n\n Nucleic Acids Research, 45(3): 1130-1143. 2017.\n cited By 23\n\n\n\n
\n\n\n\n \n \n $\"Promiscuous$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Gillinder20171130,\nauthor={Gillinder, K.R. and Ilsley, M.D. and Nébor, D. and Sachidanandam, R. and Lajoie, M. and Magor, G.W. and Tallack, M.R. and Bailey, T. and Landsberg, M.J. and Mackay, J.P. and Parker, M.W. and Miles, L.A. and Graber, J.H. and Peters, L.L. and Bieker, J.J. and Perkins, A.C.},\ntitle={Promiscuous DNA-binding of a mutant zinc finger protein corrupts the transcriptome and diminishes cell viability},\njournal={Nucleic Acids Research},\nyear={2017},\nvolume={45},\nnumber={3},\npages={1130-1143},\ndoi={10.1093/nar/gkw1014},\nnote={cited By 23},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85025175732&doi=10.1093%2fnar%2fgkw1014&partnerID=40&md5=d5756e96f0c33c47783216a9ae8210e7},\naffiliation={Cancer Genomics Group, Mater Research Institute, University of Queensland, Translational Research Institute, Woolloongabba, QLD  4102, Australia; Jackson Laboratory, Bar Harbor, ME  04609, United States; Department of Oncological Sciences, Mount Sinai School of Medicine, New York, NY  10029, United States; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD  4072, Australia; Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV  89557, United States; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD  4072, Australia; School of Life and Environmental Sciences, University of SydneyNSW  2006, Australia; ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Melbourne, VIC  3065, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC  3052, Australia; Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, NY  10029, United States; Princess Alexandra Hospital, Brisbane, QLD  4102, Australia},\nabstract={The rules of engagement between zinc finger transcription factors and DNA have been partly defined by in vitro DNA-binding and structural studies, but less is known about how these rules apply in vivo. Here, we demonstrate how a missense mutation in the second zinc finger of Krüppel-like factor-1 (KLF1) leads to degenerate DNA-binding specificity in vivo, resulting in ectopic transcription and anemia in the Nanmouse model. We employed ChIP-seq and 4sU-RNA-seq to identify aberrant DNA-binding events genome wide and ectopic transcriptional consequences of this binding. We confirmed novel sequence specificity of the mutant recombinant zinc finger domain by performing biophysical measurements ofinvitroDNA-binding affinity. Together, these results shed new light on the mechanisms by which missense mutations in DNA-binding domains of transcription factors can lead to autosomal dominant diseases. © The Author(s) 2016.},\nkeywords={kruppel like factor;  kruppel like factor 1;  messenger RNA;  transcriptome;  unclassified drug;  zinc finger protein;  DNA;  erythroid Kruppel-like factor;  kruppel like factor;  mutant protein;  protein binding;  transcriptome;  zinc finger protein, anemia;  animal cell;  animal tissue;  Article;  binding affinity;  cell viability;  chromatin immunoprecipitation;  controlled study;  down regulation;  ectopic expression;  erythroid cell;  fetus;  fetus liver;  gene expression regulation;  gene locus;  gene ontology;  genome analysis;  in vivo study;  missense mutation;  molecular recognition;  mouse;  mutational analysis;  nonhuman;  phenotype;  priority journal;  protein DNA binding;  residue analysis;  RNA sequence;  sensitivity analysis;  sequence analysis;  upregulation;  animal;  biological model;  cell line;  cell survival;  chemistry;  erythropoiesis;  genetics;  human;  metabolism;  molecular model, Animals;  Cell Line;  Cell Survival;  DNA;  Erythroid Cells;  Erythropoiesis;  Humans;  Kruppel-Like Transcription Factors;  Mice;  Models, Genetic;  Models, Molecular;  Mutant Proteins;  Mutation, Missense;  Protein Binding;  Transcriptome;  Zinc Fingers},\ncorrespondence_address1={Perkins, A.C.; Cancer Genomics Group, Australia; email: andrew.perkins@mater.uq.edu.au},\npublisher={Oxford University Press},\nissn={03051048},\ncoden={NARHA},\npubmed_id={28180284},\nlanguage={English},\nabbrev_source_title={Nucleic Acids Res.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Whaddaya Know: A Guide to Uncertainty and Subjectivity in Structural Biology.\n \n \n \n \n\n\n \n Mackay, J.; Landsberg, M.; Whitten, A.; and Bond, C.\n\n\n \n\n\n\n Trends in Biochemical Sciences, 42(2): 155-167. 2017.\n cited By 11\n\n\n\n
\n\n\n\n \n \n $\"Whaddaya$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mackay2017155,\nauthor={Mackay, J.P. and Landsberg, M.J. and Whitten, A.E. and Bond, C.S.},\ntitle={Whaddaya Know: A Guide to Uncertainty and Subjectivity in Structural Biology},\njournal={Trends in Biochemical Sciences},\nyear={2017},\nvolume={42},\nnumber={2},\npages={155-167},\ndoi={10.1016/j.tibs.2016.11.002},\nnote={cited By 11},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85009507671&doi=10.1016%2fj.tibs.2016.11.002&partnerID=40&md5=365f14348c6c6e6b755443ea85390d1d},\naffiliation={School of Life and Environmental Sciences, University of SydneyNSW  2006, Australia; School of Chemistry and Molecular Biosciences, University of QueenslandQLD, Australia; Australian Centre for Neutron Science, ANSTO, Lucas HeightsNSW, Australia; School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA  6014, Australia},\nabstract={The methods of structural biology, while powerful, are technically complex. Although the Protein Data Bank (PDB) provides a repository that allows anyone to download any structure, many users would not appreciate the caveats that should be considered when examining a structure. Here, we describe several key uncertainties associated with the application of X-ray crystallography, NMR spectroscopy, single-particle electron microscopy (SPEM), and small-angle scattering (SAS) to biological macromolecules. The take-home message is that structures are not absolute truths – they are models that fit the experimental data and therefore have uncertainty and subjectivity associated with them. These uncertainties must be appreciated – careful reading of the associated paper, and any validation report provided by the structure database, is highly recommended. © 2016 Elsevier Ltd},\nauthor_keywords={NMR spectroscopy;  single-particle cryo-electron microscopy;  small-angle scattering;  structural biology;  uncertainty;  X-ray crystallography},\nkeywords={computer model;  conformational transition;  crystal structure;  electron microscopy;  fuzzy system;  macromolecule;  molecular dynamics;  nonhuman;  nuclear magnetic resonance spectroscopy;  protein conformation;  Protein Data Bank;  protein quaternary structure;  protein structure;  Review;  single particle electron microscopy;  small angle scattering;  structural model;  structure analysis;  uncertainty;  X ray crystallography;  chemistry;  molecular biology;  molecular model, macromolecule, Crystallography, X-Ray;  Macromolecular Substances;  Magnetic Resonance Spectroscopy;  Microscopy, Electron;  Models, Molecular;  Molecular Biology;  Scattering, Small Angle;  Uncertainty},\ncorrespondence_address1={Mackay, J.P.Australia; email: joel.mackay@sydney.edu.au},\npublisher={Elsevier Ltd},\nissn={09680004},\ncoden={TBSCD},\npubmed_id={28089412},\nlanguage={English},\nabbrev_source_title={Trends Biochem. Sci.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2016\n \n \n (10)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Site-specific phosphorylation of tau inhibits amyloid-β toxicity in Alzheimer's mice.\n \n \n \n \n\n\n \n Ittner, A.; Chua, S.; Bertz, J.; Volkerling, A.; Van Der Hoven, J.; Gladbach, A.; Przybyla, M.; Bi, M.; Van Hummel, A.; Stevens, C.; Ippati, S.; Suh, L.; Macmillan, A.; Sutherland, G.; Kril, J.; Silva, A.; Mackay, J.; Poljak, A.; Delerue, F.; Ke, Y.; and Ittner, L.\n\n\n \n\n\n\n Science, 354(6314): 904-908. 2016.\n cited By 182\n\n\n\n
\n\n\n\n \n \n $\"Site-specific$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Ittner2016904,\nauthor={Ittner, A. and Chua, S.W. and Bertz, J. and Volkerling, A. and Van Der Hoven, J. and Gladbach, A. and Przybyla, M. and Bi, M. and Van Hummel, A. and Stevens, C.H. and Ippati, S. and Suh, L.S. and Macmillan, A. and Sutherland, G. and Kril, J.J. and Silva, A.P.G. and Mackay, J. and Poljak, A. and Delerue, F. and Ke, Y.D. and Ittner, L.M.},\ntitle={Site-specific phosphorylation of tau inhibits amyloid-β toxicity in Alzheimer's mice},\njournal={Science},\nyear={2016},\nvolume={354},\nnumber={6314},\npages={904-908},\ndoi={10.1126/science.aah6205},\nnote={cited By 182},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84995973237&doi=10.1126%2fscience.aah6205&partnerID=40&md5=244a650c0a184e70e1174cc0d35e2394},\naffiliation={Dementia Research Unit, School of Medical Sciences, University of New South Wales (UNSW), Sydney, NSW  2052, Australia; Motor Neuron Disease Unit, School of Medical Sciences, UNSW, Sydney, NSW  2052, Australia; Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney, NSW  2050, Australia; Biomedical Imaging Facility, Mark Wainwright Analytical Centre, UNSW, Sydney, NSW  2052, Australia; School of Molecular Bioscience, University of Sydney, Sydney, NSW  2050, Australia; Biomedical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW, Sydney, NSW  2052, Australia; Transgenic Animal Unit, Mark Wainwright Analytical Centre, UNSW, Sydney, NSW  2052, Australia; Neuroscience Research Australia, Sydney, NSW  2031, Australia},\nabstract={Amyloid-β (Aβ) toxicity in Alzheimer's disease (AD) is considered to be mediated by phosphorylated tau protein. In contrast, we found that, at least in early disease, site-specific phosphorylation of tau inhibited Aβ toxicity. This specific tau phosphorylation was mediated by the neuronal p38 mitogen-activated protein kinase p38γ and interfered with postsynaptic excitotoxic signaling complexes engaged by Aβ. Accordingly, depletion of p38γ exacerbated neuronal circuit aberrations, cognitive deficits, and premature lethality in a mousemodel of AD, whereas increasing the activity of p38γ abolished these deficits. Furthermore, mimicking site-specific tau phosphorylation alleviated Aβ-induced neuronal death and offered protection from excitotoxicity. Our work provides insights into postsynaptic processes in AD pathogenesis and challenges a purely pathogenic role of tau phosphorylation in neuronal toxicity. Copyright © 2016 by the American Association for the Advancement of Science; all rights reserved.},\nkeywords={amyloid beta protein;  mitogen activated protein kinase p38;  tau protein;  amyloid beta protein;  Dlgh4 protein, mouse;  guanylate kinase;  Mapt protein, mouse;  membrane protein;  mitogen activated protein kinase 12;  neurotoxin;  tau protein, chemical reaction;  disease incidence;  enzyme;  enzyme activity;  numerical model;  protein;  rodent;  toxicity, Alzheimer disease;  amyloid beta toxicity;  animal experiment;  animal model;  Article;  cognitive defect;  controlled study;  excitotoxicity;  experimental model;  fluorescence resonance energy transfer;  lethality;  mouse;  nerve cell necrosis;  nonhuman;  pathogenesis;  postsynaptic potential;  prematurity;  priority journal;  protein phosphorylation;  Alzheimer disease;  animal;  antagonists and inhibitors;  disease model;  genetics;  metabolism;  nerve cell;  pathology;  phosphorylation;  signal transduction;  transgenic mouse, Mus, Alzheimer Disease;  Amyloid beta-Peptides;  Animals;  Cognition Disorders;  Disease Models, Animal;  Guanylate Kinases;  Membrane Proteins;  Mice;  Mice, Transgenic;  Mitogen-Activated Protein Kinase 12;  Neurons;  Neurotoxins;  Phosphorylation;  Signal Transduction;  tau Proteins},\ncorrespondence_address1={Ittner, A.; Dementia Research Unit, Australia; email: a.ittner@unsw.edu.au},\npublisher={American Association for the Advancement of Science},\nissn={00368075},\ncoden={SCIEA},\npubmed_id={27856911},\nlanguage={English},\nabbrev_source_title={Science},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity.\n \n \n \n \n\n\n \n Wai, D.; Shihab, M.; Low, J.; and Mackay, J.\n\n\n \n\n\n\n Nucleic Acids Research, 44(19): 9153-9165. 2016.\n cited By 23\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Wai20169153,\nauthor={Wai, D.C.C. and Shihab, M. and Low, J.K.K. and Mackay, J.P.},\ntitle={The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity},\njournal={Nucleic Acids Research},\nyear={2016},\nvolume={44},\nnumber={19},\npages={9153-9165},\ndoi={10.1093/nar/gkw590},\nnote={cited By 23},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84994360397&doi=10.1093%2fnar%2fgkw590&partnerID=40&md5=de420ad7db418888b9c30d43dac39119},\naffiliation={School of Life and Environmental Sciences, University of SydneyNSW  2006, Australia},\nabstract={Classical zinc fingers (ZFs) are traditionally considered to act as sequence-specific DNA-binding domains. More recently, classical ZFs have been recognised as potential RNA-binding modules, raising the intriguing possibility that classical-ZF transcription factors are involved in post-transcriptional gene regulation via direct RNA binding. To date, however, only one classical ZF-RNA complex, that involving TFIIIA, has been structurally characterised. Yin Yang-1 (YY1) is a multi-functional transcription factor involved in many regulatory processes, and binds DNA via four classical ZFs. Recent evidence suggests that YY1 also interacts with RNA, but the molecular nature of the interaction remains unknown. In the present work, we directly assess the ability of YY1 to bind RNA using in vitro assays. Systematic Evolution of Ligands by EXponential enrichment (SELEX) was used to identify preferred RNA sequences bound by the YY1 ZFs from a randomised library over multiple rounds of selection. However, a strong motif was not consistently recovered, suggesting that the RNA sequence selectivity of these domains is modest. YY1 ZF residues involved in binding to single-stranded RNA were identified by NMR spectroscopy and found to be largely distinct from the set of residues involved in DNA binding, suggesting that interactions between YY1 and ssRNA constitute a separate mode of nucleic acid binding. Our data are consistent with recent reports that YY1 can bind to RNA in a low-specificity, yet physiologically relevant manner. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.},\nkeywords={RNA polymerase;  single stranded RNA;  transcription factor YY1;  aptamer;  DNA;  protein binding;  RNA;  transcription factor YY1;  zinc finger protein, amino acid substitution;  amino terminal sequence;  Article;  binding affinity;  binding site;  controlled study;  DNA binding;  in vitro study;  point mutation;  priority journal;  protein expression;  protein purification;  protein RNA binding;  RNA sequence;  RNA transcription;  amino acid sequence;  binding site;  chemistry;  human;  metabolism;  mutagenesis;  nuclear magnetic resonance spectroscopy;  nucleotide sequence;  systematic evolution of ligands by exponential enrichment aptamer technique, Amino Acid Sequence;  Aptamers, Nucleotide;  Base Sequence;  Binding Sites;  DNA;  Humans;  Magnetic Resonance Spectroscopy;  Mutagenesis;  Protein Binding;  RNA;  SELEX Aptamer Technique;  YY1 Transcription Factor;  Zinc Fingers},\ncorrespondence_address1={Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Oxford University Press},\nissn={03051048},\ncoden={NARHA},\npubmed_id={27369384},\nlanguage={English},\nabbrev_source_title={Nucleic Acids Res.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The Chromatin Remodelling Protein CHD1 Contains a Previously Unrecognised C-Terminal Helical Domain.\n \n \n \n \n\n\n \n Mohanty, B.; Helder, S.; Silva, A.; Mackay, J.; and Ryan, D.\n\n\n \n\n\n\n Journal of Molecular Biology, 428(21): 4298-4314. 2016.\n cited By 11\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mohanty20164298,\nauthor={Mohanty, B. and Helder, S. and Silva, A.P.G. and Mackay, J.P. and Ryan, D.P.},\ntitle={The Chromatin Remodelling Protein CHD1 Contains a Previously Unrecognised C-Terminal Helical Domain},\njournal={Journal of Molecular Biology},\nyear={2016},\nvolume={428},\nnumber={21},\npages={4298-4314},\ndoi={10.1016/j.jmb.2016.08.028},\nnote={cited By 11},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84991706628&doi=10.1016%2fj.jmb.2016.08.028&partnerID=40&md5=59dcad5fa8b4d5eec595a143ebaa1ac0},\naffiliation={School of Life and Environmental Sciences, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, New South Wales  2006, Australia; Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Building 131, Garran Road, Canberra, Australian Capital Territory  2601, Australia; Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria  3052, Australia},\nabstract={The packaging of eukaryotic DNA into nucleosomes, and the organisation of these nucleosomes into chromatin, plays a critical role in regulating all DNA-associated processes. Chromodomain helicase DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin remodelling protein that is conserved throughout eukaryotes and has an ability to assemble and organise nucleosomes both in vitro and in vivo. This activity is involved in the regulation of transcription and is implicated in mammalian development and stem cell biology. CHD1 is classically depicted as possessing a pair of tandem chromodomains that directly precede a core catalytic helicase-like domain that is then followed by a SANT-SLIDE DNA-binding domain. Here, we have identified an additional conserved domain C-terminal to the SANT-SLIDE domain and determined its structure by multidimensional heteronuclear NMR spectroscopy. We have termed this domain the CHD1 helical C-terminal (CHCT) domain as it is comprised of five α-helices arranged in a variant helical bundle topology. CHCT has a conserved, positively charged surface and is able to bind DNA and nucleosomes. In addition, we have identified another group of proteins, the as yet uncharacterised C17orf64 proteins, as also containing a conserved CHCT domain. Our data provide new structural insights into the CHD1 enzyme family. © 2016 Elsevier Ltd},\nauthor_keywords={C17orf64;  DNA-binding domain;  helical bundle;  nucleosomes;  transcription},\nkeywords={adenosine triphosphate;  chromodomain helicase DNA binding protein 1;  DNA;  DNA binding protein;  helicase;  unclassified drug;  CHD1 protein, human;  DNA;  DNA binding protein;  DNA helicase;  protein binding, alpha helix;  Article;  carboxy terminal sequence;  chromatin;  chromatin assembly and disassembly;  controlled study;  cytology;  DNA binding;  DNA packaging;  eukaryote;  genetic conservation;  in vitro study;  in vivo study;  mammal;  nonhuman;  nuclear magnetic resonance spectroscopy;  nucleosome;  open reading frame;  organogenesis;  paralogy;  priority journal;  protein domain;  protein expression;  protein family;  protein structure;  quantitative analysis;  sequence alignment;  stem cell;  surface charge;  transcription regulation;  chemistry;  metabolism;  protein domain, DNA;  DNA Helicases;  DNA-Binding Proteins;  Magnetic Resonance Spectroscopy;  Protein Binding;  Protein Conformation, alpha-Helical;  Protein Domains},\ncorrespondence_address1={Mackay, J.P.; School of Life and Environmental Sciences, Building G08, Corner Butlin Avenue and Maze Crescent, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Academic Press},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={27591891},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The yeast transcription elongation factor Spt4/5 is a sequence-specific RNA binding protein.\n \n \n \n \n\n\n \n Blythe, A.; Yazar-Klosinski, B.; Webster, M.; Chen, E.; Vandevenne, M.; Bendak, K.; Mackay, J.; Hartzog, G.; and Vrielink, A.\n\n\n \n\n\n\n Protein Science,1710-1721. 2016.\n cited By 8\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Blythe20161710,\nauthor={Blythe, A.J. and Yazar-Klosinski, B. and Webster, M.W. and Chen, E. and Vandevenne, M. and Bendak, K. and Mackay, J.P. and Hartzog, G.A. and Vrielink, A.},\ntitle={The yeast transcription elongation factor Spt4/5 is a sequence-specific RNA binding protein},\njournal={Protein Science},\nyear={2016},\npages={1710-1721},\ndoi={10.1002/pro.2976},\nnote={cited By 8},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84983078309&doi=10.1002%2fpro.2976&partnerID=40&md5=70d883dc1189bfdabad37114b46b23a2},\naffiliation={School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA  6009, Australia; Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA  95064, United States; School of Molecular Bioscience, University of Sydney, Sydney, NSW  2006, Australia; Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA  95064, United States},\nabstract={The heterodimeric transcription elongation factor Spt4/Spt5 (Spt4/5) tightly associates with RNAPII to regulate both transcriptional elongation and co-transcriptional pre-mRNA processing; however, the mechanisms by which Spt4/5 acts are poorly understood. Recent studies of the human and Drosophila Spt4/5 complexes indicate that they can bind nucleic acids in vitro. We demonstrate here that yeast Spt4/5 can bind in a sequence-specific manner to single stranded RNA containing AAN repeats. Furthermore, we show that the major protein determinants for RNA-binding are Spt4 together with the NGN domain of Spt5 and that the KOW domains are not required for RNA recognition. These findings attribute a new function to a domain of Spt4/5 that associates directly with RNAPII, making significant steps towards elucidating the mechanism behind transcriptional control by Spt4/5. © 2016 The Protein Society},\nauthor_keywords={RNA binding;  RNA polymerase;  SELEX;  Spt4/5;  transcription elongation;  transcription elongation factor},\nkeywords={RNA binding protein;  RNA polymerase II;  single stranded RNA;  transcription elongation factor;  transcription elongation factor spt4;  transcription elongation factor spt5;  unclassified drug, Article;  conformational transition;  controlled study;  molecular recognition;  nonhuman;  nucleotide repeat;  priority journal;  protein domain;  regulatory mechanism;  RNA binding;  RNA sequence;  transcription elongation;  transcription regulation;  yeast},\ncorrespondence_address1={Vrielink, A.; School of Chemistry and Biochemistry, Australia; email: alice.vrielink@uwa.edu.au},\npublisher={Blackwell Publishing Ltd},\nissn={09618368},\ncoden={PRCIE},\npubmed_id={27376968},\nlanguage={English},\nabbrev_source_title={Protein Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7.\n \n \n \n \n\n\n \n Schmidberger, J.; Sharifi Tabar, M.; Torrado, M.; Silva, A.; Landsberg, M.; Brillault, L.; AlQarni, S.; Zeng, Y.; Parker, B.; Low, J.; and Mackay, J.\n\n\n \n\n\n\n Protein Science,1472-1482. 2016.\n cited By 20\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Schmidberger20161472,\nauthor={Schmidberger, J.W. and Sharifi Tabar, M. and Torrado, M. and Silva, A.P.G. and Landsberg, M.J. and Brillault, L. and AlQarni, S. and Zeng, Y.C. and Parker, B.L. and Low, J.K.K. and Mackay, J.P.},\ntitle={The MTA1 subunit of the nucleosome remodeling and deacetylase complex can recruit two copies of RBBP4/7},\njournal={Protein Science},\nyear={2016},\npages={1472-1482},\ndoi={10.1002/pro.2943},\nnote={cited By 20},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84978998166&doi=10.1002%2fpro.2943&partnerID=40&md5=15cbc87c7db28ab52ad91904e03dbcc9},\naffiliation={School of Life and Environmental Sciences, University of SydneyNSW, Australia; School of Chemistry and Molecular Biosciences, University of QueenslandQld, Australia; Institute for Molecular Bioscience, University of QueenslandQld, Australia},\nabstract={The nucleosome remodeling and deacetylase (NuRD) complex remodels the genome in the context of both gene transcription and DNA damage repair. It is essential for normal development and is distributed across multiple tissues in organisms ranging from mammals to nematode worms. In common with other chromatin-remodeling complexes, however, its molecular mechanism of action is not well understood and only limited structural information is available to show how the complex is assembled. As a step towards understanding the structure of the NuRD complex, we have characterized the interaction between two subunits: the metastasis associated protein MTA1 and the histone-binding protein RBBP4. We show that MTA1 can bind to two molecules of RBBP4 and present negative stain electron microscopy and chemical crosslinking data that allow us to build a low-resolution model of an MTA1-(RBBP4)2 subcomplex. These data build on our understanding of NuRD complex structure and move us closer towards an understanding of the biochemical basis for the activity of this complex. © 2016 The Protein Society},\nauthor_keywords={chromatin;  MTA1;  NuRD complex;  protein structure;  RBBP4;  transcription regulation},\nkeywords={MTA1 protein;  multiprotein complex;  retinoblastoma binding protein 4;  retinoblastoma binding protein 7;  unclassified drug, Article;  biochemistry;  carboxy terminal sequence;  chromatin assembly and disassembly;  cross linking;  electron microscopy;  nucleosome;  priority journal;  protein binding;  protein function;  protein protein interaction;  protein structure},\ncorrespondence_address1={Schmidberger, J.W.; School of Life and Environmental Sciences, Australia; email: jason.schmidberger@sydney.edu.au},\npublisher={Blackwell Publishing Ltd},\nissn={09618368},\ncoden={PRCIE},\npubmed_id={27144666},\nlanguage={English},\nabbrev_source_title={Protein Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n CHD4 is a peripheral component of the nucleosome remodeling and deacetylase complex.\n \n \n \n \n\n\n \n Low, J.; Webb, S.; Silva, A.; Saathoff, H.; Ryan, D.; Torrado, M.; Brofelth, M.; Parker, B.; Shepherd, N.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 291(30): 15853-15866. 2016.\n cited By 37\n\n\n\n
\n\n\n\n \n \n $\"CHD4$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Low201615853,\nauthor={Low, J.K.K. and Webb, S.R. and Silva, A.P.G. and Saathoff, H. and Ryan, D.P. and Torrado, M. and Brofelth, M. and Parker, B.L. and Shepherd, N.E. and Mackay, J.P.},\ntitle={CHD4 is a peripheral component of the nucleosome remodeling and deacetylase complex},\njournal={Journal of Biological Chemistry},\nyear={2016},\nvolume={291},\nnumber={30},\npages={15853-15866},\ndoi={10.1074/jbc.M115.707018},\nnote={cited By 37},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84978973644&doi=10.1074%2fjbc.M115.707018&partnerID=40&md5=e133725cde68d66ff8e49099008590f7},\naffiliation={School of Life and Environmental Sciences, University of Sydney, Sydney, NSW  2006, Australia; Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, ACT  2601, Australia; Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom},\nabstract={Chromatin remodeling enzymes act to dynamically regulate gene accessibility. In many cases, these enzymes function as large multicomponent complexes that in general comprise a central ATP-dependent Snf2 family helicase that is decorated with a variable number of regulatory subunits. The nucleosome remodeling and deacetylase (NuRD) complex, which is essential for normal development in higher organisms, is one such macromolecular machine. The NuRD complex comprises ∼10 subunits, including the histone deacetylases 1 and 2 (HDAC1 and HDAC2), and is defined by the presence of a CHD family remodeling enzyme, most commonly CHD4 (chromodomain helicase DNA-binding protein 4). The existing paradigm holds that CHD4 acts as the central hub upon which the complex is built. We show here that this paradigm does not, in fact, hold and that CHD4 is a peripheral component of the NuRD complex. A complex lacking CHD4 that has HDAC activity can exist as a stable species. The addition of recombinant CHD4 to this nucleosome deacetylase complex reconstitutes a NuRD complex with nucleosome remodeling activity. These data contribute to our understanding of the architecture of the NuRD complex. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Proteins, Chromatin remodeling;  DNA-binding protein;  Histone deacetylases;  Multicomponent complexes;  Nucleosome remodeling;  Peripheral components;  Regulatory subunits;  Variable number, Enzymes, chromodomain helicase DNA binding protein 4;  DNA binding protein;  histone deacetylase;  histone deacetylase 1;  histone deacetylase 2;  metastasis associated protein 1;  metastasis associated protein 2;  metastasis associated protein 3;  methyl CpG binding protein;  methyl CpG binding protein 3;  retinoblastoma binding protein 4;  retinoblastoma binding protein 7;  transcription factor GATA;  transcription factor GATA 2A;  transcription factor GATA 2B;  tumor marker;  unclassified drug;  autoantigen;  CHD4 protein, human;  DNA helicase;  HDAC1 protein, human;  Hdac1 protein, mouse;  HDAC2 protein, human;  Hdac2 protein, mouse;  histone deacetylase;  histone deacetylase 1;  histone deacetylase 2;  Mi-2beta protein, mouse;  nucleosome, animal cell;  Article;  chromatin assembly and disassembly;  complex formation;  controlled study;  DNA cross linking;  enzyme activity;  gene expression regulation;  in vitro study;  nonhuman;  nucleosome;  priority journal;  protein DNA binding;  protein function;  protein subunit;  transcription regulation;  animal;  cell line;  genetics;  human;  metabolism;  mouse;  nucleosome, Animals;  Autoantigens;  Cell Line;  DNA Helicases;  Histone Deacetylase 1;  Histone Deacetylase 2;  Humans;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Mice;  Nucleosomes},\ncorrespondence_address1={Shepherd, N.E.; Institute of Molecular Bioscience, Australia; email: n.shepherd@imb.uq.edu.au},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={27235397},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Determinants of affinity and specificity in RNA-binding proteins.\n \n \n \n \n\n\n \n Helder, S.; Blythe, A.; Bond, C.; and Mackay, J.\n\n\n \n\n\n\n Current Opinion in Structural Biology, 38: 83-91. 2016.\n cited By 37\n\n\n\n
\n\n\n\n \n \n $\"Determinants$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Helder201683,\nauthor={Helder, S. and Blythe, A.J. and Bond, C.S. and Mackay, J.P.},\ntitle={Determinants of affinity and specificity in RNA-binding proteins},\njournal={Current Opinion in Structural Biology},\nyear={2016},\nvolume={38},\npages={83-91},\ndoi={10.1016/j.sbi.2016.05.005},\nnote={cited By 37},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84973861043&doi=10.1016%2fj.sbi.2016.05.005&partnerID=40&md5=5b9d4688aba80af759e1c94a97dab8a5},\naffiliation={School of Life and Environmental Sciences, The University of SydneyNSW  2006, Australia; School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA  6014, Australia},\nabstract={Emerging data suggest that the mechanisms by which RNA-binding proteins (RBPs) interact with RNA and the rules governing specificity might be substantially more complex than those underlying their DNA-binding counterparts. Even our knowledge of what constitutes the RNA-bound proteome is contentious; recent studies suggest that 10-30% of RBPs contain no known RNA-binding domain. Adding to this situation is a growing disconnect between the avalanche of identified interactions between proteins and long noncoding RNAs and the absence of biophysical data on these interactions. RNA-protein interactions are also at the centre of what might emerge as one of the biggest shifts in thinking about cell and molecular biology this century, following from recent reports of ribonucleoprotein complexes that drive reversible membrane-free phase separation events within the cell. Unexpectedly, low-complexity motifs are important in the formation of these structures. Here we briefly survey recent advances in our understanding of the specificity of RBPs. © 2016 Elsevier Ltd.},\nkeywords={adenosine triphosphate;  flavine adenine nucleotide;  long untranslated RNA;  nicotinamide adenine dinucleotide;  ribonucleoprotein;  RNA binding protein;  RNA recognition motif protein;  transcription factor YY1;  zinc finger protein;  long untranslated RNA;  protein binding;  RNA binding protein, binding affinity;  cell structure;  DNA binding;  gene control;  human;  nonhuman;  priority journal;  protein analysis;  protein function;  protein interaction;  protein motif;  protein RNA binding;  protein structure;  protein transport;  Review;  RNA structure;  sequence analysis;  transcription regulation;  chemistry;  enzyme specificity;  metabolism;  protein domain, Humans;  Protein Binding;  Protein Domains;  RNA, Long Noncoding;  RNA-Binding Proteins;  Substrate Specificity},\ncorrespondence_address1={Mackay, J.P.; School of Life and Environmental Sciences, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Elsevier Ltd},\nissn={0959440X},\ncoden={COSBE},\npubmed_id={27315040},\nlanguage={English},\nabbrev_source_title={Curr. Opin. Struct. Biol.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n 1H, 13C and 15N resonance assignments of a C-terminal domain of human CHD1.\n \n \n \n \n\n\n \n Mohanty, B.; Silva, A.; Mackay, J.; and Ryan, D.\n\n\n \n\n\n\n Biomolecular NMR Assignments, 10(1): 31-34. 2016.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"1H,$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mohanty201631,\nauthor={Mohanty, B. and Silva, A.P.G. and Mackay, J.P. and Ryan, D.P.},\ntitle={1H, 13C and 15N resonance assignments of a C-terminal domain of human CHD1},\njournal={Biomolecular NMR Assignments},\nyear={2016},\nvolume={10},\nnumber={1},\npages={31-34},\ndoi={10.1007/s12104-015-9631-1},\nnote={cited By 1},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84961164609&doi=10.1007%2fs12104-015-9631-1&partnerID=40&md5=1689870a49e080d3916e0ff3bcd7e34d},\naffiliation={School of Molecular Bioscience, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, NSW  2006, Australia; Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Building 131, Garran Road, Canberra, ACT  2601, Australia; Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, 3052, Australia},\nabstract={Chromatin remodelling proteins are an essential family of eukaryotic proteins. They harness the energy from ATP hydrolysis and apply it to alter chromatin structure in order to regulate all aspects of genome biology. Chromodomain helicase DNA-binding protein 1 (CHD1) is one such remodelling protein that has specialised nucleosome organising abilities and is conserved across eukaryotes. CHD1 possesses a pair of tandem chromodomains that directly precede the core catalytic Snf2 helicase-like domain, and a C-terminal SANT-SLIDE DNA-binding domain. We have identified an additional conserved domain in the C-terminal region of CHD1. Here, we report the backbone and side chain resonance assignments for this domain from human CHD1 at pH 6.5 and 25 °C (BMRB No. 25638). © 2015, Springer Science+Business Media Dordrecht.},\nauthor_keywords={C-terminal domain;  CHD1;  Chromatin remodelling;  Nucleosomes},\nkeywords={carbon;  CHD1 protein, human;  DNA binding protein;  DNA helicase;  nitrogen;  tritium, chemistry;  human;  nuclear magnetic resonance;  protein domain;  protein secondary structure, Carbon Isotopes;  DNA Helicases;  DNA-Binding Proteins;  Humans;  Nitrogen Isotopes;  Nuclear Magnetic Resonance, Biomolecular;  Protein Domains;  Protein Structure, Secondary;  Tritium},\ncorrespondence_address1={Mackay, J.P.; School of Molecular Bioscience, Building G08, Corner Butlin Avenue and Maze Crescent, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Springer Netherlands},\nissn={18742718},\npubmed_id={26286320},\nlanguage={English},\nabbrev_source_title={Biomol. NMR Assignments},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The N-terminal region of chromodomain helicase DNA-binding protein 4 (CHD4) is essential for activity and contains a high mobility group (HMG) box-like-domain that can bind poly(ADP-ribose).\n \n \n \n \n\n\n \n Silva, A.; Ryan, D.; Galanty, Y.; Low, J.; Vandevenne, M.; Jackson, S.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 291(2): 924-938. 2016.\n cited By 35\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Silva2016924,\nauthor={Silva, A.P.G. and Ryan, D.P. and Galanty, Y. and Low, J.K.K. and Vandevenne, M. and Jackson, S.P. and Mackay, J.P.},\ntitle={The N-terminal region of chromodomain helicase DNA-binding protein 4 (CHD4) is essential for activity and contains a high mobility group (HMG) box-like-domain that can bind poly(ADP-ribose)},\njournal={Journal of Biological Chemistry},\nyear={2016},\nvolume={291},\nnumber={2},\npages={924-938},\ndoi={10.1074/jbc.M115.683227},\nnote={cited By 35},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84954181424&doi=10.1074%2fjbc.M115.683227&partnerID=40&md5=282c8151000056bef2c121c1f853fa57},\naffiliation={School of Molecular Bioscience, University of Sydney, (Bldg. G08), Corner Butlin Ave. and Maze CrescentNSW  2006, Australia; Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, ACT  2601, Australia; Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom},\nabstract={Chromodomain Helicase DNA-binding protein 4 (CHD4) is a chromatin-remodeling enzyme that has been reported to regulate DNA-damage responses through its N-terminal region in a poly(ADP-ribose) polymerase-dependent manner. We have identified and determined the structure of a stable domain (CHD4-N) in this N-terminal region. The-fold consists of a four-α-helix bundle with structural similarity to the high mobility group box, a domain that is well known as a DNA binding module. We show that the CHD4-N domain binds with higher affinity to poly(ADP-ribose) than to DNA. We also show that the N-terminal region of CHD4, although not CHD4-N alone, is essential for full nucleosome remodeling activity and is important for localizing CHD4 to sites of DNA damage. Overall, these data build on our understanding of how CHD4-NuRD acts to regulate gene expression and participates in the DNA-damage response. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A.},\nkeywords={Bins;  Gene expression;  Proteins, Chromatin remodeling;  Chromodomains;  DNA damage response;  DNA-binding protein;  High-mobility groups;  Nucleosome remodeling;  Poly polymerase;  Structural similarity, DNA, chromodomain helica DNA binding protein 4;  DNA binding protein;  high mobility group protein;  nicotinamide adenine dinucleotide adenosine diphosphate ribosyltransferase 1;  poly(adenosine diphosphate ribose);  unclassified drug;  autoantigen;  CHD4 protein, human;  DNA;  histone deacetylase;  nucleosome;  peptide;  poly(adenosine diphosphate ribose);  protein binding, Article;  binding affinity;  chromatin assembly and disassembly;  controlled study;  dimerization;  DNA damage;  DNA structure;  Escherichia coli;  nonhuman;  nucleosome;  oligomerization;  priority journal;  protein binding;  protein DNA binding;  protein function;  protein localization;  protein structure;  sequence analysis;  sequence homology;  amino acid sequence;  chemistry;  conserved sequence;  double stranded DNA break;  gene deletion;  HEK293 cell line;  high mobility group box domain;  human;  metabolism;  molecular genetics;  molecular model;  protein secondary structure;  structure activity relation, Amino Acid Sequence;  Autoantigens;  Chromatin Assembly and Disassembly;  Conserved Sequence;  DNA;  DNA Breaks, Double-Stranded;  DNA Damage;  HEK293 Cells;  HMG-Box Domains;  Humans;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Models, Molecular;  Molecular Sequence Data;  Nucleosomes;  Peptides;  Poly Adenosine Diphosphate Ribose;  Protein Binding;  Protein Structure, Secondary;  Sequence Deletion;  Structure-Activity Relationship},\ncorrespondence_address1={Silva, A.P.G.; School of Molecular Bioscience, (Bldg. G08), Corner Butlin Ave. and Maze Crescent, Australia; email: ana.silva@sydney.edu.au},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={26565020},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The binding of syndapin SH3 domain to Dynamin proline-rich domain involves short and long distance elements.\n \n \n \n \n\n\n \n Luo, L.; Xue, J.; Kwan, A.; Gamsjaeger, R.; Wielens, J.; Von Kleist, L.; Cubeddu, L.; Guo, Z.; Stow, J.; Parker, M.; Mackay, J.; and Robinson, P.\n\n\n \n\n\n\n Journal of Biological Chemistry, 291(18): 9411-9424. 2016.\n cited By 14\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Luo20169411,\nauthor={Luo, L. and Xue, J. and Kwan, A. and Gamsjaeger, R. and Wielens, J. and Von Kleist, L. and Cubeddu, L. and Guo, Z. and Stow, J.L. and Parker, M.W. and Mackay, J.P. and Robinson, P.J.},\ntitle={The binding of syndapin SH3 domain to Dynamin proline-rich domain involves short and long distance elements},\njournal={Journal of Biological Chemistry},\nyear={2016},\nvolume={291},\nnumber={18},\npages={9411-9424},\ndoi={10.1074/jbc.M115.703108},\nnote={cited By 14},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84984626915&doi=10.1074%2fjbc.M115.703108&partnerID=40&md5=a1e1c8537d8cd30f43265c394d0b3ee5},\naffiliation={Cell Signalling Unit, Children's Medical Research Institute, University of Sydney, Locked Bag 23, Wentworthville, NSW  2145, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD  4072, Australia; IMB Center for Inflammation and Disease Research, University of Queensland, Brisbane, QLD  4072, Australia; School of Molecular Bioscience, University of SydneyNSW  2006, Australia; School of Science and Health, Western Sydney UniversityNSW  2751, Australia; ACRF Rational Drug Discovery Center, St. Vincent's Institute of Medical Research, Fitzroy, VIC  3065, Australia; Group of Cellular Biochemistry, Institute of Chemistry and Biochemistry, Freie Universitaet Berlin, Thielallee 63, Berlin, 14195, Germany; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC  3010, Australia},\nabstract={Dynamin is a GTPase that mediates vesicle fission during synaptic vesicle endocytosis. Its long C-terminal proline-rich domain contains 13 PXXP motifs, which orchestrate its interactions with multiple proteins. The SH3 domains of syndapin and endophilin bind the PXXP motifs called Site 2 and 3 (Pro-786-Pro-793) at the N-terminal end of the proline-rich domain, whereas the amphiphysin SH3 binds Site 9 (Pro-833-Pro-836) toward the C-terminal end. In some proteins, SH3/peptide interactions also involve short distance elements, which are 5-15 amino acid extensions flanking the central PXXP motif for high affinity binding. Here we found two previously unrecognized elements in the central and the C-terminal end of the dynamin proline-rich domain that account for a significant increase in syndapin binding affinity compared with a previously reported Site 2 and Site 3 PXXP peptide alone. The first new element (Gly-807-Gly-811) is short distance element on the C-terminal side of Site 2 PXXP, which might contact a groove identified under the RT loop of the SH3 domain. The second element (Arg-838-Pro-844) is located about 50 amino acids downstream of Site 2. These two elements provide additional specificity tothe syndapin SH3 domain outsideofthe well described polyproline-binding groove. Thus, the dynamin/syndapin interaction is mediated via a network of multiple contacts outside the core PXXP motif over a previously unrecognized extended region of the proline-rich domain. To our knowledge this is the first example among known SH3 interactions to involve spatially separated and extended long-range elements that combine to provide a higher affinity interaction. 7copy;2016 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Amino acids;  Binding energy;  Molecular biology;  Proteins, Affinity interactions;  Binding affinities;  High affinity binding;  Multiple contacts;  Poly prolines;  Proline-rich domains;  Synaptic vesicle;  Terminal sides, Bins, arginine;  dynamin;  endophilin;  guanosine triphosphatase;  proline;  syndapin;  unclassified drug;  carrier protein;  dynamin;  neuropeptide;  Pacsin1 protein, mouse;  Pacsin1 protein, rat;  phosphoprotein;  protein binding, amino terminal sequence;  Article;  binding affinity;  binding site;  carboxy terminal sequence;  controlled study;  nonhuman;  priority journal;  proline rich protein domain;  protein domain;  protein localization;  protein motif;  protein phosphorylation;  protein protein interaction;  protein targeting;  SH3 domain;  animal;  chemistry;  genetics;  human;  metabolism;  mouse;  rat;  Src homology domain, Amino Acid Motifs;  Animals;  Carrier Proteins;  Dynamins;  Humans;  Mice;  Neuropeptides;  Phosphoproteins;  Protein Binding;  Rats;  src Homology Domains},\ncorrespondence_address1={Robinson, P.J.; Cell Signalling Unit, Locked Bag 23, Australia; email: probinson@cmri.org.au},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={26893375},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2015\n \n \n (3)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Paris-Trousseau thrombocytopenia is phenocopied by the autosomal recessive inheritance of a DNA-binding domain mutation in FLI1.\n \n \n \n \n\n\n \n Stevenson, W.; Rabbolini, D.; Beutler, L.; Chen, Q.; Gabrielli, S.; Mackay, J.; Brighton, T.; Ward, C.; and Morel-Kopp, M.\n\n\n \n\n\n\n Blood, 126(17): 2027-2030. 2015.\n cited By 55\n\n\n\n
\n\n\n\n \n \n $\"Paris-Trousseau$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Stevenson20152027,\nauthor={Stevenson, W.S. and Rabbolini, D.J. and Beutler, L. and Chen, Q. and Gabrielli, S. and Mackay, J.P. and Brighton, T.A. and Ward, C.M. and Morel-Kopp, M.-C.},\ntitle={Paris-Trousseau thrombocytopenia is phenocopied by the autosomal recessive inheritance of a DNA-binding domain mutation in FLI1},\njournal={Blood},\nyear={2015},\nvolume={126},\nnumber={17},\npages={2027-2030},\ndoi={10.1182/blood-2015-06-650887},\nnote={cited By 55},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84944808427&doi=10.1182%2fblood-2015-06-650887&partnerID=40&md5=61c740a7658125e1e455315d086584b3},\naffiliation={Department of Haematology and Transfusion Medicine, Royal North Shore Hospital, Sydney, Australia; Northern Blood Research Centre, Kolling Institute of Medical Research, University of Sydney, Kolling Building Level 11, Royal North Shore Hospital, Reserve Rd, Sydney, St Leonards, NSW  2065, Australia; School of Molecular Biosciences, University of Sydney, Sydney, Australia; South Eastern Area Laboratory Services, Prince of Wales Hospital, Sydney, Australia},\nabstract={Hemizygous deletion of a variable regionon chromosome 11q containing FLI1 causes an inherited platelet-related bleeding disorder in Paris-Trousseau thrombocytopenia and Jacobsen syndrome. These multisystem disorders are also characterized by heart anomalies, changes in facial structure, and intellectual disability. We have identified a consanguineous family with autosomal recessive inheritance of a bleeding disorder that mimics Paris-Trousseau thrombocytopenia but has no other features of the 11q23 deletion syndrome. Affected individuals inthis family have moderate thrombocytopenia; absent collagen-induced platelet aggregation; and large, fused α-granules in1%to 5% of circulating platelets. This phenotype was caused by a FLI1 homozygous c.970C>T-point mutation that predicts an arginine-to-tryptophan substitution in the conserved ETS DNA-binding domain of FLI1. This mutation caused a transcription defect at the promoter of known FLI1 target genes GP6, GP9, and ITGA2B, as measured by luciferase assay in HEK293 cells, and decreased the expression of these target proteins in affected members of the family as measured by Western blotting of platelet lysates. This kindred suggests abnormalitiesin FLI1 as causative of Paris-Trousseau thrombocytopenia and confirms the important role of FLI1 in normal platelet development. © 2015 by The American Society of Hematology.},\nkeywords={glycoprotein VI;  thrombopoietin receptor;  transcription factor Fli 1;  DNA;  FLI1 protein, human;  transcription factor Fli 1, adult child;  Article;  autosomal recessive inheritance;  blood analysis;  blood cell count;  blood sampling;  case report;  Caucasian;  child;  chromosome 11q;  consanguineous marriage;  controlled study;  DNA binding;  embryo;  flow cytometry;  gene mutation;  gene targeting;  HEK293 cell line;  human;  human cell;  Jacobsen syndrome;  menorrhagia;  mucosal bleeding;  phenotype;  point mutation;  priority journal;  promoter region;  protein expression;  thrombocyte aggregation;  thrombocytopenia;  Western blotting;  amino acid sequence;  chromosome 11;  female;  follow up;  genetics;  Jacobsen syndrome;  male;  metabolism;  molecular genetics;  mutation;  pathology;  pedigree;  prognosis;  recessive gene;  sequence homology, Amino Acid Sequence;  Chromosomes, Human, Pair 11;  DNA;  Female;  Follow-Up Studies;  Genes, Recessive;  HEK293 Cells;  Humans;  Jacobsen Distal 11q Deletion Syndrome;  Male;  Molecular Sequence Data;  Mutation;  Pedigree;  Phenotype;  Prognosis;  Proto-Oncogene Protein c-fli-1;  Sequence Homology, Amino Acid},\ncorrespondence_address1={Morel-Kopp, M.-C.; Northern Blood Research Centre, Reserve Rd, Australia; email: marie-christine.kopp@sydney.edu.au},\npublisher={American Society of Hematology},\nissn={00064971},\ncoden={BLOOA},\npubmed_id={26316623},\nlanguage={English},\nabbrev_source_title={Blood},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n A peptide affinity reagent for isolating an intact and catalytically active multi-protein complex from mammalian cells.\n \n \n \n \n\n\n \n Saathoff, H.; Brofelth, M.; Trinh, A.; Parker, B.; Ryan, D.; Low, J.; Webb, S.; Silva, A.; Mackay, J.; and Shepherd, N.\n\n\n \n\n\n\n Bioorganic and Medicinal Chemistry, 23(5): 960-965. 2015.\n cited By 7\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Saathoff2015960,\nauthor={Saathoff, H. and Brofelth, M. and Trinh, A. and Parker, B.L. and Ryan, D.P. and Low, J.K.K. and Webb, S.R. and Silva, A.P.G. and Mackay, J.P. and Shepherd, N.E.},\ntitle={A peptide affinity reagent for isolating an intact and catalytically active multi-protein complex from mammalian cells},\njournal={Bioorganic and Medicinal Chemistry},\nyear={2015},\nvolume={23},\nnumber={5},\npages={960-965},\ndoi={10.1016/j.bmc.2015.01.023},\nnote={cited By 7},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84923079547&doi=10.1016%2fj.bmc.2015.01.023&partnerID=40&md5=3d78db60e737e5a0ef32875e48c63aa8},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW  2006, Australia; John Curtin School of Medical Research, Australian National University, Canberra, ACT  0200, Australia},\nabstract={We have developed an approach for directly isolating an intact multi-protein chromatin remodeling complex from mammalian cell extracts using synthetic peptide affinity reagent 4. FOG1(1-15), a short peptide sequence known to target subunits of the nucleosome remodeling and deacetylase (NuRD) complex, was joined via a 35-atom hydrophilic linker to the StreptagII peptide. Loading this peptide onto Streptactin beads enabled capture of the intact NuRD complex from MEL cell nuclear extract. Gentle biotin elution yielded the desired intact complex free of significant contaminants and in a form that was catalytically competent in a nucleosome remodeling assay. The efficiency of 4 in isolating the NuRD complex was comparable to other reported methods utilising recombinantly produced GST-FOG1(1-45). © 2015 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND.},\nauthor_keywords={Affinity purification;  Friend of GATA1 (FOG1);  Multi-protein complex;  Nucleosome remodeling and deacetylase complex peptides},\nkeywords={multiprotein complex;  affinity labeling;  histone deacetylase;  peptide, affinity chromatography;  amino terminal sequence;  animal cell;  Article;  binding affinity;  binding site;  biotinylation;  catalysis;  chromatin assembly and disassembly;  collisionally activated dissociation;  controlled study;  high performance liquid chromatography;  hydrophilicity;  mouse;  nonhuman;  peptide analysis;  polyacrylamide gel electrophoresis;  protein analysis;  protein cleavage;  protein purification;  affinity labeling;  amino acid sequence;  animal;  catalysis;  chemistry;  isolation and purification;  mass spectrometry;  metabolism;  molecular genetics;  tumor cell culture, Mammalia, Affinity Labels;  Amino Acid Sequence;  Animals;  Catalysis;  Chromatography, High Pressure Liquid;  Electrophoresis, Polyacrylamide Gel;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Mice;  Molecular Sequence Data;  Peptides;  Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization;  Tumor Cells, Cultured},\ncorrespondence_address1={Shepherd, N.E.; School of Molecular Bioscience, Australia; email: nicholas.shepherd@sydney.edu.au},\npublisher={Elsevier Ltd},\nissn={09680896},\ncoden={BMECE},\npubmed_id={25678017},\nlanguage={English},\nabbrev_source_title={Bioorg. Med. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Site directed nitroxide spin labeling of oligonucleotides for NMR and EPR studies.\n \n \n \n \n\n\n \n Shepherd, N.; Gamsjaeger, R.; Vandevenne, M.; Cubeddu, L.; and Mackay, J.\n\n\n \n\n\n\n Tetrahedron, 71(5): 813-819. 2015.\n cited By 7\n\n\n\n
\n\n\n\n \n \n $\"Site$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Shepherd2015813,\nauthor={Shepherd, N.E. and Gamsjaeger, R. and Vandevenne, M. and Cubeddu, L. and Mackay, J.P.},\ntitle={Site directed nitroxide spin labeling of oligonucleotides for NMR and EPR studies},\njournal={Tetrahedron},\nyear={2015},\nvolume={71},\nnumber={5},\npages={813-819},\ndoi={10.1016/j.tet.2014.12.056},\nnote={cited By 7},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84920742449&doi=10.1016%2fj.tet.2014.12.056&partnerID=40&md5=4581889f04ddcfd831c29865ddca124b},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW  2006, Australia; School of Science and Health, University of Western Sydney, Penrith, NSW  2751, Australia},\nabstract={Nitroxide labels are useful probes of biomolecule structure that can be detected by NMR and EPR spectroscopy. Although many methods exist for labeling oligonucleotides with nitroxides, most require reagents that are expensive or laborious to prepare. A simpler approach is described herein using commercially available phosphorothioate oligonucleotides and 2-(3-iodoacetamidomethyl)-PROXYL. We describe semi-optimized conditions for labeling DNA and RNA oligonucleotides and methodology for purifying and identifying these reagents by MALDI-MS. The nitroxide label showed some propensity to hydrolyze at high temperature and over prolonged periods at room temperature. Nitroxide-labeled DNA oligonucleotides gave characteristic EPR spectra and caused the disappearance of bound protein signals in 15N HSQC spectra consistent with the paramagnetic relaxation enhancement (PRE) effect. © 2015 The Authors. Published by Elsevier Ltd.},\nauthor_keywords={Electron paramagnetic resonance spectroscopy;  Nitroxide;  Nuclear magnetic resonance spectroscopy;  Paramagnetic relaxation enhancement;  Phosphorothioate},\nkeywords={3 (iodomethyl) 2,2,5,5 tetramethyl 1 pyrrolidinyloxyl;  DNA;  nitroxide derivative;  oligonucleotide phosphorothioate;  protein;  reagent;  RNA;  single stranded DNA binding protein;  unclassified drug, Article;  controlled study;  DNA purification;  electron spin resonance;  heteronuclear single quantum coherence;  high temperature;  hydrolysis;  long term exposure;  mass spectrometry;  nitrogen nuclear magnetic resonance;  nuclear magnetic resonance spectroscopy;  priority journal;  protein DNA interaction;  protein RNA binding;  RNA purification;  room temperature;  spin labeling},\ncorrespondence_address1={Shepherd, N.E.; School of Molecular Bioscience, University of SydneyAustralia},\npublisher={Elsevier Ltd},\nissn={00404020},\ncoden={TETRA},\nlanguage={English},\nabbrev_source_title={Tetrahedron},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2014\n \n \n (11)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Ca2+-induced PRE-NMR changes in the troponin complex reveal the possessive nature of the cardiac isoform for its regulatory switch.\n \n \n \n \n\n\n \n Cordina, N.; Liew, C.; Potluri, P.; Curmi, P.; Fajer, P.; Logan, T.; Mackay, J.; and Brown, L.\n\n\n \n\n\n\n PLoS ONE, 9(11). 2014.\n cited By 14\n\n\n\n
\n\n\n\n \n \n $\"Ca2+-induced$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Cordina2014,\nauthor={Cordina, N.M. and Liew, C.K. and Potluri, P.R. and Curmi, P.M. and Fajer, P.G. and Logan, T.M. and Mackay, J.P. and Brown, L.J.},\ntitle={Ca2+-induced PRE-NMR changes in the troponin complex reveal the possessive nature of the cardiac isoform for its regulatory switch},\njournal={PLoS ONE},\nyear={2014},\nvolume={9},\nnumber={11},\ndoi={10.1371/journal.pone.0112976},\nart_number={0112976},\nnote={cited By 14},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84911917473&doi=10.1371%2fjournal.pone.0112976&partnerID=40&md5=6462782f49b46ffd95e47758cc6f316c},\naffiliation={Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia; Department of Molecular Cardiology and Biophysics, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; School of Physics, University of New South Wales, Sydney, NSW, Australia; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States; School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW, Australia},\nabstract={The interaction between myosin and actin in cardiac muscle, modulated by the calcium (Ca2+) sensor Troponin complex (Tn), is a complex process which is yet to be fully resolved at the molecular level. Our understanding of how the binding of Ca2+ triggers conformational changes within Tn that are subsequently propagated through the contractile apparatus to initiate muscle activation is hampered by a lack of an atomic structure for the Ca2+-free state of the cardiac isoform. We have used paramagnetic relaxation enhancement (PRE)-NMR to obtain a description of the Ca2+-free state of cardiac Tn by describing the movement of key regions of the troponin I (cTnI) subunit upon the release of Ca2+ from Troponin C (cTnC). Site-directed spin-labeling was used to position paramagnetic spin labels in cTnI and the changes in the interaction between cTnI and cTnC subunits were then mapped by PRE-NMR. The functionally important regions of cTnI targeted in this study included the cTnC-binding N-region (cTnI57), the inhibitory region (cTnI143), and two sites on the regulatory switch region (cTnI151 and cTnI159). Comparison of 1H-15N-TROSY spectra of Ca2+-bound and free states for the spin labeled cTnCcTnI binary constructs demonstrated the release and modest movement of the cTnI switch region (,10 A ) away from the hydrophobic N-lobe of troponin C (cTnC) upon the removal of Ca2+. Our data supports a model where the non-bound regulatory switch region of cTnI is highly flexible in the absence of Ca2+ but remains in close vicinity to cTnC. We speculate that the close proximity of TnI to TnC in the cardiac complex is favourable for increasing the frequency of collisions between the N-lobe of cTnC and the regulatory switch region, counterbalancing the reduction in collision probability that results from the incomplete opening of the N-lobe of TnC that is unique to the cardiac isoform. © 2014 Cordina et al.},\nkeywords={calcium ion;  isoprotein;  troponin C;  troponin I;  calcium;  isoprotein;  multiprotein complex;  troponin, amino terminal sequence;  animal tissue;  Article;  calcium binding;  calcium transport;  carboxy terminal sequence;  complex formation;  conformational transition;  H1 transverse relaxation optimized spectroscopy;  heart contraction;  heart muscle;  hydrophobicity;  inhibition kinetics;  N15 transverse relaxation optimized spectroscopy;  nitrogen nuclear magnetic resonance;  nonhuman;  nuclear magnetic resonance;  paramagnetic relaxation enhancement nuclear magnetic resonance;  protein protein interaction;  protein structure;  protein subunit;  proton nuclear magnetic resonance;  rat;  regulatory mechanism;  regulatory switch region;  site directed spin labeling;  spin labeling;  animal;  chemistry;  genetics;  metabolism, Animals;  Calcium;  Multiprotein Complexes;  Myocardium;  Protein Isoforms;  Rats;  Troponin},\ncorrespondence_address1={Cordina, N.M.; Department of Chemistry and Biomolecular Sciences, Macquarie UniversityAustralia},\npublisher={Public Library of Science},\nissn={19326203},\ncoden={POLNC},\npubmed_id={25392916},\nlanguage={English},\nabbrev_source_title={PLoS ONE},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The structure of an LIM-Only protein 4 (LMO4) and Deformed Epidermal Autoregulatory Factor-1 (DEAF1) complex reveals a common mode of binding to LMO4.\n \n \n \n \n\n\n \n Joseph, S.; Kwan, A.; Stokes, P.; Mackay, J.; Cubeddu, L.; and Matthews, J.\n\n\n \n\n\n\n PLoS ONE, 9(10). 2014.\n cited By 10\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Joseph2014,\nauthor={Joseph, S. and Kwan, A.H. and Stokes, P.H. and Mackay, J.P. and Cubeddu, L. and Matthews, J.M.},\ntitle={The structure of an LIM-Only protein 4 (LMO4) and Deformed Epidermal Autoregulatory Factor-1 (DEAF1) complex reveals a common mode of binding to LMO4},\njournal={PLoS ONE},\nyear={2014},\nvolume={9},\nnumber={10},\ndoi={10.1371/journal.pone.0109108},\nart_number={e109108},\nnote={cited By 10},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84907907054&doi=10.1371%2fjournal.pone.0109108&partnerID=40&md5=2cd2cc322f865287be13896495fdfe07},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia; School of Science and Health, University of Western Sydney, Campbelltown, NSW, Australia},\nabstract={LIM-domain only protein 4 (LMO4) is a widely expressed protein with important roles in embryonic development and breast cancer. It has been reported to bind many partners, including the transcription factor Deformed epidermal autoregulatory factor-1 (DEAF1), with which LMO4 shares many biological parallels. We used yeast two-hybrid assays to show that DEAF1 binds both LIM domains of LMO4 and that DEAF1 binds the same face on LMO4 as two other LMO4-binding partners, namely LIM domain binding protein 1 (LDB1) and C-terminal binding protein interacting protein (CtIP/RBBP8). Mutagenic screening analysed by the same method, indicates that the key residues in the interaction lie in LMO4LIM2and the N-terminal half of the LMO4-binding domain in DEAF1. We generated a stable LMO4LIM2-DEAF1 complex and determined the solution structure of that complex. Although the LMO4-binding domain from DEAF1 is intrinsically disordered, it becomes structured on binding. The structure confirms that LDB1, CtIP and DEAF1 all bind to the same face on LMO4. LMO4 appears to form a hub in protein-protein interaction networks, linking numerous pathways within cells. Competitive binding for LMO4 therefore most likely provides a level of regulation between those different pathways. © 2014 Joseph et al.},\nkeywords={deformed epidermal autoregulatory factor 1;  fungal protein;  protein LIMO4;  transcription factor;  unclassified drug;  DEAF1 protein, human;  LIM protein;  LMO4 protein, human;  nuclear protein;  protein binding;  signal transducing adaptor protein, amino terminal sequence;  animal cell;  Article;  carboxy terminal sequence;  complex formation;  controlled study;  hydrophobicity;  mutagen testing;  nonhuman;  nuclear magnetic resonance;  protein binding;  protein conformation;  protein determination;  protein domain;  protein protein interaction;  yeast;  human;  metabolism;  protein tertiary structure;  two hybrid system, Adaptor Proteins, Signal Transducing;  Humans;  LIM Domain Proteins;  Nuclear Proteins;  Protein Binding;  Protein Structure, Tertiary;  Two-Hybrid System Techniques},\ncorrespondence_address1={Joseph, S.; School of Molecular Bioscience, University of SydneyAustralia},\npublisher={Public Library of Science},\nissn={19326203},\ncoden={POLNC},\npubmed_id={25310299},\nlanguage={English},\nabbrev_source_title={PLoS ONE},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Trim58 Degrades Dynein and Regulates Terminal Erythropoiesis.\n \n \n \n \n\n\n \n Thom, C.; Traxler, E.; Khandros, E.; Nickas, J.; Zhou, O.; Lazarus, J.; Silva, A.; Prabhu, D.; Yao, Y.; Aribeana, C.; Fuchs, S.; Mackay, J.; Holzbaur, E.; and Weiss, M.\n\n\n \n\n\n\n Developmental Cell, 30(6): 688-700. 2014.\n cited By 62\n\n\n\n
\n\n\n\n \n \n $\"Trim58$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Thom2014688,\nauthor={Thom, C.S. and Traxler, E.A. and Khandros, E. and Nickas, J.M. and Zhou, O.Y. and Lazarus, J.E. and Silva, A.P.G. and Prabhu, D. and Yao, Y. and Aribeana, C. and Fuchs, S.Y. and Mackay, J.P. and Holzbaur, E.L.F. and Weiss, M.J.},\ntitle={Trim58 Degrades Dynein and Regulates Terminal Erythropoiesis},\njournal={Developmental Cell},\nyear={2014},\nvolume={30},\nnumber={6},\npages={688-700},\ndoi={10.1016/j.devcel.2014.07.021},\nnote={cited By 62},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84908152438&doi=10.1016%2fj.devcel.2014.07.021&partnerID=40&md5=a2f58a8604554be18fa0a42b53bc10fb},\naffiliation={Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA  19104, United States; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA  19104, United States; Department of Physiology and Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA  19104, United States; School of Molecular Bioscience, The University of Sydney, Sydney, NSW  2006, Australia; Department of Animal Biology and Mari Lowe Comparative Oncology Center, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA  19104, United States; Department of Hematology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS #355, Memphis, TN  38105, United States},\nabstract={TRIM58 is an E3 ubiquitin ligase superfamily member implicated by genome-wide association studies to regulate human erythrocyte traits. Here, we show that Trim58 expression is induced during late erythropoiesis and that its depletion by small hairpin RNAs (shRNAs) inhibits the maturation of late-stage nucleated erythroblasts to anucleate reticulocytes. Imaging flow cytometry studies demonstrate that Trim58 regulates polarization and/or extrusion of erythroblast nuclei. Invitro, Trim58 directly binds and ubiquitinates the intermediate chain of the microtubule motor dynein. In cells, Trim58 stimulates proteasome-dependent degradation of the dynein holoprotein complex. During erythropoiesis, Trim58 expression, dynein loss, and enucleation occur concomitantly, and all are inhibited by Trim58 shRNAs. Dynein regulates nuclear positioning and microtubule organization, both of which undergo dramatic changes during erythroblast enucleation. Thus, we propose that Trim58 promotes this processby eliminating dynein. Our findings identify an erythroid-specific regulator of enucleation and elucidate a previously unrecognized mechanism for controlling dynein activity. © 2014 Elsevier Inc.},\nkeywords={dynein adenosine triphosphatase;  proteasome;  protein trim58;  short hairpin RNA;  ubiquitin protein ligase E3;  unclassified drug;  dynein adenosine triphosphatase;  protein binding;  Trim58 protein, mouse;  ubiquitin protein ligase, animal cell;  Article;  cell nucleus;  enucleation;  enzyme degradation;  erythroblast;  erythropoiesis;  flow cytometry;  microtubule;  nonhuman;  polarization;  protein binding;  protein expression;  regulatory mechanism;  reticulocyte;  ubiquitination;  animal;  cytology;  genetics;  metabolism;  mouse, Animals;  Dyneins;  Erythroblasts;  Erythropoiesis;  Mice;  Protein Binding;  Reticulocytes;  Ubiquitin-Protein Ligases;  Ubiquitination},\ncorrespondence_address1={Weiss, M.J.; Division of Hematology, United States},\npublisher={Cell Press},\nissn={15345807},\ncoden={DCEEB},\npubmed_id={25241935},\nlanguage={English},\nabbrev_source_title={Dev. Cell},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The identification and structure of an N-terminal PR domain show that FOG1 is a member of the PRDM family of proteins.\n \n \n \n \n\n\n \n Clifton, M.; Westman, B.; Thong, S.; O'Connell, M.; Webster, M.; Shepherd, N.; Quinlan, K.; Crossley, M.; Blobel, G.; and Mackay, J.\n\n\n \n\n\n\n PLoS ONE, 9(8). 2014.\n cited By 8\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Clifton2014,\nauthor={Clifton, M.K. and Westman, B.J. and Thong, S.Y. and O'Connell, M.R. and Webster, M.W. and Shepherd, N.E. and Quinlan, K.G. and Crossley, M. and Blobel, G.A. and Mackay, J.P.},\ntitle={The identification and structure of an N-terminal PR domain show that FOG1 is a member of the PRDM family of proteins},\njournal={PLoS ONE},\nyear={2014},\nvolume={9},\nnumber={8},\ndoi={10.1371/journal.pone.0106011},\nart_number={e106011},\nnote={cited By 8},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84940353391&doi=10.1371%2fjournal.pone.0106011&partnerID=40&md5=73ef2750a533a0847ccffa7165a9d07d},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia; Division of Hematology, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States},\nabstract={FOG1 is a transcriptional regulator that acts in concert with the hematopoietic master regulator GATA1 to coordinate the differentiation of platelets and erythrocytes. Despite considerable effort, however, the mechanisms through which FOG1 regulates gene expression are only partially understood. Here we report the discovery of a previously unrecognized domain in FOG1: a PR (PRD-BF1 and RIZ) domain that is distantly related in sequence to the SET domains that are found in many histone methyltransferases. We have used NMR spectroscopy to determine the solution structure of this domain, revealing that the domain shares close structural similarity with SET domains. Titration with S-adenosyl-L-homocysteine, the cofactor product synonymous with SET domain methyltransferase activity, indicated that the FOG PR domain is not, however, likely to function as a methyltransferase in the same fashion. We also sought to define the function of this domain using both pulldown experiments and gel shift assays. However, neither pulldowns from mammalian nuclear extracts nor yeast two-hybrid assays reproducibly revealed binding partners, and we were unable to detect nucleic-acid-binding activity in this domain using our high-diversity Pentaprobe oligonucleotides. Overall, our data demonstrate that FOG1 is a member of the PRDM (PR domain containing proteins, with zinc fingers) family of transcriptional regulators. The function of many PR domains, however, remains somewhat enigmatic for the time being. © 2014 Clifton et al.},\nkeywords={FOG1 protein;  methyltransferase;  PRDM protein;  regulator protein;  s adenosylhomocysteine;  unclassified drug;  zinc finger protein;  isoprotein;  nuclear protein;  recombinant protein;  transcription factor;  ZFPM1 protein, human;  Zfpm1 protein, mouse, article;  DNA binding;  enzyme activity;  nuclear magnetic resonance spectroscopy;  PR domain;  protein domain;  SET domain;  structural homology;  amino acid sequence;  animal;  chemical structure;  chemistry;  Escherichia coli;  gene expression;  genetics;  human;  metabolism;  molecular genetics;  mouse;  nucleotide sequence;  protein tertiary structure;  sequence alignment;  sequence homology;  tumor cell line, Amino Acid Sequence;  Animals;  Cell Line, Tumor;  Conserved Sequence;  Escherichia coli;  Gene Expression;  Humans;  Mice;  Models, Molecular;  Molecular Sequence Data;  Nuclear Proteins;  Protein Isoforms;  Protein Structure, Tertiary;  Recombinant Proteins;  S-Adenosylhomocysteine;  Sequence Alignment;  Sequence Homology, Amino Acid;  Transcription Factors},\nissn={19326203},\ncoden={POLNC},\npubmed_id={25162672},\nlanguage={English},\nabbrev_source_title={PLoS ONE},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Insight into the architecture of the NuRD complex: Structure of the RbAp48-MTA1 subcomplex.\n \n \n \n \n\n\n \n Alqarni, S.; Murthy, A.; Zhang, W.; Przewloka, M.; Silva, A.; Watson, A.; Lejon, S.; Pei, X.; Smits, A.; Kloet, S.; Wang, H.; Shepherd, N.; Stokes, P.; Blobel, G.; Vermeulen, M.; Glover, D.; Mackay, J.; and Laue, E.\n\n\n \n\n\n\n Journal of Biological Chemistry, 289(32): 21844-21855. 2014.\n cited By 59\n\n\n\n
\n\n\n\n \n \n $\"Insight$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Alqarni201421844,\nauthor={Alqarni, S.S.M. and Murthy, A. and Zhang, W. and Przewloka, M.R. and Silva, A.P.G. and Watson, A.A. and Lejon, S. and Pei, X.Y. and Smits, A.H. and Kloet, S.L. and Wang, H. and Shepherd, N.E. and Stokes, P.H. and Blobel, G.A. and Vermeulen, M. and Glover, D.M. and Mackay, J.P. and Laue, E.D.},\ntitle={Insight into the architecture of the NuRD complex: Structure of the RbAp48-MTA1 subcomplex},\njournal={Journal of Biological Chemistry},\nyear={2014},\nvolume={289},\nnumber={32},\npages={21844-21855},\ndoi={10.1074/jbc.M114.558940},\nnote={cited By 59},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84905842668&doi=10.1074%2fjbc.M114.558940&partnerID=40&md5=aef38249860984b1c962a944805deb7c},\naffiliation={School of Molecular Bioscience, University of Sydney, NSW 2006, Australia; Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom; Department of Genetics, University of Cambridge, CB2 3EH, United Kingdom; Department of Molecular Cancer Research, UMC Utrecht, Universiteitsweg 100, 3584CG Utrecht, Netherlands; Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, United States},\nabstract={Background: The NuRD complex controls gene expression through altering chromatin structure. Results: The MTA1-RbAp48 structure shows how the RbAp46/p48 histone chaperones are recruited to NuRD. Conclusion: The MTA subunits act as scaffolds for NuRD complex assembly. Significance: The MTA/RbAp48 interaction prevents binding of histone H4, which is crucial for understanding the role of the RbAp46/p48 chaperones in the complex. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Gene expression, Chromatin structure;  Complex assembly;  Complex control;  Histone H4, Scaffolds, histone;  histone deacetylase;  Mta1 protein, human;  nuclear protein;  nucleosome;  RBBP4 protein, human;  RBBP7 protein, human;  repressor protein;  retinoblastoma binding protein 4;  retinoblastoma binding protein 7;  transcription factor;  ZFPM1 protein, human, amino acid sequence;  animal;  chemical structure;  chemistry;  chromatin assembly and disassembly;  genetics;  human;  metabolism;  molecular genetics;  nucleosome;  nucleotide sequence;  protein domain;  sequence homology;  X ray crystallography, Amino Acid Sequence;  Animals;  Chromatin Assembly and Disassembly;  Conserved Sequence;  Crystallography, X-Ray;  Histone Deacetylases;  Histones;  Humans;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Models, Molecular;  Molecular Sequence Data;  Nuclear Proteins;  Nucleosomes;  Protein Interaction Domains and Motifs;  Repressor Proteins;  Retinoblastoma-Binding Protein 4;  Retinoblastoma-Binding Protein 7;  Sequence Homology, Amino Acid;  Transcription Factors},\ncorrespondence_address1={Laue, E.D.; Dept. of Biochemistry, Tennis Court Rd., Cambridge CB2 1GA, United Kingdom; email: e.d.laue@bioc.cam.ac.uk},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={24920672},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Engineering specificity changes on a RanBP2 zinc finger that binds single-stranded RNA.\n \n \n \n \n\n\n \n Vandevenne, M.; O'Connell, M.; Helder, S.; Shepherd, N.; Matthews, J.; Kwan, A.; Segal, D.; and Mackay, J.\n\n\n \n\n\n\n Angewandte Chemie - International Edition, 53(30): 7848-7852. 2014.\n cited By 5\n\n\n\n
\n\n\n\n \n \n $\"Engineering$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Vandevenne20147848,\nauthor={Vandevenne, M. and O'Connell, M.R. and Helder, S. and Shepherd, N.E. and Matthews, J.M. and Kwan, A.H. and Segal, D.J. and Mackay, J.P.},\ntitle={Engineering specificity changes on a RanBP2 zinc finger that binds single-stranded RNA},\njournal={Angewandte Chemie - International Edition},\nyear={2014},\nvolume={53},\nnumber={30},\npages={7848-7852},\ndoi={10.1002/anie.201402980},\nnote={cited By 5},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84904599316&doi=10.1002%2fanie.201402980&partnerID=40&md5=19671822ca224a8fa876c95ce3e02a82},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA 95616, United States; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94609, United States},\nabstract={The realization that gene transcription is much more pervasive than previously thought and that many diverse RNA species exist in simple as well as complex organisms has triggered efforts to develop functionalized RNA-binding proteins (RBPs) that have the ability to probe and manipulate RNA function. Previously, we showed that the RanBP2-type zinc finger (ZF) domain is a good candidate for an addressable single-stranded-RNA (ssRNA) binding domain that can recognize ssRNA in a modular and specific manner. In the present study, we successfully engineered a sequence specificity change onto this ZF scaffold by using a combinatorial approach based on phage display. This work constitutes a foundation from which a set of RanBP2 ZFs might be developed that is able to recognize any given RNA sequence. Variation on a theme: A combinatorial library of RanBP2-type zinc finger (ZF) domains has been engineered in an effort to select variants with distinct RNA-binding preferences. One variant was shown to successfully discriminate the sequence GCC over GGU and AAA, but only in the context of a three-ZF polypeptide. This study provides proof of principle that the specificity of RNA-binding modules based on ZF domains can be successfully altered. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},\nauthor_keywords={combinatorial chemistry;  phage display;  protein design;  RNA binding;  zinc fingers},\nkeywords={Bioassay;  Biochips;  Proteins;  Transcription;  Zinc, Combinatorial chemistry;  Phage display;  Protein design;  RNA binding;  Zinc finger, RNA, chaperone;  nucleoporin;  ran-binding protein 2;  RNA;  RNA binding protein;  zinc finger protein, amino acid sequence;  binding site;  chemistry;  genetics;  metabolism;  molecular genetics;  tissue engineering, Amino Acid Sequence;  Binding Sites;  Molecular Chaperones;  Molecular Sequence Data;  Nuclear Pore Complex Proteins;  RNA;  RNA-Binding Proteins;  Tissue Engineering;  Zinc Fingers},\ncorrespondence_address1={Mackay, J.P.; School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Wiley-VCH Verlag},\nissn={14337851},\ncoden={ACIEF},\npubmed_id={25044781},\nlanguage={English},\nabbrev_source_title={Angew. Chem. Int. Ed.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Transcription factor seeks DNA - Cognate site preferred.\n \n \n \n \n\n\n \n Mackay, J.\n\n\n \n\n\n\n Journal of Molecular Biology, 426(7): 1370-1372. 2014.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Transcription$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mackay20141370,\nauthor={Mackay, J.},\ntitle={Transcription factor seeks DNA - Cognate site preferred},\njournal={Journal of Molecular Biology},\nyear={2014},\nvolume={426},\nnumber={7},\npages={1370-1372},\ndoi={10.1016/j.jmb.2013.12.010},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84895918754&doi=10.1016%2fj.jmb.2013.12.010&partnerID=40&md5=9422cddb32f1e4b69ef4275edac5bce2},\naffiliation={School of Molecular Bioscience, University of Sydney, NSW 2006, Australia},\nkeywords={DNA;  transcription factor, DNA sequence;  human;  molecular biology;  nonhuman;  note;  priority journal;  DNA binding;  DNA transcription;  in vitro study;  in vivo study;  Note, Animals;  DNA;  Magnetic Resonance Spectroscopy;  Proto-Oncogene Proteins c-ets;  Repressor Proteins},\ncorrespondence_address1={Mackay, J.; School of Molecular Bioscience, , NSW 2006, Australia},\npublisher={Academic Press},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={24333952},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Note},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structure of the hemoglobin-isdh complex reveals the molecular basis of iron capture by staphylococcus aureus.\n \n \n \n \n\n\n \n Dickson, C.; Kumar, K.; Jacques, D.; Malmirchegini, G.; Spirig, T.; Mackay, J.; Clubb, R.; Guss, J.; and Gell, D.\n\n\n \n\n\n\n Journal of Biological Chemistry, 289(10): 6728-6738. 2014.\n cited By 38\n\n\n\n
\n\n\n\n \n \n $\"Structure$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Dickson20146728,\nauthor={Dickson, C.F. and Kumar, K.K. and Jacques, D.A. and Malmirchegini, G.R. and Spirig, T. and Mackay, J.P. and Clubb, R.T. and Guss, J.M. and Gell, D.A.},\ntitle={Structure of the hemoglobin-isdh complex reveals the molecular basis of iron capture by staphylococcus aureus},\njournal={Journal of Biological Chemistry},\nyear={2014},\nvolume={289},\nnumber={10},\npages={6728-6738},\ndoi={10.1074/jbc.M113.545566},\nnote={cited By 38},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896761833&doi=10.1074%2fjbc.M113.545566&partnerID=40&md5=643565958fd45486912dcb477ca4e85e},\naffiliation={Menzies Research Institute Tasmania, University of Tasmania, 17 Liverpool St., Hobart, TAS 7000, Australia; School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, United States; Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Medical Research Council (MRC), Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom; Dept. of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, United States},\nabstract={Background: IsdB and IsdH proteins from Staphylococcus aureus strip heme iron from human hemoglobin. Results: The IsdH·hemoglobin complex shows how globin-binding and heme-binding NEAT domains of IsdH cooperate to remove heme from both chains of hemoglobin. Conclusion: The supradomain architecture of IsdH confers activity by precisely positioning the heme acceptor domain. Significance: Multiple IsdH·hemoglobin interfaces may be targets for new antibiotics. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Bacteria;  Iron;  Porphyrins;  Proteins;  Staphylococcus aureus, Heme binding;  Heme iron;  Molecular basis, Hemoglobin, bacterial protein;  globin;  heme;  hemoglobin;  hemoglobin alpha chain;  hemoglobin beta chain;  iron;  iron regulated surface determinant H protein;  membrane protein;  unclassified drug, amino terminal sequence;  article;  carboxy terminal sequence;  controlled study;  crystal structure;  human;  NEAT domain;  nonhuman;  priority journal;  protein domain;  protein function;  protein protein interaction;  protein structure;  protein transport;  radiation scattering;  Staphylococcus aureus;  structure analysis;  X ray crystallography, Crystallography;  Heme;  Hemoglobin;  Iron-regulated Surface Determinant;  NEAT Domain;  Protein Domains;  Staphylococcus aureus, Antigens, Bacterial;  Crystallography, X-Ray;  Heme;  Hemoglobins;  Humans;  Iron;  Protein Structure, Secondary;  Protein Structure, Tertiary;  Receptors, Cell Surface;  Staphylococcal Infections;  Staphylococcus aureus},\ncorrespondence_address1={Gell, D.A.; Menzies Research Institute Tasmania, 17 Liverpool St., Hobart, TAS 7000, Australia; email: david.gell@utas.edu.au},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={24425866},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Ubiquitin fusion constructs allow the expression and purification of multi-KOW domain complexes of the Saccharomyces cerevisiae transcription elongation factor Spt4/5.\n \n \n \n \n\n\n \n Blythe, A.; Gunasekara, S.; Walshe, J.; Mackay, J.; Hartzog, G.; and Vrielink, A.\n\n\n \n\n\n\n Protein Expression and Purification, 100: 54-60. 2014.\n cited By 2\n\n\n\n
\n\n\n\n \n \n $\"Ubiquitin$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Blythe201454,\nauthor={Blythe, A. and Gunasekara, S. and Walshe, J. and Mackay, J.P. and Hartzog, G.A. and Vrielink, A.},\ntitle={Ubiquitin fusion constructs allow the expression and purification of multi-KOW domain complexes of the Saccharomyces cerevisiae transcription elongation factor Spt4/5},\njournal={Protein Expression and Purification},\nyear={2014},\nvolume={100},\npages={54-60},\ndoi={10.1016/j.pep.2014.05.005},\nnote={cited By 2},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84902173734&doi=10.1016%2fj.pep.2014.05.005&partnerID=40&md5=2e10734ce624b31a205d77daf02dcda6},\naffiliation={School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, United States},\nabstract={Spt4/5 is a hetero-dimeric transcription elongation factor that can both inhibit and promote transcription elongation by RNA polymerase II (RNAPII). However, Spt4/5's mechanism of action remains elusive. Spt5 is an essential protein and the only universally-conserved RNAP-associated transcription elongation factor. The protein contains multiple Kyrpides, Ouzounis and Woese (KOW) domains. These domains, in other proteins, are thought to bind RNA although there is little direct evidence in the literature to support such a function in Spt5. This could be due, at least in part, to difficulties in expressing and purifying recombinant Spt5. When expressed in Escherichia coli (E. coli), Spt5 is innately insoluble. Here we report a new approach for the successful expression and purification of milligram quantities of three different multi-KOW domain complexes of Saccharomyces cerevisiae Spt4/5 for use in future functional studies. Using the E. coli strain Rosetta2 (DE3) we have developed strategies for co-expression of Spt4 and multi-KOW domain Spt5 complexes from the bi-cistronic pET-Duet vector. In a second strategy, Spt4/5 was expressed via co-transformation of Spt4 in the vector pET-M11 with Spt5 ubiquitin fusion constructs in the vector pHUE. We characterized the multi-KOW domain Spt4/5 complexes by Western blot, limited proteolysis, circular dichroism, SDS-PAGE and size exclusion chromatography-multiangle light scattering and found that the proteins are folded with a Spt4:Spt5 hetero-dimeric stoichiometry of 1:1. These expression constructs encompass a larger region of Spt5 than has previously been reported, and will provide the opportunity to elucidate the biological function of the multi-KOW containing Spt5. © 2014 Elsevier Inc. All rights reserved.},\nauthor_keywords={Expression and purification;  KOW domain;  pHUE;  Spt4/5;  Ubiquitin tag},\nkeywords={hybrid protein;  nonhistone protein;  nuclear protein;  Saccharomyces cerevisiae protein;  SPT4 protein, S cerevisiae;  SPT5 transcriptional elongation factor;  transcription elongation factor;  ubiquitin, chemistry;  Escherichia coli;  genetics;  isolation and purification;  molecular cloning;  procedures;  protein tertiary structure;  transcription elongation, Chromosomal Proteins, Non-Histone;  Cloning, Molecular;  Escherichia coli;  Nuclear Proteins;  Protein Structure, Tertiary;  Recombinant Fusion Proteins;  Saccharomyces cerevisiae Proteins;  Transcription Elongation, Genetic;  Transcriptional Elongation Factors;  Ubiquitin},\ncorrespondence_address1={Vrielink, A.; School of Chemistry and Biochemistry, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; email: alice.vrielink@uwa.edu.au},\npublisher={Academic Press Inc.},\nissn={10465928},\ncoden={PEXPE},\npubmed_id={24859675},\nlanguage={English},\nabbrev_source_title={Protein Expr. Purif.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Backbone and side-chain assignments of a tethered complex between LMO4 and DEAF-1.\n \n \n \n \n\n\n \n Joseph, S.; Kwan, A.; Mackay, J.; Cubeddu, L.; and Matthews, J.\n\n\n \n\n\n\n Biomolecular NMR Assignments, 8(1): 141-144. 2014.\n cited By 3\n\n\n\n
\n\n\n\n \n \n $\"Backbone$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Joseph2014141,\nauthor={Joseph, S. and Kwan, A.H.Y. and Mackay, J.P. and Cubeddu, L. and Matthews, J.M.},\ntitle={Backbone and side-chain assignments of a tethered complex between LMO4 and DEAF-1},\njournal={Biomolecular NMR Assignments},\nyear={2014},\nvolume={8},\nnumber={1},\npages={141-144},\ndoi={10.1007/s12104-013-9470-x},\nnote={cited By 3},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84897113524&doi=10.1007%2fs12104-013-9470-x&partnerID=40&md5=c7124ed02817fd3e7ec09f2d053a081d},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; School of Science and Health, University of Western Sydney, Sydney, NSW 2751, Australia},\nabstract={The transcriptional regulator LMO4 and the transcription factor DEAF-1 are both essential for brain and skeletal development. They are also implicated in human breast cancers; overexpression of LMO4 is an indicator of poor prognosis, and overexpression of DEAF-1 promotes epithelial breast cell proliferation. We have generated a stable LMO4-DEAF-1 complex comprising the C-terminal LIM domain of LMO4 and an intrinsically disordered LMO4-interaction domain from DEAF-1 tethered by a glycine/serine linker. Here we report the 1H, 15N and 13C assignments of this construct. Analysis of the assignments indicates the presence of structure in the DEAF-1 part of the complex supporting the presence of a physical interaction between the two proteins. © 2013 Springer Science+Business Media Dordrecht.},\nauthor_keywords={Breast cancer;  DEAF-1;  Embryonic development;  LMO4;  Transcriptional complex},\nkeywords={Deaf1 protein, mouse;  LIM protein;  Lmo4 protein, mouse;  signal transducing adaptor protein;  transcription factor, amino acid sequence;  animal;  article;  chemistry;  human;  molecular genetics;  mouse;  nuclear magnetic resonance;  protein secondary structure, Adaptor Proteins, Signal Transducing;  Amino Acid Sequence;  Animals;  Humans;  LIM Domain Proteins;  Mice;  Molecular Sequence Data;  Nuclear Magnetic Resonance, Biomolecular;  Protein Structure, Secondary;  Transcription Factors},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; email: jacqui.matthews@sydney.edu.au},\npublisher={Kluwer Academic Publishers},\nissn={18742718},\npubmed_id={23417771},\nlanguage={English},\nabbrev_source_title={Biomol. NMR Assignments},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n 1H, 13C and 15N resonance assignments of an N-terminal domain of CHD4.\n \n \n \n \n\n\n \n Silva, A.; Kwan, A.; and Mackay, J.\n\n\n \n\n\n\n Biomolecular NMR Assignments, 8(1): 137-139. 2014.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"1H,$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Silva2014137,\nauthor={Silva, A.P.G. and Kwan, A.H. and Mackay, J.P.},\ntitle={1H, 13C and 15N resonance assignments of an N-terminal domain of CHD4},\njournal={Biomolecular NMR Assignments},\nyear={2014},\nvolume={8},\nnumber={1},\npages={137-139},\ndoi={10.1007/s12104-013-9469-3},\nnote={cited By 1},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84897113392&doi=10.1007%2fs12104-013-9469-3&partnerID=40&md5=a6b05cf067f1f03e2dab6a552a36c60f},\naffiliation={School of Molecular Bioscience, University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, NSW 2006, Australia},\nabstract={Chromatin-remodeling proteins have a pivotal role in normal cell function and development, catalyzing conformational changes in DNA that ultimately result in changes in gene expression patterns. Chromodomain helicase DNA-binding protein 4 (CHD4), the defining subunit of the nucleosome remodeling and deacetylase (NuRD) complex, is a nucleosome-remodeling protein of the SNF2/ISWI2 family, members of which contain two chromo domains and an ATP-dependent helicase module. CHD3, CHD4 and CHD5 also contain two contiguous PHD domains and have an extended N-terminal region that has not previously been characterized. We have identified a stable domain in the N-terminal region of CHD4 and report here the backbone and side chain resonance assignments for this domain at pH 7.5 and 25 °C (BMRB No. 18906). © 2013 Springer Science+Business Media Dordrecht.},\nauthor_keywords={CHD4;  Chromatin remodeling;  N-terminal domain;  NuRD complex;  PAR-binding motif},\nkeywords={autoantigen;  carbon;  CHD4 protein, human;  histone deacetylase;  hydrogen;  nitrogen, article;  chemistry;  human;  nuclear magnetic resonance;  protein secondary structure;  protein tertiary structure, Autoantigens;  Carbon Isotopes;  Humans;  Hydrogen;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Nitrogen Isotopes;  Nuclear Magnetic Resonance, Biomolecular;  Protein Structure, Secondary;  Protein Structure, Tertiary},\ncorrespondence_address1={Silva, A.P.G.; School of Molecular Bioscience, University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, NSW 2006, Australia; email: ana.silva@sydney.edu.au},\npublisher={Kluwer Academic Publishers},\nissn={18742718},\npubmed_id={23417793},\nlanguage={English},\nabbrev_source_title={Biomol. NMR Assignments},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2013\n \n \n (8)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n A structural analysis of DNA binding by myelin transcription factor 1 double zinc fingers.\n \n \n \n \n\n\n \n Gamsjaeger, R.; O'Connell, M.; Cubeddu, L.; Shepherd, N.; Lowry, J.; Kwan, A.; Vandevenne, M.; Swanton, M.; Matthews, J.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 288(49): 35180-35191. 2013.\n cited By 16\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Gamsjaeger201335180,\nauthor={Gamsjaeger, R. and O'Connell, M.R. and Cubeddu, L. and Shepherd, N.E. and Lowry, J.A. and Kwan, A.H. and Vandevenne, M. and Swanton, M.K. and Matthews, J.M. and Mackay, J.P.},\ntitle={A structural analysis of DNA binding by myelin transcription factor 1 double zinc fingers},\njournal={Journal of Biological Chemistry},\nyear={2013},\nvolume={288},\nnumber={49},\npages={35180-35191},\ndoi={10.1074/jbc.M113.482075},\nnote={cited By 16},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84890260897&doi=10.1074%2fjbc.M113.482075&partnerID=40&md5=3ef4d427c5566580347be43ba1bedc74},\naffiliation={School of Molecular Biosciences, University of Sydney, NSW 2006, Australia; School of Science and Health, University of Western Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia; Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010, Australia},\nabstract={Background: Myelin transcription factor 1 (MyT1) contains seven similar zinc finger domains that bind DNA specifically. Results: A three-dimensional structural model explains how a double zinc finger unit is able to recognize DNA. Conclusion: DNA-binding residues are conserved among all MyT1 zinc fingers, suggesting an identical DNA binding mode. Significance: Determination of the molecular details of DNA interaction will be crucial in understanding MyT1 function. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={DNA interaction;  DNA-binding;  DNA-binding modes;  Structural modeling;  Zinc finger;  Zinc finger domains, Binding energy;  DNA;  Transcription factors, Zinc, DNA;  myelin transcription factor 1;  unclassified drug;  zinc finger protein, article;  DNA binding;  DNA sequence;  human;  molecular cloning;  molecular docking;  mouse;  nonhuman;  nuclear magnetic resonance spectroscopy;  priority journal;  protein expression;  protein interaction;  protein motif;  protein purification;  protein structure;  surface plasmon resonance, Computer Modeling;  Myelin;  Nuclear Magnetic Resonance;  Protein Structure;  Zinc Finger, Amino Acid Sequence;  Animals;  Base Sequence;  Binding Sites;  DNA;  DNA-Binding Proteins;  Humans;  Mice;  Models, Molecular;  Molecular Sequence Data;  Mutagenesis, Site-Directed;  Neurogenesis;  Neurons;  Nuclear Magnetic Resonance, Biomolecular;  Promoter Regions, Genetic;  Protein Binding;  Protein Conformation;  Receptors, Retinoic Acid;  Sequence Homology, Amino Acid;  Sequence Homology, Nucleic Acid;  Surface Plasmon Resonance;  Transcription Factors;  Zinc Fingers},\ncorrespondence_address1={Mackay, J.P.; School of Molecular Biosciences, , NSW 2006, Australia; email: joel.mackay@sydney.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={24097990},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Is there a telltale RH fingerprint in zinc fingers that recognizes methylated CpG dinucleotides?.\n \n \n \n \n\n\n \n Mackay, J.; Segal, D.; and Crossley, M.\n\n\n \n\n\n\n Trends in Biochemical Sciences, 38(9): 421-422. 2013.\n cited By 2\n\n\n\n
\n\n\n\n \n \n $\"Is$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mackay2013421,\nauthor={Mackay, J.P. and Segal, D.J. and Crossley, M.},\ntitle={Is there a telltale RH fingerprint in zinc fingers that recognizes methylated CpG dinucleotides?},\njournal={Trends in Biochemical Sciences},\nyear={2013},\nvolume={38},\nnumber={9},\npages={421-422},\ndoi={10.1016/j.tibs.2013.06.005},\nnote={cited By 2},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84883176133&doi=10.1016%2fj.tibs.2013.06.005&partnerID=40&md5=5a8c6cbd0bada2d4b01af7dcdf12b9b9},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney NSW 2006, Australia; Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, United States; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia},\nkeywords={arginine;  CpG dinucleotide;  dinucleotide;  DNA binding protein;  guanine;  histidine;  kruppel like factor 4;  lysine;  RNA binding protein;  thymine;  unclassified drug;  zinc finger protein;  zinc finger protein 1;  zinc finger protein 2;  zinc finger protein 3;  zinc finger protein 4;  zinc finger protein 5, Caenorhabditis elegans;  Ciona intestinalis;  DNA binding;  DNA fingerprinting;  DNA methylation;  DNA modification;  Drosophila melanogaster;  epigenetics;  hydrogen bond;  letter;  molecular recognition;  nonhuman;  nucleotide binding site;  nucleotide motif;  organisms;  priority journal;  protein domain, CpG Islands;  DNA Methylation;  Humans;  Repressor Proteins},\ncorrespondence_address1={Mackay, J.P.; 1School of Molecular Bioscience, , Sydney NSW 2006, Australia; email: joel.mackay@sydney.edu.au},\nissn={09680004},\ncoden={TBSCD},\npubmed_id={23992945},\nlanguage={English},\nabbrev_source_title={Trends Biochem. Sci.},\ndocument_type={Letter},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n α-Hemoglobin-stabilizing Protein (AHSP) perturbs the proximal heme pocket of oxy-α-hemoglobin and weakens the iron-oxygen bond.\n \n \n \n \n\n\n \n Dickson, C.; Rich, A.; D'Avigdor, W.; Collins, D.; Lowry, J.; Mollan, T.; Khandros, E.; Olson, J.; Weiss, M.; MacKay, J.; Lay, P.; and Gell, D.\n\n\n \n\n\n\n Journal of Biological Chemistry, 288(27): 19986-20001. 2013.\n cited By 12\n\n\n\n
\n\n\n\n \n \n $\"α-Hemoglobin-stabilizing$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Dickson201319986,\nauthor={Dickson, C.F. and Rich, A.M. and D'Avigdor, W.M.H. and Collins, D.A.T. and Lowry, J.A. and Mollan, T.L. and Khandros, E. and Olson, J.S. and Weiss, M.J. and MacKay, J.P. and Lay, P.A. and Gell, D.A.},\ntitle={α-Hemoglobin-stabilizing Protein (AHSP) perturbs the proximal heme pocket of oxy-α-hemoglobin and weakens the iron-oxygen bond},\njournal={Journal of Biological Chemistry},\nyear={2013},\nvolume={288},\nnumber={27},\npages={19986-20001},\ndoi={10.1074/jbc.M112.437509},\nnote={cited By 12},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84880056136&doi=10.1074%2fjbc.M112.437509&partnerID=40&md5=90dca23f3867ad70e08950e3e73e1a11},\naffiliation={Menzies Research Institute Tasmania, University of Tasmania, 17 Liverpool St., Hobart, TAS 7000, Australia; School of Chemistry, University of Sydney, NSW 2006, Australia; School of Molecular Bioscience, University of Sydney, NSW 2006, Australia; Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251, United States; Cell and Molecular Biology Group, University of Pennsylvania, Philadelphia, PA 19104, United States},\nabstract={α-Hemoglobin (αHb)-stabilizing protein (AHSP) is a molecular chaperone that assists hemoglobin assembly. AHSP induces changes in αHb heme coordination, but how these changes are facilitated by interactions at the αHb·AHSP interface is not well understood. To address this question we have used NMR, x-ray absorption spectroscopy, and ligand binding measurements to probe αHb conformational changes induced by AHSP binding.NMRchemical shift analyses of free CO-αHb and CO- αHb·AHSP indicated that the seven helical elements of the native αHb structure are retained and that the heme Fe(II) remains coordinated to the proximal His-87 side chain. However, chemical shift differences revealed alterations of the F, G, and H helices and the heme pocket of CO-αHb bound to AHSP. Comparisons of iron-ligand geometry using extended x-ray absorption fine structure spectroscopy showed that AHSP binding induces a small 0.03 Å lengthening of the Fe-O2 bond, explaining previous reports that AHSP decreases αHb O2 affinity roughly 4-fold and promotes autooxidation due primarily to a 3-4-fold increase in the rate ofO2 dissociation. Pro-30 mutations diminished NMR chemical shift changes in the proximal heme pocket, restored normal O2 dissociation rate and equilibrium constants, and reduced O2-αHb autooxidation rates. Thus, the contacts mediated by Pro-30 in wild-type AHSP promote αHb autooxidation by introducing strain into the proximal heme pocket. As a chaperone, AHSP facilitates rapid assembly of αHb into Hb when βHb is abundant but diverts αHb to a redox resistant holding state when βHb is limiting. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Chemical shift;  Dissociation;  Equilibrium constants;  Extended X ray absorption fine structure spectroscopy;  Hemoglobin;  Iron metallography;  Ligands;  Oxygen;  Porphyrins;  Proteins;  Rate constants, Autooxidation;  Autooxidation rate;  Conformational change;  Dissociation rates;  Ligand binding;  Molecular chaperones;  NMR chemical shifts;  Oxygen bonds, Iron compounds, alpha hemoglobin stabilizing protein;  helicase;  heme;  hemoglobin;  histidine;  iron;  iron oxide;  oxy alpha hemoglobin;  oxygen;  proline;  unclassified drug, article;  autooxidation;  binding affinity;  chemical bond;  controlled study;  geometry;  human;  human cell;  image analysis;  molecular imaging;  nonhuman;  nuclear magnetic resonance;  oxidation reduction reaction;  oxygen dissociation curve;  priority journal;  protein binding;  protein conformation;  protein expression;  protein function;  protein protein interaction;  protein structure;  structure analysis;  X ray absorption spectroscopy},\ncorrespondence_address1={Gell, D.A.; Menzies Research Institute Tasmania, 17 Liverpool St., Hobart, TAS 7000, Australia; email: david.gell@utas.edu.au},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={23696640},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Analysis of disease-causing GATA1 mutations in murine gene complementation systems.\n \n \n \n \n\n\n \n Campbell, A.; Wilkinson-White, L.; MacKay, J.; Matthews, J.; and Blobel, G.\n\n\n \n\n\n\n Blood, 121(26): 5218-5227. 2013.\n cited By 38\n\n\n\n
\n\n\n\n \n \n $\"Analysis$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Campbell20135218,\nauthor={Campbell, A.E. and Wilkinson-White, L. and MacKay, J.P. and Matthews, J.M. and Blobel, G.A.},\ntitle={Analysis of disease-causing GATA1 mutations in murine gene complementation systems},\njournal={Blood},\nyear={2013},\nvolume={121},\nnumber={26},\npages={5218-5227},\ndoi={10.1182/blood-2013-03-488080},\nnote={cited By 38},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84884190615&doi=10.1182%2fblood-2013-03-488080&partnerID=40&md5=ef72ac5b5dda277d26501065152e806d},\naffiliation={Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia},\nabstract={Missense mutations in transcription factor GATA1 underlie a spectrum of congenital red blood cell and platelet disorders. We investigated how these alterations cause distinct clinical phenotypes by combining structural, biochemical, and genomic approaches with gene complementation systems that examine GATA1 function in biologically relevant cellular contexts. Substitutions that disrupt FOG1 cofactor binding impair both gene activation and repression and are associated with pronounced clinical phenotypes. Moreover, clinical severity correlates with the degree of FOG1 disruption. Surprisingly, 2 mutations shown to impair DNA binding of GATA1 in vitro did not measurably affect in vivo target gene occupancy. Rather, one of these disrupted binding to the TAL1 complex, implicating it in diseases caused by GATA1 mutations. Diminished TAL1 complex recruitment mainly impairs transcriptional activation and is linked to relatively mild disease. Notably, different substitutions at the same amino acid can selectively inhibit TAL1 complex or FOG1 binding, producing distinct cellular and clinical phenotypes. The structure-function relationships elucidated here were not predicted by prior in vitro or computational studies. Thus, our findings uncover novel disease mechanisms underlying GATA1 mutations and highlight the power of gene complementation assays for elucidating the molecular basis of genetic diseases. © 2013 by The American Society of Hematology.},\nkeywords={transcription factor GATA 1;  basic helix loop helix transcription factor;  biological marker;  messenger RNA;  nuclear protein;  oncoprotein;  TAL1 protein, human;  transcription factor;  transcription factor GATA 1;  ZFPM1 protein, human, animal cell;  Article;  cell proliferation;  controlled study;  DNA binding;  gene expression profiling;  gene mutation;  genetic complementation;  human;  human cell;  megakaryocyte erythroid progenitor;  missense mutation;  nonhuman;  priority journal;  reverse transcription polymerase chain reaction;  structure activity relation;  transcription initiation;  animal;  article;  cell differentiation;  chemistry;  chromatin immunoprecipitation;  cytology;  DNA microarray;  erythroid cell;  genetics;  hematologic disease;  megakaryocyte;  metabolism;  missense mutation;  mouse;  pathology;  real time polymerase chain reaction;  Western blotting, Animals;  Basic Helix-Loop-Helix Transcription Factors;  Biological Markers;  Blotting, Western;  Cell Differentiation;  Cell Proliferation;  Chromatin Immunoprecipitation;  Erythroid Cells;  GATA1 Transcription Factor;  Gene Expression Profiling;  Genetic Complementation Test;  Hematologic Diseases;  Humans;  Megakaryocytes;  Mice;  Mutation, Missense;  Nuclear Proteins;  Oligonucleotide Array Sequence Analysis;  Proto-Oncogene Proteins;  Real-Time Polymerase Chain Reaction;  Reverse Transcriptase Polymerase Chain Reaction;  RNA, Messenger;  Structure-Activity Relationship;  Transcription Factors},\npublisher={American Society of Hematology},\nissn={00064971},\ncoden={BLOOA},\npubmed_id={23704091},\nlanguage={English},\nabbrev_source_title={Blood},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217.\n \n \n \n \n\n\n \n Vandevenne, M.; Jacques, D.; Artuz, C.; Nguyen, C.; Kwan, A.; Segal, D.; Matthews, J.; Crossley, M.; Guss, J.; and MacKay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 288(15): 10616-10627. 2013.\n cited By 31\n\n\n\n
\n\n\n\n \n \n $\"New$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Vandevenne201310616,\nauthor={Vandevenne, M. and Jacques, D.A. and Artuz, C. and Nguyen, C.D. and Kwan, A.H.Y. and Segal, D.J. and Matthews, J.M. and Crossley, M. and Guss, J.M. and MacKay, J.P.},\ntitle={New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217},\njournal={Journal of Biological Chemistry},\nyear={2013},\nvolume={288},\nnumber={15},\npages={10616-10627},\ndoi={10.1074/jbc.M112.441451},\nnote={cited By 31},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84876238286&doi=10.1074%2fjbc.M112.441451&partnerID=40&md5=4108c25584901cb8584586bce427e3ad},\naffiliation={School of Molecular Bioscience, Darlington Campus, University of Sydney, Butlin Ave. and Maze Crescent, NSW 2006, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, United States},\nabstract={Background: Classical zinc finger proteins are extremely abundant and interact with DNA using a well defined recognition code. Results: We solved the structure of ZNF217 bound to its cognate DNA. Conclusion: ZNF217 presents a unique DNA interaction pattern including a new type of protein-DNA contact. Significance: This study deepens our understanding of DNA recognition by classical zinc fingers. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={DNA interaction;  DNA recognition;  Oncoproteins;  Zinc finger;  Zinc finger protein, DNA;  Proteins;  Zinc, Gene encoding, oncoprotein;  protein ZNF 217;  unclassified drug;  zinc finger protein, amino terminal sequence;  anisotropy;  article;  binding affinity;  binding site;  controlled study;  crystallization;  DNA determination;  enzyme specificity;  human;  human cell;  nonhuman;  priority journal;  promoter region;  protein binding;  protein DNA binding;  protein function;  protein protein interaction;  protein structure;  sequence alignment;  stoichiometry;  structure analysis;  transcription regulation;  X ray crystallography, Crystallography, X-Ray;  DNA;  Humans;  Models, Molecular;  Neoplasm Proteins;  Structure-Activity Relationship;  Trans-Activators;  Zinc Fingers},\ncorrespondence_address1={MacKay, J.P.; School of Molecular Bioscience, Butlin Ave. and Maze Crescent, NSW 2006, Australia; email: joel.mackay@sydney.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={23436653},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structural basis of the interaction of the breast cancer Oncogene LMO4 with the tumour suppressor CtIP/RBBP8.\n \n \n \n \n\n\n \n Stokes, P.; Liew, C.; Kwan, A.; Foo, P.; Barker, H.; Djamirze, A.; O'Reilly, V.; Visvader, J.; Mackay, J.; and Matthews, J.\n\n\n \n\n\n\n Journal of Molecular Biology, 425(7): 1101-1110. 2013.\n cited By 7\n\n\n\n
\n\n\n\n \n \n $\"Structural$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Stokes20131101,\nauthor={Stokes, P.H. and Liew, C.W. and Kwan, A.H. and Foo, P. and Barker, H.E. and Djamirze, A. and O'Reilly, V. and Visvader, J.E. and Mackay, J.P. and Matthews, J.M.},\ntitle={Structural basis of the interaction of the breast cancer Oncogene LMO4 with the tumour suppressor CtIP/RBBP8},\njournal={Journal of Molecular Biology},\nyear={2013},\nvolume={425},\nnumber={7},\npages={1101-1110},\ndoi={10.1016/j.jmb.2013.01.017},\nnote={cited By 7},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84875225595&doi=10.1016%2fj.jmb.2013.01.017&partnerID=40&md5=2824a4a8373cf4dfcfa87bb97b6eea1f},\naffiliation={School of Molecular Bioscience, University of Sydney, NSW 2006, Australia; Division of Stem Cells and Cancer, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 2050, Australia},\nabstract={LIM-only protein 4 (LMO4) is strongly linked to the progression of breast cancer. Although the mechanisms underlying this phenomenon are not well understood, a role is emerging for LMO4 in regulation of the cell cycle. We determined the solution structure of LMO4 in complex with CtIP (C-terminal binding protein interacting protein)/RBBP8, a tumour suppressor protein that is involved in cell cycle progression, DNA repair and transcriptional regulation. Our data reveal that CtIP and the essential LMO cofactor LDB1 (LIM-domain binding protein 1) bind to the same face on LMO4 and cannot simultaneously bind to LMO4. We hypothesise that overexpression of LMO4 may disrupt some of the normal tumour suppressor activities of CtIP, thereby contributing to breast cancer progression. © 2013 Elsevier Ltd.},\nauthor_keywords={breast cancer;  cell cycle control;  intrinsically disordered domains;  LIM domains;  protein-protein interactions},\nkeywords={c terminal binding protein interacting protein;  lim only protein 4;  oncoprotein;  rbbp8 protein;  tumor suppressor protein;  unclassified drug, article;  breast cancer;  cancer growth;  cell cycle progression;  controlled study;  DNA repair;  embryo;  gene interaction;  human;  human cell;  oncogene;  priority journal;  protein binding;  protein expression;  protein structure;  transcription regulation},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, , NSW 2006, Australia; email: jacqui.matthews@sydney.edu.au},\npublisher={Academic Press},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={23353824},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Effects of calcium binding and the hypertrophic cardiomyopathy A8V mutation on the dynamic equilibrium between closed and open conformations of the regulatory N-domain of isolated cardiac troponin C.\n \n \n \n \n\n\n \n Cordina, N.; Liew, C.; Gell, D.; Fajer, P.; MacKay, J.; and Brown, L.\n\n\n \n\n\n\n Biochemistry, 52(11): 1950-1962. 2013.\n cited By 26\n\n\n\n
\n\n\n\n \n \n $\"Effects$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Cordina20131950,\nauthor={Cordina, N.M. and Liew, C.K. and Gell, D.A. and Fajer, P.G. and MacKay, J.P. and Brown, L.J.},\ntitle={Effects of calcium binding and the hypertrophic cardiomyopathy A8V mutation on the dynamic equilibrium between closed and open conformations of the regulatory N-domain of isolated cardiac troponin C},\njournal={Biochemistry},\nyear={2013},\nvolume={52},\nnumber={11},\npages={1950-1962},\ndoi={10.1021/bi4000172},\nnote={cited By 26},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84875416080&doi=10.1021%2fbi4000172&partnerID=40&md5=de3572752d4811baf45ec06f769a0d3f},\naffiliation={Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, United States; Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute, 405 Liverpool St., Darlinghurst, NSW 2010, Australia; Menzies Research Institute, University of Tasmania, TAS 7000, Australia},\nabstract={Troponin C (TnC) is the calcium-binding subunit of the troponin complex responsible for initiating striated muscle contraction in response to calcium influx. In the skeletal TnC isoform, calcium binding induces a structural change in the regulatory N-domain of TnC that involves a transition from a closed to open structural state and accompanying exposure of a large hydrophobic patch for troponin I (TnI) to subsequently bind. However, little is understood about how calcium primes the N-domain of the cardiac isoform (cTnC) for interaction with the TnI subunit as the open conformation of the regulatory domain of cTnC has been observed only in the presence of bound TnI. Here we use paramagnetic relaxation enhancement (PRE) to characterize the closed to open transition of isolated cTnC in solution, a process that cannot be observed by traditional nuclear magnetic resonance methods. Our PRE data from four spin-labeled monocysteine constructs of isolated cTnC reveal that calcium binding triggers movement of the N-domain helices toward an open state. Fitting of the PRE data to a closed to open transition model reveals the presence of a small population of cTnC molecules in the absence of calcium that possess an open conformation, the level of which increases substantially upon Ca2+ binding. These data support a model in which calcium binding creates a dynamic equilibrium between the closed and open structural states to prime cTnC for interaction with its target peptide. We also used PRE data to assess the structural effects of a familial hypertrophic cardiomyopathy point mutation located within the N-domain of cTnC (A8V). The PRE data show that the Ca2+ switch mechanism is perturbed by the A8V mutation, resulting in a more open N-domain conformation in both the apo and holo states. © 2013 American Chemical Society.},\nkeywords={Cardiac troponin C;  Dynamic equilibria;  Familial hypertrophic cardiomyopathies;  Hydrophobic patch;  Hypertrophic cardiomyopathy;  Open conformation;  Paramagnetic relaxation enhancements;  Structural effect, Calcium;  Muscle;  Paramagnetism;  Population statistics, Conformations, calcium;  cysteine;  magnesium ion;  troponin C, analysis;  article;  binding affinity;  calcium binding;  calcium cell level;  calcium transport;  heart muscle cell;  hypertrophic cardiomyopathy;  mutation;  nonhuman;  paramagnetic relaxation enhancement;  priority journal;  protein conformation;  protein domain;  protein structure;  rat, Animals;  Calcium;  Cardiomyopathy, Hypertrophic;  Chickens;  Humans;  Models, Molecular;  Point Mutation;  Protein Structure, Tertiary;  Rats;  Troponin C},\ncorrespondence_address1={Brown, L.J.; Department of Chemistry and Biomolecular Sciences, , Sydney, NSW 2109, Australia; email: louise.brown@mq.edu.au},\nissn={00062960},\ncoden={BICHA},\npubmed_id={23425245},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Semiquantitative and quantitative analysis of protein-DNA interactions using steady-state measurements in surface plasmon resonance competition experiments.\n \n \n \n \n\n\n \n Gamsjaeger, R.; Kariawasam, R.; Bang, L.; Touma, C.; Nguyen, C.; Matthews, J.; Cubeddu, L.; and Mackay, J.\n\n\n \n\n\n\n Analytical Biochemistry, 440(2): 178-185. 2013.\n cited By 17\n\n\n\n
\n\n\n\n \n \n $\"Semiquantitative$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Gamsjaeger2013178,\nauthor={Gamsjaeger, R. and Kariawasam, R. and Bang, L.H. and Touma, C. and Nguyen, C.D. and Matthews, J.M. and Cubeddu, L. and Mackay, J.P.},\ntitle={Semiquantitative and quantitative analysis of protein-DNA interactions using steady-state measurements in surface plasmon resonance competition experiments},\njournal={Analytical Biochemistry},\nyear={2013},\nvolume={440},\nnumber={2},\npages={178-185},\ndoi={10.1016/j.ab.2013.04.030},\nnote={cited By 17},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84884951197&doi=10.1016%2fj.ab.2013.04.030&partnerID=40&md5=9cd1a8aaa2e7eabb53952dc7b4044dca},\naffiliation={School of Science and Health, University of Western Sydney, Penrith, NSW 2751, Australia; School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={One method commonly used to characterize protein-DNA interactions is surface plasmon resonance (SPR). In a typical SPR experiment, chip-bound DNA is exposed to increasing concentrations of protein; the resulting binding data are used to calculate a dissociation constant for the interaction. However, in cases in which knowledge of the specificity of the interaction is required, a large set of DNA variants has to be tested; this is time consuming and costly, in part because of the requirement for multiple SPR chips. We have developed a new protocol that uses steady-state binding levels in SPR competition experiments to determine protein-binding dissociation constants for a set of DNA variants. This approach is rapid and straightforward and requires the use of only a single SPR chip. Additionally, in contrast to other methods, our approach does not require prior knowledge of parameters such as on or off rates, using an estimate of the wild-type interaction as the sole input. Utilizing relative steady-state responses, our protocol also allows for the rapid, reliable, and simultaneous determination of protein-binding dissociation constants of a large series of DNA mutants in a single experiment in a semiquantitative fashion. We compare our approach to existing methods, highlighting specific advantages as well as limitations. © 2013 Elsevier Inc. All rights reserved.},\nauthor_keywords={Competition experiments;  Kinetics;  Protein-DNA interaction;  SPR},\nkeywords={Biochemistry;  Dissociation;  DNA;  Enzyme kinetics;  Plasmons;  Proteins, Dissociation constant;  New protocol;  Prior knowledge;  Protein binding;  Protein-DNA interactions;  Simultaneous determinations;  Steady-state measurements;  Steady-state response, Surface plasmon resonance, DNA;  DNA binding protein;  protein, analytic method;  article;  binding competition;  Caenorhabditis elegans;  controlled study;  dissociation constant;  nonhuman;  parameters;  priority journal;  protein analysis;  protein DNA binding;  protein DNA interaction;  quantitative analysis;  steady state;  surface plasmon resonance;  wild type, Competition experiments;  Kinetics;  Protein-DNA interaction;  SPR, Binding, Competitive;  DNA;  DNA, Single-Stranded;  DNA-Binding Proteins;  Protein Binding;  Proteins;  Surface Plasmon Resonance;  Time Factors},\ncorrespondence_address1={Gamsjaeger, R.; School of Science and Health, , Penrith, NSW 2751, Australia; email: r.gamsjaeger@uws.edu.au},\npublisher={Academic Press Inc.},\nissn={00032697},\ncoden={ANBCA},\npubmed_id={23727560},\nlanguage={English},\nabbrev_source_title={Anal. Biochem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2012\n \n \n (12)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Solution structure of a tethered Lmo2LIM2/Ldb1LID complex.\n \n \n \n \n\n\n \n Dastmalchi, S.; Wilkinson-White, L.; Kwan, A.; Gamsjaeger, R.; Mackay, J.; and Matthews, J.\n\n\n \n\n\n\n Protein Science, 21(11): 1768-1774. 2012.\n cited By 7\n\n\n\n
\n\n\n\n \n \n $\"Solution$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Dastmalchi20121768,\nauthor={Dastmalchi, S. and Wilkinson-White, L. and Kwan, A.H. and Gamsjaeger, R. and Mackay, J.P. and Matthews, J.M.},\ntitle={Solution structure of a tethered Lmo2LIM2/Ldb1LID complex},\njournal={Protein Science},\nyear={2012},\nvolume={21},\nnumber={11},\npages={1768-1774},\ndoi={10.1002/pro.2153},\nnote={cited By 7},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84867672609&doi=10.1002%2fpro.2153&partnerID=40&md5=3c73becb6de8338190e9c56bdd333c84},\naffiliation={Schoolof Molecular Bioscience, Building G08, University of Sydney, Sydney, NSW 2006, Australia; Biotechnology Research Centre, School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; School of Science and Health, Universityof Western Sydney, Penrith, NSW 2751, Australia},\nabstract={LIM-only protein 2, Lmo2, is a regulatory protein that is essential for hematopoietic development and inappropriate overexpression of Lmo2 in T-cells contributes to T-cell leukemia. It exerts its functions by mediating protein-protein interactions and nucleating multicomponent transcriptional complexes. Lmo2 interacts with LIM domain binding protein 1 (Ldb1) through the tandem LIM domains of Lmo2 and the LIM interaction domain (LID) of Ldb1. Here, we present the solution structure of the LIM2 domain of Lmo2 bound to Ldb1 LID. The ordered regions of Ldb1 in this complex correspond well with binding hotspots previously defined by mutagenic studies. Comparisons of this Lmo2LIM2-Ldb1LID structure with previously determined structures of the Lmo2/Ldb1LID complexes lead to the conclusion that modular binding of tandem LIM domains in Lmo2 to tandem linear motifs in Ldb1 is accompanied by several disorder-to-order transitions and/or conformational changes in both proteins. © 2012 The Protein Society.},\nauthor_keywords={Ldb1;  Lmo2;  Modular binding;  NMR structure},\nkeywords={binding protein;  LIM domain binding protein 1;  LIM only protein 2;  regulator protein;  unclassified drug, article;  controlled study;  mutagenesis;  nonhuman;  priority journal;  protein binding;  protein conformation;  protein protein interaction;  protein structure, Adaptor Proteins, Signal Transducing;  Animals;  DNA-Binding Proteins;  LIM Domain Proteins;  Mice;  Models, Molecular;  Nuclear Magnetic Resonance, Biomolecular;  Protein Conformation;  Protein Structure, Tertiary;  Recombinant Proteins},\ncorrespondence_address1={Matthews, J.M.; Schoolof Molecular Bioscience, , Sydney, NSW 2006, Australia; email: jacqui.matthews@sydney.edu.au},\nissn={09618368},\ncoden={PRCIE},\npubmed_id={22936624},\nlanguage={English},\nabbrev_source_title={Protein Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n A rapid method for assessing the RNA-binding potential of a protein.\n \n \n \n \n\n\n \n Bendak, K.; Loughlin, F.; Cheung, V.; O'Connell, M.; Crossley, M.; and MacKay, J.\n\n\n \n\n\n\n Nucleic Acids Research, 40(14): e105. 2012.\n cited By 27\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Bendak2012,\nauthor={Bendak, K. and Loughlin, F.E. and Cheung, V. and O'Connell, M.R. and Crossley, M. and MacKay, J.P.},\ntitle={A rapid method for assessing the RNA-binding potential of a protein},\njournal={Nucleic Acids Research},\nyear={2012},\nvolume={40},\nnumber={14},\npages={e105},\ndoi={10.1093/nar/gks285},\nnote={cited By 27},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84861390479&doi=10.1093%2fnar%2fgks285&partnerID=40&md5=0faa624583820cfa94d0abd92ed8bbef},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Institute for Molecular Biology and Biophysics, ETH, 8093 Zürich, Switzerland; Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia},\nabstract={In recent years, evidence has emerged for the existence of many diverse types of RNA, which play roles in a wide range of biological processes in all kingdoms of life. These molecules generally do not, however, act in isolation, and identifying which proteins partner with RNA is a major challenge. Many methods, in vivo and in vitro, have been used to address this question, including combinatorial or high-throughput approaches, such as systematic evolution of ligands, cross-linking and immunoprecipitation and RNA immunoprecipitation combined with deep sequencing. However, most of these methods are not trivial to pursue and often require substantial optimization before results can be achieved. Here, we demonstrate a simple technique that allows one to screen proteins for RNA-binding properties in a gel-shift experiment and can be easily implemented in any laboratory. This assay should be a useful first-pass tool for assessing whether a protein has RNA- or DNA-binding properties, prior to committing resources to more complex procedures. © The Author(s) 2012.},\nkeywords={double stranded DNA;  heparin;  heterogeneous nuclear ribonucleoprotein f;  protein Fox 1;  protein ZNF180;  protein ZRANB2;  RNA binding protein;  single stranded RNA;  unclassified drug, amino terminal sequence;  article;  combinatorial chemistry;  cross linking;  gel mobility shift assay;  immunoprecipitation;  in vitro study;  molecular recognition;  priority journal;  protein determination;  protein DNA binding;  protein function;  protein RNA binding;  protein targeting;  RNA probe;  RNA sequence, Electrophoretic Mobility Shift Assay;  Heparin;  RNA Probes;  RNA-Binding Proteins},\ncorrespondence_address1={MacKay, J.P.; School of Molecular Bioscience, , Sydney, NSW 2006, Australia; email: joel.mackay@sydney.edu.au},\nissn={03051048},\ncoden={NARHA},\npubmed_id={22492509},\nlanguage={English},\nabbrev_source_title={Nucleic Acids Res.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Solution structure of the LIM-homeodomain transcription factor complex Lhx3/Ldb1 and the effects of a pituitary mutation on key Lhx3 interactions.\n \n \n \n \n\n\n \n Bhati, M.; Lee, C.; Gadd, M.; Jeffries, C.; Kwan, A.; Whitten, A.; Trewhella, J.; Mackay, J.; and Matthews, J.\n\n\n \n\n\n\n PLoS ONE, 7(7). 2012.\n cited By 8\n\n\n\n
\n\n\n\n \n \n $\"Solution$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Bhati2012,\nauthor={Bhati, M. and Lee, C. and Gadd, M.S. and Jeffries, C.M. and Kwan, A. and Whitten, A.E. and Trewhella, J. and Mackay, J.P. and Matthews, J.M.},\ntitle={Solution structure of the LIM-homeodomain transcription factor complex Lhx3/Ldb1 and the effects of a pituitary mutation on key Lhx3 interactions},\njournal={PLoS ONE},\nyear={2012},\nvolume={7},\nnumber={7},\ndoi={10.1371/journal.pone.0040719},\nart_number={e40719},\nnote={cited By 8},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84864346714&doi=10.1371%2fjournal.pone.0040719&partnerID=40&md5=481b43f43ec8ed577eda778b1e75ccb9},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Bragg Institute, Australian Nuclear Science and Technology Organisation, Kirrawee DC, NSW, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia},\nabstract={Lhx3 is a LIM-homeodomain (LIM-HD) transcription factor that regulates neural cell subtype specification and pituitary development in vertebrates, and mutations in this protein cause combined pituitary hormone deficiency syndrome (CPHDS). The recently published structures of Lhx3 in complex with each of two key protein partners, Isl1 and Ldb1, provide an opportunity to understand the effect of mutations and posttranslational modifications on key protein-protein interactions. Here, we use small-angle X-ray scattering of an Ldb1-Lhx3 complex to confirm that in solution the protein is well represented by our previously determined NMR structure as an ensemble of conformers each comprising two well-defined halves (each made up of LIM domain from Lhx3 and the corresponding binding motif in Ldb1) with some flexibility between the two halves. NMR analysis of an Lhx3 mutant that causes CPHDS, Lhx3(Y114C), shows that the mutation does not alter the zinc-ligation properties of Lhx3, but appears to cause a structural rearrangement of the hydrophobic core of the LIM2 domain of Lhx3 that destabilises the domain and/or reduces the affinity of Lhx3 for both Ldb1 and Isl1. Thus the mutation would affect the formation of Lhx3-containing transcription factor complexes, particularly in the pituitary gland where these complexes are required for the production of multiple pituitary cell types and hormones. © 2012 Bhati et al.},\nkeywords={binding protein;  islet 1 protein;  LIM domain binding protein 1;  mutant protein;  protein LIM2;  structural protein;  transcription factor LHX3;  unclassified drug;  zinc, amino acid sequence;  article;  binding affinity;  binding site;  carboxy terminal sequence;  complex formation;  controlled study;  hormone synthesis;  hydrophobicity;  hypophysis;  hypophysis cell;  mutational analysis;  nuclear magnetic resonance;  protein domain;  protein expression;  protein localization;  protein phosphorylation;  protein protein interaction;  protein stability;  structure analysis;  X ray crystallography, Amino Acid Motifs;  Animals;  DNA-Binding Proteins;  Humans;  LIM Domain Proteins;  LIM-Homeodomain Proteins;  Mice;  Mutation;  Nuclear Magnetic Resonance, Biomolecular;  Protein Binding;  Protein Structure, Quaternary;  Protein Structure, Tertiary;  Transcription Factors, Vertebrata},\ncorrespondence_address1={Matthews, J. M.; School of Molecular Bioscience, , Sydney, NSW, Australia; email: Jacqui.Matthews@sydney.edu.au},\nissn={19326203},\npubmed_id={22848397},\nlanguage={English},\nabbrev_source_title={PLoS ONE},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Determination of ribonuclease sequence-specificity using Pentaprobes and mass spectrometry.\n \n \n \n \n\n\n \n Mckenzie, J.; Duyvestyn, J.; Smith, T.; Bendak, K.; Mackay, J.; Cursons, R.; Cook, G.; and Arcus, V.\n\n\n \n\n\n\n RNA, 18(6): 1267-1278. 2012.\n cited By 35\n\n\n\n
\n\n\n\n \n \n $\"Determination$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mckenzie20121267,\nauthor={Mckenzie, J.L. and Duyvestyn, J.M. and Smith, T. and Bendak, K. and Mackay, J. and Cursons, R.A.Y. and Cook, G.M. and Arcus, V.L.},\ntitle={Determination of ribonuclease sequence-specificity using Pentaprobes and mass spectrometry},\njournal={RNA},\nyear={2012},\nvolume={18},\nnumber={6},\npages={1267-1278},\ndoi={10.1261/rna.031229.111},\nnote={cited By 35},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84861397933&doi=10.1261%2frna.031229.111&partnerID=40&md5=f88483f85f454af1e24d41c8c1479b0a},\naffiliation={Department of Biological Sciences, University of Waikato, Hamilton 3240, New Zealand; Department of Computer Science, University of Waikato, Hamilton 3240, New Zealand; School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia; Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand},\nabstract={The VapBC toxin-antitoxin (TA) family is the largest of nine identified TA families. The toxin, VapC, is a metal-dependent ribonuclease that is inhibited by its cognate antitoxin, VapB. Although the VapBCs are the largest TA family, little is known about their biological roles. Here we describe a new general method for the overexpression and purification of toxic VapC proteins and subsequent determination of their RNase sequence-specificity. Functional VapC was isolated by expression of the nontoxic VapBC complex, followed by removal of the labile antitoxin (VapB) using limited trypsin digestion. We have then developed a sensitive and robust method for determining VapC ribonuclease sequence-specificity. This technique employs the use of Pentaprobes as substrates for VapC. These are RNA sequences encoding every combination of five bases. We combine the RNase reaction with MALDI-TOF MS to detect and analyze the cleavage products and thus determine the RNA cut sites. Successful MALDI-TOF MS analysis of RNA fragments is acutely dependent on sample preparation methods. The sequencespecificity of four VapC proteins from two different organisms (VapCPAE0151 and VapCPAE2754 from Pyrobaculum aerophilum, and VapCRv0065 and VapCRv0617 from Mycobacterium tuberculosis) was successfully determined using the described strategy. This rapid and sensitive method can be applied to determine the sequence-specificity of VapC ribonucleases along with other RNA interferases (such as MazF) from a range of organisms. Published by Cold Spring Harbor Laboratory Press. Copyright © 2012 RNA Society.},\nauthor_keywords={Mycobacteria;  PIN-domain;  RNA interferase;  RNase;  Toxin-antitoxin;  VapC},\nkeywords={ribonuclease;  trypsin;  unclassified drug;  VapC protein, analytic method;  article;  controlled study;  matrix assisted laser desorption ionization time of flight mass spectrometry;  Mycobacterium tuberculosis;  nonhuman;  Pentaprobe;  priority journal;  protein expression;  protein isolation;  protein purification;  Pyrobaculum aerophilum;  RNA sequence, Bacterial Proteins;  Mycobacterium tuberculosis;  Pyrobaculum;  Ribonucleases;  RNA Probes;  Sequence Analysis, RNA;  Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization;  Substrate Specificity, Corynebacterineae;  Mycobacterium tuberculosis;  Pyrobaculum aerophilum},\ncorrespondence_address1={Arcus, V.L.; Department of Biological Sciences, , Hamilton 3240, New Zealand; email: varcus@waikato.ac.nz},\nissn={13558382},\ncoden={RNARF},\npubmed_id={22539524},\nlanguage={English},\nabbrev_source_title={RNA},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Two-timing zinc finger transcription factors liaising with RNA.\n \n \n \n \n\n\n \n Burdach, J.; O'Connell, M.; Mackay, J.; and Crossley, M.\n\n\n \n\n\n\n Trends in Biochemical Sciences, 37(5): 199-205. 2012.\n cited By 33\n\n\n\n
\n\n\n\n \n \n $\"Two-timing$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Burdach2012199,\nauthor={Burdach, J. and O'Connell, M.R. and Mackay, J.P. and Crossley, M.},\ntitle={Two-timing zinc finger transcription factors liaising with RNA},\njournal={Trends in Biochemical Sciences},\nyear={2012},\nvolume={37},\nnumber={5},\npages={199-205},\ndoi={10.1016/j.tibs.2012.02.001},\nnote={cited By 33},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84860533858&doi=10.1016%2fj.tibs.2012.02.001&partnerID=40&md5=246210f2a7e1886e7502d73bc4031a1f},\naffiliation={School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia; School of Molecular Biosciences, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Classical zinc fingers (ZFs) are one of the most common protein domains in higher eukaryotes and have been known for almost 30 years to act as sequence-specific DNA-binding domains. This knowledge has come, however, from the study of a small number of archetypal proteins, and a larger picture is beginning to emerge that ZF functions are far more diverse than originally suspected. Here, we review the evidence that a subset of ZF proteins live double lives, binding to both DNA and RNA targets and frequenting both the cytoplasm and the nucleus. This duality can create an important additional level of gene regulation that serves to connect transcriptional and post-transcriptional control. © 2012 Elsevier Ltd.},\nkeywords={DNA directed RNA polymerase III;  isoprotein;  protein TRA 1;  RNA 5S;  RNA polymerase II;  transcription factor;  transcription factor YY1;  unclassified drug;  WT1 protein;  zinc finger protein, binding affinity;  cell membrane transport;  cell nucleus;  cellular distribution;  cytoplasm;  human;  molecular mechanics;  nonhuman;  priority journal;  protein DNA binding;  protein function;  protein localization;  protein RNA binding;  protein targeting;  review;  RNA analysis;  RNA structure;  transcription regulation, DNA;  DNA-Binding Proteins;  Gene Expression Regulation;  Humans;  Models, Molecular;  Protein Binding;  RNA;  RNA-Binding Proteins;  Transcription Factors;  Zinc Fingers, Eukaryota},\ncorrespondence_address1={Crossley, M.; School of Biotechnology and Biomolecular Sciences, , NSW 2052, Australia; email: m.crossley@unsw.edu.au},\nissn={09680004},\ncoden={TBSCD},\npubmed_id={22405571},\nlanguage={English},\nabbrev_source_title={Trends Biochem. Sci.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Synthesis of the bacteriocin glycopeptide sublancin 168 and S-glycosylated variants.\n \n \n \n \n\n\n \n Hsieh, Y.; Wilkinson, B.; O'Connell, M.; MacKay, J.; Matthews, J.; and Payne, R.\n\n\n \n\n\n\n Organic Letters, 14(7): 1910-1913. 2012.\n cited By 40\n\n\n\n
\n\n\n\n \n \n $\"Synthesis$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Hsieh20121910,\nauthor={Hsieh, Y.S.Y. and Wilkinson, B.L. and O'Connell, M.R. and MacKay, J.P. and Matthews, J.M. and Payne, R.J.},\ntitle={Synthesis of the bacteriocin glycopeptide sublancin 168 and S-glycosylated variants},\njournal={Organic Letters},\nyear={2012},\nvolume={14},\nnumber={7},\npages={1910-1913},\ndoi={10.1021/ol300557g},\nnote={cited By 40},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84859620443&doi=10.1021%2fol300557g&partnerID=40&md5=da6b6dda445db8719b1df1ef780b7243},\naffiliation={School of Chemistry, School of Molecular Bioscience, University of Sydney, NSW 2006, Australia},\nabstract={The synthesis of sublancin 168, a unique S-glucosylated bacteriocin antibiotic, is described. The natural product and two S-glycosylated variants were successfully prepared via native chemical ligation followed by folding. The synthetic glycopeptides were shown to possess primarily an α-helical secondary structure by CD and NMR studies. © 2012 American Chemical Society.},\nkeywords={bacteriocin;  glycopeptide;  sublancin 168, amino acid sequence;  article;  chemical structure;  chemistry;  circular dichroism;  nuclear magnetic resonance;  synthesis, Amino Acid Sequence;  Bacteriocins;  Circular Dichroism;  Glycopeptides;  Molecular Structure;  Nuclear Magnetic Resonance, Biomolecular},\ncorrespondence_address1={Payne, R.J.; School of Chemistry, , NSW 2006, Australia; email: richard.payne@sydney.edu.au},\nissn={15237060},\ncoden={ORLEF},\npubmed_id={22455748},\nlanguage={English},\nabbrev_source_title={Org. Lett.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Self-assembly of functional, amphipathic amyloid monolayers by the fungal hydrophobin EAS.\n \n \n \n \n\n\n \n Macindoe, I.; Kwan, A.; Ren, Q.; Morris, V.; Yang, W.; Mackay, J.; and Sunde, M.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 109(14): E804-E811. 2012.\n cited By 104\n\n\n\n
\n\n\n\n \n \n $\"Self-assembly$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Macindoe2012,\nauthor={Macindoe, I. and Kwan, A.H. and Ren, Q. and Morris, V.K. and Yang, W. and Mackay, J.P. and Sunde, M.},\ntitle={Self-assembly of functional, amphipathic amyloid monolayers by the fungal hydrophobin EAS},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2012},\nvolume={109},\nnumber={14},\npages={E804-E811},\ndoi={10.1073/pnas.1114052109},\nnote={cited By 104},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84859466168&doi=10.1073%2fpnas.1114052109&partnerID=40&md5=d436952fc403739ba247d191798d815c},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Discipline of Pharmacology, University of Sydney, Sydney, NSW 2006, Australia; School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3217, Australia},\nabstract={The hydrophobin EAS from the fungus Neurospora crassa forms functional amyloid fibrils called rodlets that facilitate spore formation and dispersal. Self-assembly of EAS into fibrillar rodlets occurs spontaneously at hydrophobic:hydrophilic interfaces and the rodlets further associate laterally to form amphipathic monolayers. We have used site-directed mutagenesis and peptide experiments to identify the region of EAS that drives intermolecular association and formation of the cross-β rodlet structure. Transplanting this region into a nonamyloidogenic hydrophobin enables it to form rodlets. We have also determined the structure and dynamics of an EAS variant with reduced rodlet-forming ability. Taken together, these data allow us to pinpoint the conformational changes that take place when hydrophobins self-assemble at an interface and to propose a model for the amphipathic EAS rodlet structure.},\nkeywords={amyloid;  fungal protein;  hydrophobin;  peptide;  protein variant, article;  beta sheet;  conformational transition;  hydrophilicity;  hydrophobicity;  molecular dynamics;  molecular model;  Neurospora crassa;  nonhuman;  priority journal;  protein assembly;  protein structure;  site directed mutagenesis;  sporogenesis, Amino Acid Sequence;  Amyloid;  Fungi;  Magnetic Resonance Spectroscopy;  Mass Spectrometry;  Microscopy, Electron, Transmission;  Molecular Sequence Data;  Mutagenesis, Site-Directed;  Sequence Homology, Amino Acid, Fungi;  Neurospora crassa},\ncorrespondence_address1={Sunde, M.; School of Molecular Bioscience, , Sydney, NSW 2006, Australia; email: margaret.sunde@sydney.edu.au},\nissn={00278424},\ncoden={PNASA},\npubmed_id={22308366},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Backbone and sidechain 1H, 13C and 15N chemical shift assignments of the hydrophobin DewA from Aspergillus nidulans.\n \n \n \n \n\n\n \n Morris, V.; Kwan, A.; MacKay, J.; and Sunde, M.\n\n\n \n\n\n\n Biomolecular NMR Assignments, 6(1): 83-86. 2012.\n cited By 5\n\n\n\n
\n\n\n\n \n \n $\"Backbone$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Morris201283,\nauthor={Morris, V.K. and Kwan, A.H. and MacKay, J.P. and Sunde, M.},\ntitle={Backbone and sidechain 1H, 13C and 15N chemical shift assignments of the hydrophobin DewA from Aspergillus nidulans},\njournal={Biomolecular NMR Assignments},\nyear={2012},\nvolume={6},\nnumber={1},\npages={83-86},\ndoi={10.1007/s12104-011-9330-5},\nnote={cited By 5},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84858295602&doi=10.1007%2fs12104-011-9330-5&partnerID=40&md5=8e0ca92884867890557fb77819e919d2},\naffiliation={School of Molecular Bioscience, Building G08, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Hydrophobins are proteins secreted by filamentous fungi that are able to self-assemble into monolayers at hydrophobic:hydrophilic interfaces. The layers are amphipathic and can reverse the wettability of surfaces. Hydrophobins have several roles in fungal development, including the formation of coatings on fungal structures to render them hydrophobic. Here we report the backbone and sidechain assignments for the class I hydrophobin DewA from the fungus Aspergillus nidulans. © 2011 Springer Science+Business Media B.V.},\nauthor_keywords={DewA;  Functional amyloid;  Hydrophobin;  NMR assignment},\nkeywords={DEWA protein, Asperigillus nidulans;  fungal protein, amino acid sequence;  article;  Aspergillus nidulans;  chemistry;  molecular genetics;  nuclear magnetic resonance;  protein secondary structure, Amino Acid Sequence;  Aspergillus nidulans;  Fungal Proteins;  Molecular Sequence Data;  Nuclear Magnetic Resonance, Biomolecular;  Protein Structure, Secondary, Emericella nidulans;  Fungi},\ncorrespondence_address1={Sunde, M.; School of Molecular Bioscience, , Sydney, NSW 2006, Australia; email: margaret.sunde@sydney.edu.au},\nissn={18742718},\npubmed_id={21845363},\nlanguage={English},\nabbrev_source_title={Biomol. NMR Assignments},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n 1H, 15N and 13C assignments of an intramolecular LMO4-LIM1/CtIP complex.\n \n \n \n \n\n\n \n Liew, C.; Kwan, A.; Stokes, P.; MacKay, J.; and Matthews, J.\n\n\n \n\n\n\n Biomolecular NMR Assignments, 6(1): 31-34. 2012.\n cited By 3\n\n\n\n
\n\n\n\n \n \n $\"1H,$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Liew201231,\nauthor={Liew, C.W. and Kwan, A.H. and Stokes, P.H. and MacKay, J.P. and Matthews, J.M.},\ntitle={1H, 15N and 13C assignments of an intramolecular LMO4-LIM1/CtIP complex},\njournal={Biomolecular NMR Assignments},\nyear={2012},\nvolume={6},\nnumber={1},\npages={31-34},\ndoi={10.1007/s12104-011-9319-0},\nnote={cited By 3},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84858181828&doi=10.1007%2fs12104-011-9319-0&partnerID=40&md5=ee5f78e9904057a707f67088f5987376},\naffiliation={School of Molecular Bioscience, University of Sydney, Building G08, Sydney, NSW 2006, Australia},\nabstract={LMO4 is a broadly expressed LIM-only protein that is involved in neural tube development and implicated in breast cancer. Here we report backbone and side chain NMR assignments for an engineered intramolecular complex of the N-terminal LIM domain from LMO4 tethered to residues 641-685 of C-terminal binding protein interacting protein (CtIP/RBBP8). © 2011 Springer Science+Business Media B.V.},\nauthor_keywords={Breast cancer;  CtIP;  LMO4;  Neural development;  NMR assignments},\nkeywords={carrier protein;  LIM homeodomain protein, amino acid sequence;  article;  chemistry;  metabolism;  molecular genetics;  nuclear magnetic resonance, Amino Acid Sequence;  Carrier Proteins;  LIM-Homeodomain Proteins;  Molecular Sequence Data;  Nuclear Magnetic Resonance, Biomolecular},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, , Sydney, NSW 2006, Australia; email: jacqui.matthews@sydney.edu.au},\nissn={18742718},\npubmed_id={21643835},\nlanguage={English},\nabbrev_source_title={Biomol. NMR Assignments},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Bivalent recognition of nucleosomes by the tandem PHD fingers of the CHD4 ATPase is required for CHD4-mediated repression.\n \n \n \n \n\n\n \n Musselman, C.; Ramiŕez, J.; Sims, J.; Mansfield, R.; Oliver, S.; Denu, J.; Mackay, J.; Wade, P.; Hagman, J.; and Kutateladze, T.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 109(3): 787-792. 2012.\n cited By 83\n\n\n\n
\n\n\n\n \n \n $\"Bivalent$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Musselman2012787,\nauthor={Musselman, C.A. and Ramiŕez, J. and Sims, J.K. and Mansfield, R.E. and Oliver, S.S. and Denu, J.M. and Mackay, J.P. and Wade, P.A. and Hagman, J. and Kutateladze, T.G.},\ntitle={Bivalent recognition of nucleosomes by the tandem PHD fingers of the CHD4 ATPase is required for CHD4-mediated repression},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2012},\nvolume={109},\nnumber={3},\npages={787-792},\ndoi={10.1073/pnas.1113655109},\nnote={cited By 83},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856383786&doi=10.1073%2fpnas.1113655109&partnerID=40&md5=4d2a65c28bfef9051873d7efabd60bbd},\naffiliation={Department of Pharmacology, University of Colorado Denver, School of Medicine, Aurora, CO 80045, United States; Integrated Department of Immunology, National Jewish Health, Denver, CO 80206, United States; Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, United States; School of Molecular Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, United States},\nabstract={CHD4 is a catalytic subunit of the NuRD (nucleosome remodeling and deacetylase) complex essential in transcriptional regulation, chromatin assembly and DNA damage repair. CHD4 contains tandem plant homeodomain (PHD) fingers connected by a short linker, the biological function of which remains unclear. Here we explore the combinatorial action of the CHD4 PHD1/2 fingers and detail the molecular basis for their association with chromatin. We found that PHD1/2 targets nucleosomes in a multivalent manner, concomitantly engaging two histone H3 tails. This robust synergistic interaction displaces HP1γ from pericentric sites, inducing changes in chromatin structure and leading to the dispersion of the heterochromatic mark H3K9me3. We demonstrate that recognition of the histone H3 tails by the PHD fingers is required for repressive activity of the CHD4/NuRD complex. Together, our data elucidate the molecular mechanism of multivalent association of the PHD fingers with chromatin and reveal their critical role in the regulation of CHD4 functions.},\nauthor_keywords={Epigenetics;  Gene repression;  Histone;  Posttranslational modifications},\nkeywords={adenosine triphosphatase;  chromodomain helicase DNA binding protein 4;  DNA binding protein;  heterochromatin protein 1;  histone deacetylase;  histone H3;  homeodomain protein;  unclassified drug, animal cell;  article;  chromatin;  controlled study;  dispersion;  molecular recognition;  nonhuman;  nucleosome;  priority journal, Amino Acid Sequence;  HEK293 Cells;  Heterochromatin;  Histones;  Homeodomain Proteins;  Humans;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Models, Molecular;  Molecular Sequence Data;  Nucleosomes;  Protein Processing, Post-Translational;  Protein Structure, Tertiary;  Repressor Proteins;  Transcription, Genetic},\ncorrespondence_address1={Kutateladze, T.G.; Department of Pharmacology, , Aurora, CO 80045, United States; email: Tatiana.Kutateladze@UCDenver.edu},\nissn={00278424},\ncoden={PNASA},\npubmed_id={22215588},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The detection and quantitation of protein oligomerization.\n \n \n \n \n\n\n \n Gell, D.; Grant, R.; and MacKay, J.\n\n\n \n\n\n\n Advances in Experimental Medicine and Biology, 747: 19-41. 2012.\n cited By 39\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Gell201219,\nauthor={Gell, D.A. and Grant, R.P. and MacKay, J.P.},\ntitle={The detection and quantitation of protein oligomerization},\njournal={Advances in Experimental Medicine and Biology},\nyear={2012},\nvolume={747},\npages={19-41},\ndoi={10.1007/978-1-4614-3229-6_2},\nnote={cited By 39},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84866783899&doi=10.1007%2f978-1-4614-3229-6_2&partnerID=40&md5=e1c0dafdddfedca5af135c8166a33183},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia; Menzies Research Institute, University of Tasmania, Hobart, TAS, Australia},\nabstract={There are many different techniques available to biologists and biochemists that can be used to detect and characterize the self-association of proteins. Each technique has strengths and weaknesses and it is often useful to combine several approaches to maximize the former and minimize the latter. Here we review a range of methodologies that identify protein self-association and/or allow the stoichiometry and affinity of the interaction to be determined, placing an emphasis on what type of information can be obtained and outlining the advantages and disadvantages involved. In general, in vitro biophysical techniques, such as size exclusion chromatography, analytical ultracentrifugation, scattering techniques, NMR spectroscopy, isothermal titration calorimetry, fluorescence anisotropy and mass spectrometry, provide information on stoichiometry and/or binding affinities. Other approaches such as cross-linking, fluorescence methods (e.g., fluorescence correlation spectroscopy, FCS; Förster resonance energy transfer, FRET; fluorescence recovery after photobleaching, FRAP; and proximity imaging, PRIM) and complementation approaches (e.g., yeast two hybrid assays and bimolecular fluorescence complementation, BiFC) can be used to detect protein self-association in a cellular context. © 2012 Springer Science+Business Media, LLC.},\nkeywords={transcription factor GAL4;  protein, anisotropy;  binding affinity;  binding site;  chromatography;  fluorescence correlation spectroscopy;  fluorescence recovery after photobleaching;  fluorescence resonance energy transfer;  gel permeation chromatography;  in vivo study;  isothermal titration calorimetry;  light scattering;  mass spectrometry;  molecular dynamics;  molecular imaging;  nuclear magnetic resonance spectroscopy;  oligomerization;  priority journal;  protein assembly;  protein binding;  protein cross linking;  protein determination;  protein protein interaction;  quantitative analysis;  review;  sedimentation rate;  stoichiometry;  ultracentrifugation;  X ray crystallography;  calorimetry;  chemistry;  gel chromatography;  light;  metabolism;  nuclear magnetic resonance;  protein multimerization;  protein subunit;  small angle scattering;  spectrofluorometry, Calorimetry;  Chromatography, Gel;  Fluorescence Resonance Energy Transfer;  Light;  Mass Spectrometry;  Molecular Imaging;  Nuclear Magnetic Resonance, Biomolecular;  Protein Multimerization;  Protein Subunits;  Proteins;  Scattering, Small Angle;  Spectrometry, Fluorescence;  Ultracentrifugation},\ncorrespondence_address1={MacKay, J.P.; School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia; email: j.mackay@mmb.usyd.edu.au},\npublisher={Springer New York LLC},\nissn={00652598},\nisbn={9781461432289},\ncoden={AEMBA},\npubmed_id={22949109},\nlanguage={English},\nabbrev_source_title={Adv. Exp. Med. Biol.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Interdomain orientation of cardiac troponin C characterized by paramagnetic relaxation enhancement NMR reveals a compact state.\n \n \n \n \n\n\n \n Cordina, N.; Liew, C.; Gell, D.; Fajer, P.; Mackay, J.; and Brown, L.\n\n\n \n\n\n\n Protein Science, 21(9): 1376-1387. 2012.\n cited By 15\n\n\n\n
\n\n\n\n \n \n $\"Interdomain$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Cordina20121376,\nauthor={Cordina, N.M. and Liew, C.K. and Gell, D.A. and Fajer, P.G. and Mackay, J.P. and Brown, L.J.},\ntitle={Interdomain orientation of cardiac troponin C characterized by paramagnetic relaxation enhancement NMR reveals a compact state},\njournal={Protein Science},\nyear={2012},\nvolume={21},\nnumber={9},\npages={1376-1387},\ndoi={10.1002/pro.2124},\nnote={cited By 15},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84865416690&doi=10.1002%2fpro.2124&partnerID=40&md5=ca11ef70492a6b1c96faf597e98ade62},\naffiliation={Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States; Department of Molecular Cardiology and Biophysics, Victor Chang Cardiac Research Institute, 405 Liverpool St., Darlinghurst, NSW 2010, Australia; Menzies Research Institute, University of Tasmania, TAS 7000, Australia},\nabstract={Cardiac troponin C (cTnC) is the calcium binding subunit of the troponin complex that triggers the thin filament response to calcium influx into the sarcomere. cTnC consists of two globular EF-hand domains (termed the N- and C-domains) connected by a flexible linker. While the conformation of each domain of cTnC has been thoroughly characterized through NMR studies involving either the isolated N-domain (N-cTnC) or C-domain (C-cTnC), little attention has been paid to the range of interdomain orientations possible in full-length cTnC that arises as a consequence of the flexibility of the domain linker. Flexibility in the domain linker of cTnC is essential for effective regulatory function of troponin. We have therefore utilized paramagnetic relaxation enhancement (PRE) NMR to assess the interdomain orientation of cTnC. Ensemble fitting of our interdomain PRE measurements reveals that isolated cTnC has considerable interdomain flexibility and preferentially adopts a bent conformation in solution, with a defined range of relative domain orientations. Published by Wiley-Blackwell. © 2012 The Protein Society.},\nauthor_keywords={Cardiac troponin C;  Ensemble states;  Paramagnetic relaxation enhancement;  Site-directed spin labeling;  Solution NMR},\nkeywords={troponin C, article;  contrast enhancement;  data analysis;  heart function;  nuclear magnetic resonance;  paramagnetic relaxation enhancement nuclear magnetic resonance;  priority journal;  protein analysis;  protein conformation;  regulatory mechanism;  spectroscopy},\ncorrespondence_address1={Brown, L.J.; Department of Chemistry and Biomolecular Sciences, , Sydney, NSW 2109, Australia; email: Louise.Brown@mq.edu.au},\npublisher={Blackwell Publishing Ltd},\nissn={09618368},\ncoden={PRCIE},\npubmed_id={22811351},\nlanguage={English},\nabbrev_source_title={Protein Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2011\n \n \n (14)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n The multi-zinc finger protein ZNF217 contacts DNA through a two-finger domain.\n \n \n \n \n\n\n \n Nunez, N.; Clifton, M.; Funnell, A.; Artuz, C.; Hallal, S.; Quinlan, K.; Font, J.; Vandevenne, M.; Setiyaputra, S.; Pearson, R.; Mackay, J.; and Crossley, M.\n\n\n \n\n\n\n Journal of Biological Chemistry, 286(44): 38190-38201. 2011.\n cited By 18\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Nunez201138190,\nauthor={Nunez, N. and Clifton, M.M.K. and Funnell, A.P.W. and Artuz, C. and Hallal, S. and Quinlan, K.G.R. and Font, J. and Vandevenne, M. and Setiyaputra, S. and Pearson, R.C.M. and Mackay, J.P. and Crossley, M.},\ntitle={The multi-zinc finger protein ZNF217 contacts DNA through a two-finger domain},\njournal={Journal of Biological Chemistry},\nyear={2011},\nvolume={286},\nnumber={44},\npages={38190-38201},\ndoi={10.1074/jbc.M111.301234},\nnote={cited By 18},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-80055099277&doi=10.1074%2fjbc.M111.301234&partnerID=40&md5=68ce9c8d249b0886e109230476860b26},\naffiliation={School of Molecular Bioscience, University of Sydney, NSW 2006, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia},\nabstract={Classical C2H2 zinc finger proteins are among the most abundant transcription factors found in eukaryotes, and the mechanisms through which they recognize their target genes have been extensively investigated. In general, a tandem array of three fingers separated by characteristic TGERP links is required for sequence-specific DNA recognition. Nevertheless, a significant number of zinc finger proteins do not contain a hallmark three-finger array of this type, raising the question of whether and how they contact DNA. We have examined the multi-finger protein ZNF217, which contains eight classical zinc fingers. ZNF217 is implicated as an oncogene and in repressing the E-cadherin gene. We show that two of its zinc fingers, 6 and 7, can mediate contacts with DNA. We examine its putative recognition site in the E-cadherin promoter and demonstrate that this is a suboptimal site. NMR analysis and mutagenesis is used to define the DNA binding surface of ZNF217, and we examine the specificity of the DNA binding activity using fluorescence anisotropy titrations. Finally, sequence analysis reveals that a variety of multi-finger proteins also contain two-finger units, and our data support the idea that these may constitute a distinct subclass of DNA recognition motif. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in the U.S.A.},\nkeywords={Data support;  DNA binding;  DNA binding activity;  DNA recognition;  E-cadherins;  Fluorescence anisotropy titration;  NMR analysis;  Recognition site;  Sequence analysis;  Tandem arrays;  Target genes;  Zinc finger;  Zinc finger protein, Genes;  Transcription;  Transcription factors;  Zinc, DNA, DNA;  unclassified drug;  uvomorulin;  zinc finger protein;  ZNF217 protein, article;  base pairing;  binding affinity;  binding site;  controlled study;  DNA sequence;  E cadherin gene;  fluorescence analysis;  gene;  gene repression;  human;  molecular recognition;  mutagenesis;  nonhuman;  nuclear magnetic resonance spectroscopy;  oncogene;  priority journal;  promoter region;  protein DNA binding;  protein domain;  protein function;  protein motif;  protein structure;  sequence analysis, Amino Acid Motifs;  Binding Sites;  Cell Nucleus;  DNA;  Gene Expression Regulation;  HEK293 Cells;  Humans;  Magnetic Resonance Spectroscopy;  Models, Molecular;  Protein Binding;  Protein Interaction Mapping;  Protein Structure, Tertiary;  Trans-Activators;  Transcription, Genetic;  Zinc Fingers, Eukaryota},\ncorrespondence_address1={Crossley, M.; School of Molecular Bioscience, , NSW 2006, Australia; email: m.crossley@unsw.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={21908891},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structural basis for hemoglobin capture by Staphylococcus aureus cell-surface protein, IsdH.\n \n \n \n \n\n\n \n Kumar, K.; Jacques, D.; Pishchany, G.; Caradoc-Davies, T.; Spirig, T.; Malmirchegini, G.; Langley, D.; Dickson, C.; Mackay, J.; Clubb, R.; Skaar, E.; Guss, J.; and Gell, D.\n\n\n \n\n\n\n Journal of Biological Chemistry, 286(44): 38439-38447. 2011.\n cited By 48\n\n\n\n
\n\n\n\n \n \n $\"Structural$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Kumar201138439,\nauthor={Kumar, K.K. and Jacques, D.A. and Pishchany, G. and Caradoc-Davies, T. and Spirig, T. and Malmirchegini, G.R. and Langley, D.B. and Dickson, C.F. and Mackay, J.P. and Clubb, R.T. and Skaar, E.P. and Guss, J.M. and Gell, D.A.},\ntitle={Structural basis for hemoglobin capture by Staphylococcus aureus cell-surface protein, IsdH},\njournal={Journal of Biological Chemistry},\nyear={2011},\nvolume={286},\nnumber={44},\npages={38439-38447},\ndoi={10.1074/jbc.M111.287300},\nnote={cited By 48},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-80055092837&doi=10.1074%2fjbc.M111.287300&partnerID=40&md5=dcd309b6bee03df8fe6c1dedd25cd439},\naffiliation={School of Molecular Bioscience, University of Sydney, NSW 2006, Australia; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical School, Nashville, TN 37232, United States; Australian Synchrotron, Clayton, VIC 3168, Australia; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, United States; Menzies Research Institute, University of Tasmania, TAS 7000, Australia},\nabstract={Pathogens must steal iron from their hosts to establish infection. In mammals, hemoglobin (Hb) represents the largest reservoir of iron, and pathogens express Hb-binding proteins to access this source. Here, we show how one of the commonest and most significant human pathogens, Staphylococcus aureus, captures Hb as the first step of an iron-scavenging pathway. The x-ray crystal structure of Hb bound to a domain from the Isd (iron-regulated surface determinant) protein, IsdH, is the first structure of a Hb capture complex to be determined. Surface mutations in Hb that reduce binding to the Hb-receptor limit the capacity of S. aureus to utilize Hb as an iron source, suggesting that Hb sequence is a factor in host susceptibility to infection. The demonstration that pathogens make highly specific recognition complexes with Hb raises the possibility of developing inhibitors of Hb binding as antibacterial agents. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Bacteria;  Cell membranes;  Hemoglobin;  Iron;  Mammals;  Pathogens;  Proteins;  Staphylococcus aureus, Binding proteins;  Cell surface proteins;  Host susceptibility;  Human pathogens;  Iron sources;  Specific recognition;  Structural basis;  X ray crystal structures, Crystal structure, bacterial protein;  hemoglobin;  hemoglobin receptor;  iron;  IsdH protein;  unclassified drug, article;  bacterial growth;  bacterial metabolism;  controlled study;  crystal structure;  host susceptibility;  human;  mutational analysis;  nonhuman;  priority journal;  protein structure;  receptor binding;  Staphylococcus aureus, Mammalia;  Staphylococcus aureus},\ncorrespondence_address1={Gell, D.A.; Menzies Research Institute Tasmania, 17 Liverpool St., Hobart, TAS 7000, Australia; email: david.gell@utas.edu.au},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={21917915},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structural basis of simultaneous recruitment of the transcriptional regulators LMO2 and FOG1/ZFPM1 by the transcription factor GATA1.\n \n \n \n \n\n\n \n Wilkinson-White, L.; Gamsjaeger, R.; Dastmalchi, S.; Wienert, B.; Stokes, P.; Crossley, M.; Mackay, J.; and Matthews, J.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 108(35): 14443-14448. 2011.\n cited By 34\n\n\n\n
\n\n\n\n \n \n $\"Structural$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Wilkinson-White201114443,\nauthor={Wilkinson-White, L. and Gamsjaeger, R. and Dastmalchi, S. and Wienert, B. and Stokes, P.H. and Crossley, M. and Mackay, J.P. and Matthews, J.M.},\ntitle={Structural basis of simultaneous recruitment of the transcriptional regulators LMO2 and FOG1/ZFPM1 by the transcription factor GATA1},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2011},\nvolume={108},\nnumber={35},\npages={14443-14448},\ndoi={10.1073/pnas.1105898108},\nnote={cited By 34},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-80052284219&doi=10.1073%2fpnas.1105898108&partnerID=40&md5=7b04909bcb5fe6347e1995d62f822169},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; School of Biomedical Sciences, University of Western Sydney, Penrith, NSW 2751, Australia; School of Pharmacy and Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz 51656-65813, Iran; Westfälische-Wilhelms-University, 48149 Münster, Germany},\nabstract={The control of red blood cell and megakaryocyte development by the regulatory protein GATA1 is a paradigm for transcriptional regulation of gene expression in cell lineage differentiation and maturation. Most GATA1-regulated events require GATA1 to bind FOG1, and essentially all GATA1-activated genes are cooccupied by a TAL1/E2A/LMO2/LDB1 complex; however, it is not known whether FOG1 and TAL1/E2A/LMO2/LDB1 are simultaneously recruited by GATA1. Our structural data reveal that the FOG1-binding domain of GATA1, the N finger, can also directly contact LMO2 and show that, despite the small size (<50 residues) of the GATA1 N finger, both FOG1 and LMO2 can simultaneously bind this domain. LMO2 in turn can simultaneously contact both GATA1 and the DNA-binding protein TAL1/E2A at bipartite E-box/WGATAR sites. Taken together, our data provide the first structural snapshot of multiprotein complex formation at GATA1-dependent genes and support a model in which FOG1 and TAL1/E2A/LMO2/LDB1 can cooccupy E-box/WGATAR sites to facilitate GATA1-mediated activation of gene activation.},\nauthor_keywords={Haematopoiesis;  Protein-DNA interactions;  Protein-protein interactions;  Transcription factor complex},\nkeywords={binding protein;  cell protein;  DNA binding protein;  protein FOG1;  protein LDB1;  protein Lmo2;  protein ZFPM1;  transcription factor E2A;  transcription factor GATA 1;  transcription factor TAL1;  unclassified drug;  zinc finger protein, article;  complex formation;  DNA binding;  E box element;  gene activation;  priority journal;  promoter region;  protein binding;  protein domain;  transcription regulation, Binding, Competitive;  DNA;  DNA-Binding Proteins;  GATA1 Transcription Factor;  Metalloproteins;  Models, Anatomic;  Nuclear Proteins;  Protein Structure, Quaternary;  Protein Structure, Tertiary;  Transcription Factors;  Transcription, Genetic},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, , Sydney, NSW 2006, Australia; email: Jacqui.Matthews@sydney.edu.au},\nissn={00278424},\ncoden={PNASA},\npubmed_id={21844373},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Protein-protein interactions: Analysis of a false positive GST pulldown result.\n \n \n \n \n\n\n \n Wissmueller, S.; Font, J.; Liew, C.; Cram, E.; Schroeder, T.; Turner, J.; Crossley, M.; Mackay, J.; and Matthews, J.\n\n\n \n\n\n\n Proteins: Structure, Function and Bioinformatics, 79(8): 2365-2371. 2011.\n cited By 21\n\n\n\n
\n\n\n\n \n \n $\"Protein-protein$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Wissmueller20112365,\nauthor={Wissmueller, S. and Font, J. and Liew, C.W. and Cram, E. and Schroeder, T. and Turner, J. and Crossley, M. and Mackay, J.P. and Matthews, J.M.},\ntitle={Protein-protein interactions: Analysis of a false positive GST pulldown result},\njournal={Proteins: Structure, Function and Bioinformatics},\nyear={2011},\nvolume={79},\nnumber={8},\npages={2365-2371},\ndoi={10.1002/prot.23068},\nnote={cited By 21},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79960084378&doi=10.1002%2fprot.23068&partnerID=40&md5=5c09c2d89b7e782269667bef030de5c8},\naffiliation={School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia; Centenary Institute, Royal Price Alfred Hospital, NSW 2050, Australia; Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland; School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2050, Australia},\nabstract={One of the most common ways to demonstrate a direct protein-protein interaction in vitro is the glutathione-S-transferse (GST)-pulldown. Here we report the detailed characterization of a putative interaction between two transcription factor proteins, GATA-1 and Krüppel-like factor 3 (KLF3/BKLF) that show robust interactions in GST-pulldown experiments. Attempts to map the interaction interface of GATA-1 on KLF3 using a mutagenic screening approach did not yield a contiguous binding face on KLF3, suggesting that the interaction might be non-specific. NMR experiments showed that the proteins do not interact at protein concentrations of 50-100 μM. Rather, the GST tag can cause part of KLF3 to misfold. In addition to misfolding, the fact that both proteins are DNA-binding domains appears to introduce binding artifacts (possibly nucleic acid bridging) that cannot be resolved by the addition of nucleases or ethidium bromide (EtBr). This study emphasizes the need for caution in relying on GST-pulldown results and related methods, without convincing confirmation from different approaches. © 2011 Wiley-Liss, Inc.},\nauthor_keywords={Binding artifact;  Misfolding;  NMR spectroscopy;  Nucleic acid bridging;  Transcription factors},\nkeywords={DNA;  ethidium bromide;  glutathione transferase;  kruppel like factor;  kruppel like factor 3;  transcription factor GATA 1;  unclassified drug, article;  DNA binding motif;  false positive result;  in vitro study;  nuclear magnetic resonance spectroscopy;  nucleotide sequence;  priority journal;  protein analysis;  protein expression;  protein folding;  protein protein interaction;  protein purification, Animals;  GATA1 Transcription Factor;  Kruppel-Like Transcription Factors;  Mice;  Nuclear Magnetic Resonance, Biomolecular;  Protein Binding},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, , NSW 2006, Australia; email: jacqui.matthews@sydney.edu.au},\nissn={08873585},\npubmed_id={21638332},\nlanguage={English},\nabbrev_source_title={Proteins Struct. Funct. Bioinformatics},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structural basis and specificity of acetylated transcription factor GATA1 recognition by BET family bromodomain protein Brd3.\n \n \n \n \n\n\n \n Gamsjaeger, R.; Webb, S.; Lamonica, J.; Billin, A.; Blobel, G.; and Mackay, J.\n\n\n \n\n\n\n Molecular and Cellular Biology, 31(13): 2632-2640. 2011.\n cited By 89\n\n\n\n
\n\n\n\n \n \n $\"Structural$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Gamsjaeger20112632,\nauthor={Gamsjaeger, R. and Webb, S.R. and Lamonica, J.M. and Billin, A. and Blobel, G.A. and Mackay, J.P.},\ntitle={Structural basis and specificity of acetylated transcription factor GATA1 recognition by BET family bromodomain protein Brd3},\njournal={Molecular and Cellular Biology},\nyear={2011},\nvolume={31},\nnumber={13},\npages={2632-2640},\ndoi={10.1128/MCB.05413-11},\nnote={cited By 89},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79959402979&doi=10.1128%2fMCB.05413-11&partnerID=40&md5=07b503d23576d926a78db5b90642a13f},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Division of Hematology, The Children's Hospital of Philadelphia, The University of Pennsylvania School of Medicine, Philadelphia, PA 19104, United States; GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, United Kingdom},\nabstract={Recent data demonstrate that small synthetic compounds specifically targeting bromodomain proteins can modulate the expression of cancer-related or inflammatory genes. Although these studies have focused on the ability of bromodomains to recognize acetylated histones, it is increasingly becoming clear that histone-like modifications exist on other important proteins, such as transcription factors. However, our understanding of the molecular mechanisms through which these modifications modulate protein function is far from complete. The transcription factor GATA1 can be acetylated at lysine residues adjacent to the zinc finger domains, and this acetylation is essential for the normal chromatin occupancy of GATA1. We have recently identified the bromodomain-containing protein Brd3 as a cofactor that interacts with acetylated GATA1 and shown that this interaction is essential for the targeting of GATA1 to chromatin. Here we describe the structural basis for this interaction. Our data reveal for the first time the molecular details of an interaction between a transcription factor bearing multiple acetylation modifications and its cognate recognition module. We also show that this interaction can be inhibited by an acetyllysine mimic, highlighting the importance of further increasing the specificity of compounds that target bromodomain and extraterminal (BET) bromodomains in order to fully realize their therapeutic potential. © 2011, American Society for Microbiology.},\nkeywords={bromodomain and extraterminal domain protein;  cell protein;  lysine;  protein brd3;  transcription factor;  trascription factor gata1;  unclassified drug, acetylation;  article;  complex formation;  gene expression regulation;  histone modification;  priority journal;  protein processing;  protein protein interaction;  protein structure, Acetylation;  Amino Acid Sequence;  GATA1 Transcription Factor;  Humans;  Hydrophobic and Hydrophilic Interactions;  Lysine;  Molecular Sequence Data;  Protein Structure, Secondary;  RNA-Binding Proteins},\ncorrespondence_address1={Mackay, J.P.; School of Molecular Bioscience, , Sydney, NSW 2006, Australia; email: joel.mackay@sydney.edu.au},\nissn={02707306},\ncoden={MCEBD},\npubmed_id={21555453},\nlanguage={English},\nabbrev_source_title={Mol. Cell. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Bromodomain protein Brd3 associates with acetylated GATA1 to promote its chromatin occupancy at erythroid target genes.\n \n \n \n \n\n\n \n Lamonica, J.; Deng, W.; Kadauke, S.; Campbell, A.; Gamsjaeger, R.; Wang, H.; Cheng, Y.; Billin, A.; Hardison, R.; Mackay, J.; and Blobel, G.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 108(22): E159-E168. 2011.\n cited By 172\n\n\n\n
\n\n\n\n \n \n $\"Bromodomain$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Lamonica2011,\nauthor={Lamonica, J.M. and Deng, W. and Kadauke, S. and Campbell, A.E. and Gamsjaeger, R. and Wang, H. and Cheng, Y. and Billin, A.N. and Hardison, R.C. and Mackay, J.P. and Blobel, G.A.},\ntitle={Bromodomain protein Brd3 associates with acetylated GATA1 to promote its chromatin occupancy at erythroid target genes},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2011},\nvolume={108},\nnumber={22},\npages={E159-E168},\ndoi={10.1073/pnas.1102140108},\nnote={cited By 172},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79959365005&doi=10.1073%2fpnas.1102140108&partnerID=40&md5=44741816361039a5e1f35fdb87f832ed},\naffiliation={Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States; University of Pennsylvania School of Medicine, Philadelphia, PA 19104, United States; Department of Biology, University of Pennsylvania, Philadelphia, PA, United States; School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, United States; GlaxoSmithKline, Durham, NC 27709, United States},\nabstract={Acetylation of histones triggers association with bromodomaincontaining proteins that regulate diverse chromatin-related processes. Although acetylation of transcription factors has been appreciated for some time, the mechanistic consequences are less well understood. The hematopoietic transcription factor GATA1 is acetylated at conserved lysines that are required for its stable association with chromatin. We show that the BET family protein Brd3 binds via its first bromodomain (BD1) to GATA1 in an acetylation-dependent manner in vitro and in vivo. Mutation of a single residue in BD1 that is involved in acetyl-lysine binding abrogated recruitment of Brd3 by GATA1, demonstrating that acetylation of GATA1 is essential for Brd3 association with chromatin. Notably, Brd3 is recruited by GATA1 to both active and repressed target genes in a fashion seemingly independent of histone acetylation. Anti-Brd3 ChIP followed by massively parallel sequencing in GATA1-deficient erythroid precursor cells and those that are GATA1 replete qrevealed that GATA1 is a major determinant of Brd3 recruitment to genomic targets within chromatin. A pharmacologic compound that occupies the acetyl-lysine binding pockets of Brd3 bromodomains disrupts the Brd3-GATA1 interaction, diminishes the chromatin occupancy of both proteins, and inhibits erythroid maturation. Together these findings provide a mechanism for GATA1 acetylation and suggest that Brd3 "reads" acetyl marks on nuclear factors to promote their stable association with chromatin.},\nauthor_keywords={Gene regulation;  Hematopoiesis;  Posttranslational modifications},\nkeywords={bromodomain 3 protein;  bromodomain 4 protein;  protein;  transcription factor GATA 1;  unclassified drug, acetylation;  amino acid sequence;  animal cell;  article;  chromatin;  erythroid precursor cell;  erythroleukemia cell;  gene targeting;  histone acetylation;  in vitro study;  in vivo study;  mouse;  nonhuman;  priority journal;  protein binding;  protein protein interaction, Acetylation;  Animals;  Chromatin;  Chromatin Immunoprecipitation;  Erythroid Cells;  GATA1 Transcription Factor;  Gene Expression Regulation;  Hematopoiesis;  Histones;  Mice;  Mutation;  Nuclear Proteins;  Protein Binding;  Protein Processing, Post-Translational;  Protein Structure, Tertiary},\ncorrespondence_address1={Blobel, G. A.; Division of Hematology, , Philadelphia, PA 19104, United States; email: blobel@email.chop.edu},\nissn={00278424},\ncoden={PNASA},\npubmed_id={21536911},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The structure of a truncated phosphoribosylanthranilate isomerase suggests a unified model for evolution of the (βα)8 barrel fold.\n \n \n \n \n\n\n \n Setiyaputra, S.; MacKay, J.; and Patrick, W.\n\n\n \n\n\n\n Journal of Molecular Biology, 408(2): 291-303. 2011.\n cited By 14\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Setiyaputra2011291,\nauthor={Setiyaputra, S. and MacKay, J.P. and Patrick, W.M.},\ntitle={The structure of a truncated phosphoribosylanthranilate isomerase suggests a unified model for evolution of the (βα)8 barrel fold},\njournal={Journal of Molecular Biology},\nyear={2011},\nvolume={408},\nnumber={2},\npages={291-303},\ndoi={10.1016/j.jmb.2011.02.048},\nnote={cited By 14},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79953675666&doi=10.1016%2fj.jmb.2011.02.048&partnerID=40&md5=664b39b8620fab6d5c847ebdf5d46720},\naffiliation={School of Molecular Bioscience, Darlington Campus, University of Sydney, NSW 2006, Australia; Institute of Natural Sciences, Massey University, Private Bag 102 904, North Shore, Auckland 0745, New Zealand},\nabstract={The (βα)8 barrel is one of the most common protein folds, and enzymes with this architecture display a remarkable range of catalytic activities. Many of these functions are associated with ancient metabolic pathways, and phylogenetic reconstructions suggest that the (βα)8 barrel was one of the very first protein folds to emerge. Consequently, there is considerable interest in understanding the evolutionary processes that gave rise to this fold. In particular, much attention has been focused on the plausibility of (βα)8 barrel evolution from homodimers of half barrels. However, we previously isolated a three-quarter-barrel-sized fragment of a (βα)8 barrel, termed truncated phosphoribosylanthranilate isomerase (trPRAI), that is soluble and almost as thermostable as full-length N-(5′-phosphoribosyl) anthranilate isomerase (PRAI). Here, we report the NMR-derived structure of trPRAI. The subdomain is monomeric, is well ordered and adopts a native-like structure in solution. Side chains from strands β1 (Glu3 and Lys5), β2 (Tyr25) and β6 (Lys122) of trPRAI repack to shield the hydrophobic core from the solvent. This result demonstrates that three-quarter barrels were viable intermediates in the evolution of the (βα)8 barrel fold. We propose a unified model for (βα)8 barrel evolution that combines our data, previously published work and plausible scenarios for the emergence of (initially error-prone) genetic systems. In this model, the earliest proto-cells contained diverse pools of part-barrel subdomains. Combinatorial assembly of these subdomains gave rise to many distinct lineages of (βα)8 barrel proteins, that is, our model excludes the possibility that there was a single (βα)8 barrel from which all present examples are descended. © 2011 Elsevier Ltd. All rights reserved.},\nauthor_keywords={NMR;  protein evolution;  protein structure;  subdomain},\nkeywords={homodimer;  isomerase;  monomer;  n (5' phosphoribosyl)anthranilate isomerase;  phosphoribosylanthranilate isomerase;  solvent;  unclassified drug, article;  barrel fold;  genetic analysis;  hydrophobicity;  isolation procedure;  nuclear magnetic resonance;  priority journal;  protein domain;  protein folding;  protein multimerization;  structure analysis},\ncorrespondence_address1={MacKay, J. P.; School of Molecular Bioscience, , NSW 2006, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Academic Press},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={21354426},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Erratum: The prospects for designer single-stranded RNA-binding proteins (Nature Structural and Molecular Biology (2011) 18 (256-261)).\n \n \n \n \n\n\n \n MacKay, J.; Font, J.; and Segal, D.\n\n\n \n\n\n\n Nature Structural and Molecular Biology, 18(4): 516. 2011.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Erratum:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@ARTICLE{MacKay2011516,\nauthor={MacKay, J.P. and Font, J. and Segal, D.J.},\ntitle={Erratum: The prospects for designer single-stranded RNA-binding proteins (Nature Structural and Molecular Biology (2011) 18 (256-261))},\njournal={Nature Structural and Molecular Biology},\nyear={2011},\nvolume={18},\nnumber={4},\npages={516},\ndoi={10.1038/nsmb0411-516e},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79953794821&doi=10.1038%2fnsmb0411-516e&partnerID=40&md5=18a35aa5b153bea5147b08af32f4740e},\nkeywords={erratum;  error;  priority journal},\ncorrespondence_address1={MacKay, J. P.},\nissn={15459993},\ncoden={NSMBC},\nlanguage={English},\nabbrev_source_title={Nat. Struct. Mol. Biol.},\ndocument_type={Erratum},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Plant homeodomain (PHD) fingers of CHD4 are histone H3-binding modules with preference for unmodified H3K4 and methylated H3K9.\n \n \n \n \n\n\n \n Mansfield, R.; Musselman, C.; Kwan, A.; Oliver, S.; Garske, A.; Davrazou, F.; Denu, J.; Kutateladze, T.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 286(13): 11779-11791. 2011.\n cited By 124\n\n\n\n
\n\n\n\n \n \n $\"Plant$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mansfield201111779,\nauthor={Mansfield, R.E. and Musselman, C.A. and Kwan, A.H. and Oliver, S.S. and Garske, A.L. and Davrazou, F. and Denu, J.M. and Kutateladze, T.G. and Mackay, J.P.},\ntitle={Plant homeodomain (PHD) fingers of CHD4 are histone H3-binding modules with preference for unmodified H3K4 and methylated H3K9},\njournal={Journal of Biological Chemistry},\nyear={2011},\nvolume={286},\nnumber={13},\npages={11779-11791},\ndoi={10.1074/jbc.M110.208207},\nnote={cited By 124},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79953180590&doi=10.1074%2fjbc.M110.208207&partnerID=40&md5=259536d36401023f7b85d708efffe604},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Department of Pharmacology, School of Medicine, University of Colorado Denver, Aurora, CO 80045, United States; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, United States},\nabstract={A major challenge in chromatin biology is to understand the mechanisms by which chromatin is remodeled into active or inactive states as required during development and cell differentiation. One complex implicated in these processes is the nucleosome remodeling and histone deacetylase (NuRD) complex, which contains both histone deacetylase and nucleosome remodeling activities and has been implicated in the silencing of subsets of genes involved in various stages of cellular development. Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a core component of the NuRD complex and contains a nucleosome remodeling ATPase domain along with two chromodomains and two plant homeodomain (PHD) fingers. We have previously demonstrated that the second PHD finger of CHD4 binds peptides corresponding to the N terminus of histone H3 methylated at Lys9. Here, we determine the solution structure of PHD2 in complex with H3K9me3, revealing the molecular basis of histone recognition, including a cation-π recognition mechanism for methylated Lys9. Additionally, we demonstrate that the first PHD finger also exhibits binding to the N terminus of H3, and we establish the histone-binding surface of this domain. This is the first instance where histone binding ability has been demonstrated for two separate PHD modules within the one protein. These findings suggest that CHD4 could bind to two H3 N-terminal tails on the same nucleosome or on two separate nucleosomes simultaneously, presenting exciting implications for the mechanism by which CHD4 and the NuRD complex could direct chromatin remodeling. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={ATPase domain;  Binding abilities;  Binding surface;  Cell differentiation;  Cellular development;  Chromatin remodeling;  Chromodomains;  Core components;  DNA-binding protein;  Helicases;  Histone deacetylases;  Histone H3;  Homeodomain;  Molecular basis;  N-terminals;  Nucleosome remodeling;  Nucleosomes;  Recognition mechanism;  Solution structures, Genes;  Plants (botany), Proteins, chromodomain helicase DNA binding protein 4;  DNA binding protein;  histone H3;  histone H3K4;  histone h3k9;  homeodomain protein;  plant homeodomain finger 2 protein;  unclassified drug, amino terminal sequence;  article;  binding affinity;  binding site;  complex formation;  controlled study;  histone methylation;  molecular dynamics;  molecular recognition;  nonhuman;  plant homeodomain finger;  priority journal;  protein binding;  protein protein interaction;  protein structure, Adenosine Triphosphatases;  Autoantigens;  Chromatin Assembly and Disassembly;  Histones;  Humans;  K562 Cells;  Methylation;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Nucleosomes;  Plants;  Protein Structure, Tertiary},\ncorrespondence_address1={Mackay, J. P.; School of Molecular Bioscience, , Sydney, NSW 2006, Australia; email: joel.mackay@sydney.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={21278251},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Characterization of a family of RanBP2-Type zinc fingers that can recognize single-stranded RNA.\n \n \n \n \n\n\n \n Nguyen, C.; Mansfield, R.; Leung, W.; Vaz, P.; Loughlin, F.; Grant, R.; and MacKay, J.\n\n\n \n\n\n\n Journal of Molecular Biology, 407(2): 273-283. 2011.\n cited By 80\n\n\n\n
\n\n\n\n \n \n $\"Characterization$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Nguyen2011273,\nauthor={Nguyen, C.D. and Mansfield, R.E. and Leung, W. and Vaz, P.M. and Loughlin, F.E. and Grant, R.P. and MacKay, J.P.},\ntitle={Characterization of a family of RanBP2-Type zinc fingers that can recognize single-stranded RNA},\njournal={Journal of Molecular Biology},\nyear={2011},\nvolume={407},\nnumber={2},\npages={273-283},\ndoi={10.1016/j.jmb.2010.12.041},\nnote={cited By 80},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79952317624&doi=10.1016%2fj.jmb.2010.12.041&partnerID=40&md5=991f3a047c42a996ee680eac98b74791},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={The recognition of single-stranded RNA (ssRNA) is an important aspect of gene regulation, and a number of different classes of protein domains that recognize ssRNA in a sequence-specific manner have been identified. Recently, we demonstrated that the RanBP2-type zinc finger (ZnF) domains from the human splicing factor ZnF Ran binding domain-containing protein 2 (ZRANB2) can bind to a sequence containing the consensus AGGUAA. Six other human proteins, namely, Ewing's sarcoma (EWS), translocated in liposarcoma (TLS)/FUS, RNA-binding protein 56 (RBP56), RNA-binding motif 5 (RBM5), RNA-binding motif 10 (RBM10) and testis-expressed sequence 13A (TEX13A), each contains a single ZnF with homology to the ZRANB2 ZnFs, and several of these proteins have been implicated in the regulation of mRNA processing. Here, we show that all of these ZnFs are able to bind with micromolar affinities to ssRNA containing a GGU motif. NMR titration data reveal that binding is mediated by the corresponding surfaces on each ZnF, and we also show that sequence selectivity is largely limited to the GGU core motif and that substitution of the three flanking adenines that were selected in our original selection experiment has a minimal effect on binding affinity. These data establish a subset of RanBP2-type ZnFs as a new family of ssRNA-binding motifs. © 2011 Elsevier Ltd.},\nauthor_keywords={EWS;  RBM5;  TEX13A;  TLS/FUS;  ZRANB2},\nkeywords={adenine;  rabp2 type zinc finger protein;  single stranded RNA;  unclassified drug;  zinc finger protein, amino acid sequence;  article;  binding affinity;  complex formation;  human;  molecular recognition;  nucleic acid base substitution;  nucleotide sequence;  priority journal;  protein analysis;  protein motif;  protein RNA binding;  protein structure;  RNA sequence;  stoichiometry},\ncorrespondence_address1={MacKay, J. P.; School of Molecular Bioscience, , Sydney, NSW 2006, Australia; email: joel.mackay@sydney.edu.au},\npublisher={Academic Press},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={21256132},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The prospects for designer single-stranded RNA-binding proteins.\n \n \n \n \n\n\n \n MacKay, J.; Font, J.; and Segal, D.\n\n\n \n\n\n\n Nature Structural and Molecular Biology, 18(3): 256-261. 2011.\n cited By 47\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{MacKay2011256,\nauthor={MacKay, J.P. and Font, J. and Segal, D.J.},\ntitle={The prospects for designer single-stranded RNA-binding proteins},\njournal={Nature Structural and Molecular Biology},\nyear={2011},\nvolume={18},\nnumber={3},\npages={256-261},\ndoi={10.1038/nsmb.2005},\nnote={cited By 47},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79952363146&doi=10.1038%2fnsmb.2005&partnerID=40&md5=b768d48d6f4d83f34405b4dd13e5c18c},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia; Department of Pharmacology, University of California at Davis, Davis, CA, United States; Genome Center, University of California at Davis, Davis, CA, United States},\nabstract={Spectacular progress has been made in the design of proteins that recognize double-stranded DNA with a chosen specificity, to the point that designer DNA-binding proteins can be ordered commercially. This success raises the question of whether it will be possible to engineer libraries of proteins that can recognize RNA with tailored specificity. Given the recent explosion in the number and diversity of RNA species demonstrated to play roles in biology, designer RNA-binding proteins are set to become valuable tools, both in the research laboratory and potentially in the clinic. Here we discuss the prospects for the realization of this idea. © 2011 Nature America, Inc. All rights reserved.},\nkeywords={nucleocapsid protein;  RNA binding protein;  scaffold protein;  single stranded RNA;  zinc finger protein, crystal structure;  hydrogen bond;  molecular recognition;  priority journal;  protein domain;  protein engineering;  protein motif;  protein structure;  review, Animals;  Bacteria;  Bacterial Proteins;  Binding Sites;  Humans;  Models, Molecular;  Protein Engineering;  Protein Interaction Domains and Motifs;  RNA;  RNA-Binding Proteins;  Tristetraprolin;  Zinc Fingers},\ncorrespondence_address1={MacKay, J. P.; School of Molecular Bioscience, , Sydney, NSW, Australia; email: joel.mackay@sydney.edu.au},\nissn={15459993},\ncoden={NSMBC},\npubmed_id={21358629},\nlanguage={English},\nabbrev_source_title={Nat. Struct. Mol. Biol.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Macromolecular NMR spectroscopy for the non-spectroscopist: Beyond macromolecular solution structure determination.\n \n \n \n \n\n\n \n Bieri, M.; Kwan, A.; Mobli, M.; King, G.; MacKay, J.; and Gooley, P.\n\n\n \n\n\n\n FEBS Journal, 278(5): 704-715. 2011.\n cited By 46\n\n\n\n
\n\n\n\n \n \n $\"Macromolecular$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Bieri2011704,\nauthor={Bieri, M. and Kwan, A.H. and Mobli, M. and King, G.F. and MacKay, J.P. and Gooley, P.R.},\ntitle={Macromolecular NMR spectroscopy for the non-spectroscopist: Beyond macromolecular solution structure determination},\njournal={FEBS Journal},\nyear={2011},\nvolume={278},\nnumber={5},\npages={704-715},\ndoi={10.1111/j.1742-4658.2011.08005.x},\nnote={cited By 46},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79951931431&doi=10.1111%2fj.1742-4658.2011.08005.x&partnerID=40&md5=01b6e438d288f676997c8652c7384cc7},\naffiliation={Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; School of Molecular Bioscience, University of Sydney, Australia; Institute for Molecular Bioscience, University of Queensland, St. Lucia, Australia},\nabstract={A strength of NMR spectroscopy is its ability to monitor, on an atomic level, molecular changes and interactions. In this review, which is intended for non-spectroscopist, we describe major uses of NMR in protein science beyond solution structure determination. After first touching on how NMR can be used to quickly determine whether a mutation induces structural perturbations in a protein, we describe the unparalleled ability of NMR to monitor binding interactions over a wide range of affinities, molecular masses and solution conditions. We discuss the use of NMR to measure the dynamics of proteins at the atomic level and over a wide range of timescales. Finally, we outline new and expanding areas such as macromolecular structure determination in multicomponent systems, as well as in the solid state and in vivo. © 2011 FEBS.},\nauthor_keywords={chemical shift mapping;  NMR;  NOE;  protein;  protein complex;  protein dynamics;  protein folding;  protein interaction;  protein mutagenesis;  saturation difference},\nkeywords={transcription factor;  zinc finger protein, binding affinity;  computer program;  gene mutation;  heteronuclear single quantum coherence;  in vivo study;  macromolecule;  molecular dynamics;  molecular interaction;  molecular weight;  nuclear magnetic resonance spectroscopy;  nuclear Overhauser effect;  priority journal;  protein conformation;  protein domain;  protein folding;  protein interaction;  protein structure;  review;  site directed mutagenesis;  solid state;  structure analysis, Magnetic Resonance Spectroscopy;  Molecular Structure;  Protein Binding;  Protein Folding;  Proteins},\ncorrespondence_address1={Gooley, P. R.; Department of Biochemistry and Molecular Biology, , Parkville, VIC 3010, Australia; email: prg@unimelb.edu.au},\nissn={1742464X},\npubmed_id={21214861},\nlanguage={English},\nabbrev_source_title={FEBS J.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Macromolecular NMR spectroscopy for the non-spectroscopist.\n \n \n \n \n\n\n \n Kwan, A.; Mobli, M.; Gooley, P.; King, G.; and MacKay, J.\n\n\n \n\n\n\n FEBS Journal, 278(5): 687-703. 2011.\n cited By 127\n\n\n\n
\n\n\n\n \n \n $\"Macromolecular$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Kwan2011687,\nauthor={Kwan, A.H. and Mobli, M. and Gooley, P.R. and King, G.F. and MacKay, J.P.},\ntitle={Macromolecular NMR spectroscopy for the non-spectroscopist},\njournal={FEBS Journal},\nyear={2011},\nvolume={278},\nnumber={5},\npages={687-703},\ndoi={10.1111/j.1742-4658.2011.08004.x},\nnote={cited By 127},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79951919101&doi=10.1111%2fj.1742-4658.2011.08004.x&partnerID=40&md5=8bade4f924897455b7ef11efab9e1a78},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia},\nabstract={NMR spectroscopy is a powerful tool for studying the structure, function and dynamics of biological macromolecules. However, non-spectroscopists often find NMR theory daunting and data interpretation nontrivial. As the first of two back-to-back reviews on NMR spectroscopy aimed at non-spectroscopists, the present review first provides an introduction to the basics of macromolecular NMR spectroscopy, including a discussion of typical sample requirements and what information can be obtained from simple NMR experiments. We then review the use of NMR spectroscopy for determining the 3D structures of macromolecules and examine how to judge the quality of NMR-derived structures. © 2011 FEBS.},\nauthor_keywords={HSQC;  nuclear magnetic resonance (NMR) spectroscopy;  protein folding;  protein NMR spectroscopy;  protein stability;  protein structure determination;  TROSY},\nkeywords={carbon 13;  DNA;  nitrogen 15;  proton;  RNA, chemical structure;  computer program;  data analysis;  heteronuclear single quantum coherence;  macromolecule;  nuclear magnetic resonance spectroscopy;  nuclear Overhauser effect;  priority journal;  protein aggregation;  protein folding;  protein stability;  protein structure;  proton nuclear magnetic resonance;  quality control;  review;  sampling;  structure analysis;  X ray crystallography, Magnetic Resonance Spectroscopy;  Protein Conformation;  Protein Folding;  Protein Stability;  Proteins},\ncorrespondence_address1={MacKay, J. P.; School of Molecular Bioscience, , Sydney, NSW 2006, Australia; email: joel.mackay@sydney.edu.au},\nissn={1742464X},\npubmed_id={21214860},\nlanguage={English},\nabbrev_source_title={FEBS J.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Insights into association of the NuRD complex with FOG-1 from the crystal structure of an RbAp48·FOG-1 complex.\n \n \n \n \n\n\n \n Lejon, S.; Thong, S.; Murthy, A.; AlQarni, S.; Murzina, N.; Blobel, G.; Laue, E.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 286(2): 1196-1203. 2011.\n cited By 69\n\n\n\n
\n\n\n\n \n \n $\"Insights$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Lejon20111196,\nauthor={Lejon, S. and Thong, S.Y. and Murthy, A. and AlQarni, S. and Murzina, N.V. and Blobel, G.A. and Laue, E.D. and Mackay, J.P.},\ntitle={Insights into association of the NuRD complex with FOG-1 from the crystal structure of an RbAp48·FOG-1 complex},\njournal={Journal of Biological Chemistry},\nyear={2011},\nvolume={286},\nnumber={2},\npages={1196-1203},\ndoi={10.1074/jbc.M110.195842},\nnote={cited By 69},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-78651380341&doi=10.1074%2fjbc.M110.195842&partnerID=40&md5=733fb6641fab7da3761edcd2158973d6},\naffiliation={Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom; School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States},\nabstract={Chromatin-modifying complexes such as the NuRD complex are recruited to particular genomic sites by gene-specific nuclear factors. Overall, however, little is known about the molecular basis for these interactions. Here, we present the 1.9 Å resolution crystal structure of the NuRD subunit RbAp48 bound to the 15 N-terminal amino acids of the GATA-1 cofactor FOG-1. The FOG-1 peptide contacts a negatively charged binding pocket on top of the RbAp48 β-propeller that is distinct from the binding surface used by RpAp48 to contact histone H4. We further show that RbAp48 interacts with the NuRD subunit MTA-1 via a surface that is distinct from its FOG-binding pocket, providing a first glimpse into the way in which NuRD assembly facilitates interactions with cofactors. Our RbAp48·FOG-1 structure provides insight into the molecular determinants of FOG-1-dependent association with the NuRD complex and into the links between transcription regulation and nucleosome remodeling. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Binding pockets;  Binding surface;  Cofactors;  Histone H4;  Molecular basis;  Molecular determinants;  N-terminals;  Nuclear factors;  Nucleosome remodeling;  Transcription regulations, Amino acids;  Complexation;  Fog;  Transcription, Crystal structure, friend of GATA 1;  histone deacetylase;  histone H4;  nucleosome remodeling and deacetylase;  retinoblastoma binding protein 4;  transcription factor;  unclassified drug, amino terminal sequence;  article;  binding site;  chromatin assembly and disassembly;  complex formation;  controlled study;  crystal structure;  enzyme subunit;  gene function;  nonhuman;  priority journal;  protein binding;  protein protein interaction;  transcription regulation, Amino Acid Sequence;  Animals;  Binding Sites;  Cells, Cultured;  Conserved Sequence;  Crystallography, X-Ray;  Histone Deacetylases;  Histones;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Microfilament Proteins;  Molecular Sequence Data;  Nuclear Proteins;  Protein Interaction Domains and Motifs;  Protein Structure, Tertiary;  Recombinant Proteins;  Repressor Proteins;  Retinoblastoma-Binding Protein 4;  Spodoptera;  Transcription Factors;  Transcription, Genetic},\ncorrespondence_address1={Laue, E. D.; Department of Biochemistry, , Cambridge CB2 1GA, United Kingdom; email: e.d.laue@bioc.cam.ac.uk},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={21047798},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2010\n \n \n (7)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Protein Recognition.\n \n \n \n \n\n\n \n Mansfield, R.; Cross, A.; Matthews, J.; and Mackay, J.\n\n\n \n\n\n\n Volume 2 Wiley-VCH, 2010.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Protein$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@BOOK{Mansfield2010505,\nauthor={Mansfield, R.E. and Cross, A.J. and Matthews, J.M. and Mackay, J.P.},\ntitle={Protein Recognition},\njournal={Amino Acids, Peptides and Proteins in Organic Chemistry},\nyear={2010},\nvolume={2},\npages={505-532},\ndoi={10.1002/9783527631780.ch12},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84886022954&doi=10.1002%2f9783527631780.ch12&partnerID=40&md5=c710af96b580c855ff6e8bc05ede6d6e},\naffiliation={University of Sydney, School of Molecular and Microbial Biosciences, G08 Biochemistry Building, Sydney, NSW 2006, Australia},\nauthor_keywords={Coupled folding and binding;  Hotspots;  Post-translational modifications;  Protein interfaces;  Protein recognition},\ncorrespondence_address1={Mansfield, R.E.; University of Sydney, G08 Biochemistry Building, Sydney, NSW 2006, Australia},\npublisher={Wiley-VCH},\nisbn={9783527320981},\nlanguage={English},\nabbrev_source_title={Amino Acids, Peptides and Proteins in Organic Chem.},\ndocument_type={Book Chapter},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Preface.\n \n \n \n \n\n\n \n MacKay, J.; and Segal, D.\n\n\n \n\n\n\n Methods in Molecular Biology, 649: V-VI. 2010.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Preface$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{MacKay2010,\nauthor={MacKay, J.P. and Segal, D.J.},\ntitle={Preface},\njournal={Methods in Molecular Biology},\nyear={2010},\nvolume={649},\npages={V-VI},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84858235053&partnerID=40&md5=8b33ec033ee3f025dd27bd154e155908},\ncorrespondence_address1={MacKay, J.P., Sydney, Australia},\neditor={Mackay J.P., Segal D.J.},\nissn={10643745},\nisbn={9781607617525},\nlanguage={English},\nabbrev_source_title={Methods Mol. Biol.},\ndocument_type={Editorial},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Beyond DNA: Zinc finger domains as RNA-binding modules.\n \n \n \n \n\n\n \n Font, J.; and MacKay, J.\n\n\n \n\n\n\n Methods in Molecular Biology, 649: 479-491. 2010.\n cited By 35\n\n\n\n
\n\n\n\n \n \n $\"Beyond$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Font2010479,\nauthor={Font, J. and MacKay, J.P.},\ntitle={Beyond DNA: Zinc finger domains as RNA-binding modules},\njournal={Methods in Molecular Biology},\nyear={2010},\nvolume={649},\npages={479-491},\ndoi={10.1007/978-1-60761-753-2_29},\nnote={cited By 35},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-80053189897&doi=10.1007%2f978-1-60761-753-2_29&partnerID=40&md5=0987d824eb53a7b3ca359870f5d7100f},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia},\nabstract={Over the last 25 years, we have learned that many structural classes of zinc-binding domains (zinc fingers, ZFs) exist and it has become clear that the molecular functions of these domains are by no means limited to the sequence-specific recognition of double-stranded DNA. For example, ZFs can act as protein recognition or RNA-binding modules, and some domains can exhibit more than one function. In this chapter we describe the progress that has been made in understanding the role of ZF domains as RNA-recognition modules, and we speculate about both the prevalence of such functions and the prospects for creating designer ZFs that target RNA. © 2010 Springer Science+Business Media, LLC.},\nauthor_keywords={protein design;  protein interaction domain;  RNA-binding domain;  Zinc fingers},\nkeywords={protein;  RNA binding protein;  zinc finger protein, animal;  article;  chemical structure;  chemistry;  genetics;  human;  metabolism;  protein binding;  protein secondary structure, Animals;  Humans;  Models, Molecular;  Protein Binding;  Protein Structure, Secondary;  Proteins;  RNA-Binding Proteins;  Zinc Fingers},\ncorrespondence_address1={Font, J.; School of Molecular Bioscience, , Sydney, NSW, Australia},\neditor={Mackay J.P., Segal D.J.},\nissn={10643745},\nisbn={9781607617525},\npubmed_id={20680853},\nlanguage={English},\nabbrev_source_title={Methods Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n AHSP (α-haemoglobin-stabilizing protein) stabilizes apo-α-haemoglobin in a partially folded state.\n \n \n \n \n\n\n \n Krishna Kumar, K.; Dickson, C.; Weiss, M.; Mackay, J.; and Gell, D.\n\n\n \n\n\n\n Biochemical Journal, 432(2): 275-282. 2010.\n cited By 13\n\n\n\n
\n\n\n\n \n \n $\"AHSP$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{KrishnaKumar2010275,\nauthor={Krishna Kumar, K. and Dickson, C.F. and Weiss, M.J. and Mackay, J.P. and Gell, D.A.},\ntitle={AHSP (α-haemoglobin-stabilizing protein) stabilizes apo-α-haemoglobin in a partially folded state},\njournal={Biochemical Journal},\nyear={2010},\nvolume={432},\nnumber={2},\npages={275-282},\ndoi={10.1042/BJ20100642},\nnote={cited By 13},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-78649597558&doi=10.1042%2fBJ20100642&partnerID=40&md5=a26a3073525115dc98a528be7dc1cc46},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Menzies Research Institute, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia; Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, United States},\nabstract={To produce functional Hb (haemoglobin), nascent α-globin (αo) and β-globin (βo) chains must each bind a single haem molecule (to form αh and βh) and interact together to form heterodimers.The precise sequence of binding events is unknown, and it has been suggested that additional factors might enhance the efficiency of Hb folding. AHSP (α-haemoglobin-stabilizing protein) has been shown previously to bind αh and regulate redox activity of the haem iron. In the present study, we used a combination of classical and dynamic light scattering and NMR spectroscopy to demonstrate that AHSP forms a heterodimeric complex with αo that inhibits αo aggregation and promotes αo folding in the absence of haem. These findings indicate that AHSP may function as an αo-specific chaperone, and suggest an important role for αo in guiding Hb assembly by stabilizing βo and inhibiting off-pathway self-association of βh. © The Authors Journal compilation © 2010 Biochemical Society.},\nauthor_keywords={α-haemoglobin-stabilizing protein (AHSP);  Aggregation;  Apo-α-haemoglobin;  Chaperone},\nkeywords={Aggregation;  Binding events;  Chaperone;  Folded state;  Haem iron;  Haemoglobins;  Heterodimeric complexes;  NMR spectroscopy;  Redox activity;  Self-associations, Hemoglobin;  Nuclear magnetic resonance spectroscopy;  Redox reactions, Association reactions, alpha hemoglobin stabilizing protein;  chaperone;  heme;  hemoglobin;  iron binding protein;  unclassified drug, alpha helix;  article;  complex formation;  dimerization;  iron binding capacity;  oxidation reduction reaction;  priority journal;  protein conformation;  protein denaturation;  protein folding;  protein stability;  protein tertiary structure;  thermostability, Apoproteins;  Blood Proteins;  Circular Dichroism;  Dimerization;  Drug Stability;  Hemoglobin A;  Hemoglobins;  Humans;  Models, Molecular;  Molecular Chaperones;  Peptide Fragments;  Protein Denaturation;  Protein Folding;  Protein Structure, Tertiary;  Protein Subunits;  Scattering, Radiation;  Solubility;  Thermodynamics},\ncorrespondence_address1={Gell, D. A.; Menzies Research Institute, 17 Liverpool Street, Hobart, TAS 7000, Australia; email: david.gell@utas.edu.au},\nissn={02646021},\ncoden={BIJOA},\npubmed_id={20860551},\nlanguage={English},\nabbrev_source_title={Biochem. J.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n 1H, 13C and 15N backbone and side chain resonance assignments of the N-terminal domain of the histidine kinase inhibitor KipI from Bacillus subtilis.\n \n \n \n \n\n\n \n Hynson, R.; Kwan, A.; Jacques, D.; MacKay, J.; and Trewhella, J.\n\n\n \n\n\n\n Biomolecular NMR Assignments, 4(2): 167-169. 2010.\n cited By 2\n\n\n\n
\n\n\n\n \n \n $\"1H,$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Hynson2010167,\nauthor={Hynson, R.M.G. and Kwan, A.H. and Jacques, D.A. and MacKay, J.P. and Trewhella, J.},\ntitle={1H, 13C and 15N backbone and side chain resonance assignments of the N-terminal domain of the histidine kinase inhibitor KipI from Bacillus subtilis},\njournal={Biomolecular NMR Assignments},\nyear={2010},\nvolume={4},\nnumber={2},\npages={167-169},\ndoi={10.1007/s12104-010-9237-6},\nnote={cited By 2},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77957942398&doi=10.1007%2fs12104-010-9237-6&partnerID=40&md5=b1821e37d36097295a9c990e9c38cf64},\naffiliation={School of Molecular Biosciences, University of Sydney, New South Wales 2006, Australia},\nabstract={KipI is a sporulation inhibitor in Bacillus subtilis which acts by binding to the dimerisation and histidine phosphotransfer (DHp) domain of KinA, the principle input kinase in the phosphorelay responsible for sporulation. The 15N, 13C and 1H chemical shift assignments of the N-terminal domain of KipI were determined using multidimensional, multinuclear NMR experiments. The N-terminal domain has two conformers and resonance assignments have been made for both conformers. © 2010 Springer Science+Business Media B.V.},\nauthor_keywords={Bacillus subtilis;  Bacterial signal transduction;  Histidine kinase inhibition;  KipI},\nkeywords={Bacillus subtilis;  Bacteria (microorganisms), bacterial protein;  carbon;  hydrogen;  nitrogen;  protein histidine kinase;  protein kinase;  protein-histidine kinase, article;  Bacillus subtilis;  chemistry;  metabolism;  nuclear magnetic resonance;  protein secondary structure;  protein tertiary structure, Bacillus subtilis;  Bacterial Proteins;  Carbon Isotopes;  Hydrogen;  Nitrogen Isotopes;  Nuclear Magnetic Resonance, Biomolecular;  Protein Kinases;  Protein Structure, Secondary;  Protein Structure, Tertiary},\ncorrespondence_address1={Hynson, R. M. G.; School of Molecular Biosciences, , New South Wales 2006, Australia; email: robert.hynson@sydney.edu.au},\nissn={18742718},\npubmed_id={20524093},\nlanguage={English},\nabbrev_source_title={Biomol. NMR Assignments},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n 1H, 15N and 13C assignments of an intramolecular Lmo2-LIM2/Ldb1-LID complex.\n \n \n \n \n\n\n \n Wilkinson-White, L.; Dastmalchi, S.; Kwan, A.; Ryan, D.; MacKay, J.; and Matthews, J.\n\n\n \n\n\n\n Biomolecular NMR Assignments, 4(2): 203-206. 2010.\n cited By 6\n\n\n\n
\n\n\n\n \n \n $\"1H,$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Wilkinson-White2010203,\nauthor={Wilkinson-White, L.E. and Dastmalchi, S. and Kwan, A.H. and Ryan, D.P. and MacKay, J.P. and Matthews, J.M.},\ntitle={1H, 15N and 13C assignments of an intramolecular Lmo2-LIM2/Ldb1-LID complex},\njournal={Biomolecular NMR Assignments},\nyear={2010},\nvolume={4},\nnumber={2},\npages={203-206},\ndoi={10.1007/s12104-010-9240-y},\nnote={cited By 6},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77957941346&doi=10.1007%2fs12104-010-9240-y&partnerID=40&md5=dbb84534513024589788d866ffb43c88},\naffiliation={School of Molecular Bioscience, Building G08, University of Sydney, Sydney, NSW 2006, Australia; School of Pharmacy, Biotechnology Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran; Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom},\nabstract={Lmo2 is a LIM-only protein involved in hematopoiesis and the development of T-cell acute lymphoblastic leukaemia. Here we report backbone and side chain NMR assignments for an engineered intramolecular complex of the C-terminal LIM domain from Lmo2 tethered to the LIM interaction domain (LID) from LIM domain binding protein 1 (Ldb1). © 2010 Springer Science+Business Media B.V.},\nauthor_keywords={Ldb1;  Leukaemia;  Lmo2;  NMR assignments},\nkeywords={carbon;  DNA binding protein;  hydrogen;  nitrogen;  transcription factor, amino acid sequence;  article;  chemistry;  metabolism;  molecular genetics;  nuclear magnetic resonance;  protein secondary structure;  protein tertiary structure, Amino Acid Sequence;  Carbon Isotopes;  DNA-Binding Proteins;  Hydrogen;  Molecular Sequence Data;  Nitrogen Isotopes;  Nuclear Magnetic Resonance, Biomolecular;  Protein Structure, Secondary;  Protein Structure, Tertiary;  Transcription Factors},\ncorrespondence_address1={Matthews, J. M.; School of Molecular Bioscience, , Sydney, NSW 2006, Australia; email: jacqui.matthews@sydney.edu.au},\nissn={18742718},\npubmed_id={20563763},\nlanguage={English},\nabbrev_source_title={Biomol. NMR Assignments},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Two-state conformational equilibrium in the Par-4 leucine zipper domain.\n \n \n \n \n\n\n \n Schwalbe, M.; Dutta, K.; Libich, D.; Venugopal, H.; Claridge, J.; Gell, D.; Mackay, J.; Edwards, P.; and Pascal, S.\n\n\n \n\n\n\n Proteins: Structure, Function and Bioinformatics, 78(11): 2433-2449. 2010.\n cited By 6\n\n\n\n
\n\n\n\n \n \n $\"Two-state$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Schwalbe20102433,\nauthor={Schwalbe, M. and Dutta, K. and Libich, D.S. and Venugopal, H. and Claridge, J.K. and Gell, D.A. and Mackay, J.P. and Edwards, P.J.B. and Pascal, S.M.},\ntitle={Two-state conformational equilibrium in the Par-4 leucine zipper domain},\njournal={Proteins: Structure, Function and Bioinformatics},\nyear={2010},\nvolume={78},\nnumber={11},\npages={2433-2449},\ndoi={10.1002/prot.22752},\nnote={cited By 6},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77955786914&doi=10.1002%2fprot.22752&partnerID=40&md5=b873f28445414250192257a247a1eb32},\naffiliation={Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Turitea Site, Private Bag 11222, Palmerston North 4442, New Zealand; New York Structural Biology Centre, 89 Convent Avenue, New York, NY 10027, United States; School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia},\nabstract={Prostate apoptosis response factor-4 (Par-4) is a pro-apoptotic and tumor-suppressive protein. A highly conserved heptad repeat sequence at the Par-4 C-terminus suggests the presence of a leucine zipper (LZ). This C-terminal region is essential for Par-4 self-association and interaction with various effector proteins. We have used nuclear magnetic resonance (NMR) spectroscopy to fully assign the chemical shift resonances of a peptide comprising the LZ domain of Par-4 at neutral pH. Further, we have investigated the properties of the Par-4 LZ domain and two point mutants under a variety of conditions using NMR, circular dichroism (CD), light scattering, and bioinformatics. Results indicate an environment-dependent conformational equilibrium between a partially ordered monomer (POM) and a predominantly coiled coil dimer (CCD). The combination of techniques used allows the time scales of the equilibrium to be probed and also helps to identify features of the amino acid sequence that may influence the equilibrium. © 2010 Wiley-Liss, Inc.},\nauthor_keywords={Circular dichroism;  Leucine zipper;  Prostate apoptosis response factor 4;  Solution NMR spectroscopy},\nkeywords={dimer;  leucine zipper protein;  monomer;  peptide;  prostate apoptosis response factor 4;  tumor suppressor protein;  unclassified drug;  apoptosis regulatory protein;  hybrid protein;  prostate apoptosis response-4 protein, amino acid sequence;  article;  basic leucine zipper motif;  bioinformatics;  circular dichroism;  conformation;  light scattering;  nuclear magnetic resonance spectroscopy;  pH;  point mutation;  priority journal;  proton nuclear magnetic resonance;  chemical structure;  chemistry;  Escherichia coli;  gel chromatography;  genetics;  light;  metabolism;  nuclear magnetic resonance;  protein conformation;  radiation scattering;  temperature, Apoptosis Regulatory Proteins;  Chromatography, Gel;  Circular Dichroism;  Escherichia coli;  Hydrogen-Ion Concentration;  Leucine Zippers;  Light;  Models, Molecular;  Nuclear Magnetic Resonance, Biomolecular;  Peptides;  Protein Conformation;  Recombinant Fusion Proteins;  Scattering, Radiation;  Temperature},\ncorrespondence_address1={Pascal, S. M.; Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Turitea Site, Private Bag 11222, Palmerston North 4442, New Zealand; email: s.pascal@massey.ac.nz},\npublisher={John Wiley and Sons Inc.},\nissn={08873585},\npubmed_id={20602362},\nlanguage={English},\nabbrev_source_title={Proteins Struct. Funct. Bioinformatics},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2009\n \n \n (8)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n It takes two to tango: The structure and function of LIM, RING, PHD and MYND domains.\n \n \n \n \n\n\n \n Matthews, J.; Bhati, M.; Lehtomaki, E.; Mansfield, R.; Cubeddu, L.; and Mackay, J.\n\n\n \n\n\n\n Current Pharmaceutical Design, 15(31): 3681-3696. 2009.\n cited By 64\n\n\n\n
\n\n\n\n \n \n $\"It$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Matthews20093681,\nauthor={Matthews, J.M. and Bhati, M. and Lehtomaki, E. and Mansfield, R.E. and Cubeddu, L. and Mackay, J.P.},\ntitle={It takes two to tango: The structure and function of LIM, RING, PHD and MYND domains},\njournal={Current Pharmaceutical Design},\nyear={2009},\nvolume={15},\nnumber={31},\npages={3681-3696},\ndoi={10.2174/138161209789271861},\nnote={cited By 64},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-70449558328&doi=10.2174%2f138161209789271861&partnerID=40&md5=45013714e3c397319d381cf6f7449752},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney NSW 2006, Australia},\nabstract={LIM (Lin-11, Isl-1, Mec-3), RING (Really interesting new gene), PHD (Plant homology domain) and MYND (myeloid, Nervy, DEAF-1) domains are all zinc-binding domains that ligate two zinc ions. Unlike the better known classical zinc fingers, these domains do not bind DNA, but instead mediate interactions with other proteins. LIM-domain containing proteins have diverse functions as regulators of gene expression, cell adhesion and motility and signal transduction. RING finger proteins are generally associated with ubiquitination; the presence of such a domain is the defining feature of a class of E3 ubiquitin protein ligases. PHD proteins have been associated with SUMOylation but most recently have emerged as a chromatin recognition motif that reads the methylation state of histones. The function of the MYND domain is less clear, but MYND domains are also found in proteins that have ubiquitin ligase and/or histone methyltransferase activity. Here we review the structure-function relationships for these domains and discuss strategies to modulate their activity. © 2009 Bentham Science Publishers Ltd.},\nkeywords={4 [4 (4' chloro 2 biphenylylmethyl) 1 piperazinyl] n [4 [3 dimethylamino 1 (phenylthiomethyl)propylamino] 3 nitrobenzenesulfonyl]benzamide;  BMI1 protein;  BRCA1 associated RING domain 1 protein;  breast cancer 1 protein;  deformed epidermal autoregulatory factor 1;  histone;  Islet 1 protein;  myeloid translocation protein 8;  Nervy protein;  phosphatidylinositide;  plant homology domain protein;  proline;  protein Lin 11;  protein MDM2;  protein Mec 3;  protein p53;  really interestining new gene domain protein;  RING finger protein 13;  Ring finger protein 1b;  scaffold protein;  ubiquitin protein ligase E3;  unclassified drug;  zinc binding protein, binding site;  carboxy terminal sequence;  DNA binding;  down regulation;  in vivo study;  malignant neoplastic disease;  molecular recognition;  mutagenesis;  nonhuman;  prediction;  priority journal;  protein binding;  protein function;  protein motif;  protein protein interaction;  protein structure;  review;  sequence homology;  signal transduction;  structure activity relation;  structure analysis, Animals;  Binding Sites;  DNA-Binding Proteins;  Homeodomain Proteins;  Humans;  Protein Conformation;  Protein Folding;  RING Finger Domains;  Sequence Homology, Amino Acid;  Zinc Fingers},\ncorrespondence_address1={Matthews, J. M.; School of Molecular and Microbial Biosciences, , Sydney NSW 2006, Australia; email: j.matthews@mmb.usyd.edu.au},\nissn={13816128},\ncoden={CPDEF},\npubmed_id={19925420},\nlanguage={English},\nabbrev_source_title={Curr. Pharm. Des.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n A cis-proline in α-hemoglobin stabilizing protein directs the structural reorganization of α-hemoglobin.\n \n \n \n \n\n\n \n Gell, D.; Feng, L.; Zhou, S.; Jeffrey, P.; Bendak, K.; Gow, A.; Weiss, M.; Shi, Y.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 284(43): 29462-29469. 2009.\n cited By 18\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Gell200929462,\nauthor={Gell, D.A. and Feng, L. and Zhou, S. and Jeffrey, P.D. and Bendak, K. and Gow, A. and Weiss, M.J. and Shi, Y. and Mackay, J.P.},\ntitle={A cis-proline in α-hemoglobin stabilizing protein directs the structural reorganization of α-hemoglobin},\njournal={Journal of Biological Chemistry},\nyear={2009},\nvolume={284},\nnumber={43},\npages={29462-29469},\ndoi={10.1074/jbc.M109.027045},\nnote={cited By 18},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-70350365377&doi=10.1074%2fjbc.M109.027045&partnerID=40&md5=e90a57ab2de87cb207496040ddd3eb37},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, United States; The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, United States; Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, United States},\nabstract={α-Hemoglobin (αHb) stabilizing protein (AHSP) is expressed in erythropoietic tissues as an accessory factor in hemoglobin synthesis. AHSP forms a specific complex with αHb and suppresses the heme-catalyzed evolution of reactive oxygen species by converting αHb to a conformation in which the heme is coordinated at both axial positions by histidine side chains (bis-histidyl coordination). Currently, the detailed mechanism by which AHSP induces structural changes in αHb has not been determined. Here, we present x-ray crystallography, NMR spectroscopy, and mutagenesis data that identify, for the first time, the importance of an evolutionarily conserved proline, Pro30, in loop 1 of AHSP. Mutation of Pro30 to a variety of residue types results in reduced ability to convert αHb. In complex with-Hb, AHSP Pro30 adopts a cis-peptidyl conformation and makes contact with the N terminus of helix G in αHb. Mutations that stabilize the cis-peptidyl conformation of free AHSP, also enhance the αHb conversion activity. These findings suggest that AHSP loop 1 can transmit structural changes to the heme pocket of αHb, and, more generally, highlight the importance of cis-peptidyl prolyl residues in defining the conformation of regulatory protein loops. © 2009 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Axial positions;  Heme pockets;  NMR spectroscopy;  Reactive oxygen species;  Regulatory protein;  Side chains;  Structural change;  Structural reorganization, Coordination reactions;  Nuclear magnetic resonance spectroscopy;  Oxygen;  Porphyrins;  X ray crystallography, Hemoglobin, alpha hemoglobin stabilizing protein;  binding protein;  hemoglobin A;  proline;  unclassified drug, amino acid sequence;  article;  complex formation;  conformational transition;  genetic conservation;  mutagenesis;  nuclear magnetic resonance spectroscopy;  priority journal;  protein function;  protein stability;  protein structure;  X ray crystallography, Blood Proteins;  Crystallography, X-Ray;  Hemoglobin A;  Humans;  Molecular Chaperones;  Mutation;  Nuclear Magnetic Resonance, Biomolecular;  Proline;  Protein Stability;  Protein Structure, Quaternary;  Protein Structure, Secondary;  Structure-Activity Relationship},\ncorrespondence_address1={Gell, D.A.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: dagell@mail.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={19706593},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Binding of the CHD4 PHD2 finger to histone H3 is modulated by covalent modifications.\n \n \n \n \n\n\n \n Musselman, C.; Mansfield, R.; Garske, A.; Davrazou, F.; Kwan, A.; Oliver, S.; O'Leary, H.; Denu, J.; Mackay, J.; and Kutateladze, T.\n\n\n \n\n\n\n Biochemical Journal, 423(2): 179-187. 2009.\n cited By 93\n\n\n\n
\n\n\n\n \n \n $\"Binding$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Musselman2009179,\nauthor={Musselman, C.A. and Mansfield, R.E. and Garske, A.L. and Davrazou, F. and Kwan, A.H. and Oliver, S.S. and O'Leary, H. and Denu, J.M. and Mackay, J.P. and Kutateladze, T.G.},\ntitle={Binding of the CHD4 PHD2 finger to histone H3 is modulated by covalent modifications},\njournal={Biochemical Journal},\nyear={2009},\nvolume={423},\nnumber={2},\npages={179-187},\ndoi={10.1042/BJ20090870},\nnote={cited By 93},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-70350115247&doi=10.1042%2fBJ20090870&partnerID=40&md5=d1fce430047477449a279813c42e1a2e},\naffiliation={Department of Pharmacology, School of Medicine, University of Colorado Denver, Aurora, CO 80045, United States; School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, United States},\nabstract={CHD4 (chromodomain helicase DNA-binding protein 4) ATPase is a major subunit of the repressive NuRD (nucleosome remodelling and deacetylase) complex, which is involved in transcriptional regulation and development. CHD4 contains two PHD (plant homeodomain) fingers of unknown function. Here we show that the second PHD finger (PHD2) of CHD4 recognizes the N-terminus of histone H3 and that this interaction is facilitated by acetylation ormethylation of Lys9 (H3K9ac and H3K9me respectively) but is inhibited by methylation of Lys4 (H3K4me) or acetylation of Ala1 (H3A1ac). An 18 μM binding affinity toward unmodified H3 rises to 0.6 μM for H3K9ac and to 0.9 μM for H3K9me3, whereas it drops to 2.0 mM for H3K4me3, as measured by tryptophan fluorescence and NMR. A peptide library screen further shows that phosphorylation of Thr3, Thr6 or Ser10 abolishes this interaction. A model of the PHD2-H3 complex, generated using a combination of NMR, data-driven docking and mutagenesis data, reveals an elongated site on the PHD2 surface where the H3 peptide is bound. Together our findings suggest that the PHD2 finger plays a role in targeting of the CHD4/NuRD complex to chromatin. © The Authors Journal compilation. © 2009 Biochemical Society.},\nauthor_keywords={Chromodomain helicase DNA-binding protein 4 (CHD4);  Histone;  Methylation;  Plant homeodomain (PHD)},\nkeywords={Binding affinities;  Chromodomain helicase DNA-binding protein 4 (CHD4);  Chromodomains;  Covalent modifications;  Data-driven;  Deacetylase;  DNA-binding protein;  Helicases;  Histone;  Histone H3;  Homeodomain;  Nucleosomes;  Peptide library;  Plant homeodomain (PHD);  Transcriptional regulation;  Tryptophan fluorescence, Acetylation;  Alkylation;  Amines;  Amino acids;  Binding energy;  DNA;  Methylation;  Nuclear magnetic resonance;  Nucleic acids;  Peptides, Genes, binding protein;  chromodomain helicase DNA binding protein 4;  histone H3;  plant homeodomain 2;  unclassified drug, acetylation;  amino terminal sequence;  article;  binding affinity;  binding site;  controlled study;  hydrophobicity;  immunoprecipitation;  methylation;  molecular docking;  mutagenesis;  nonhuman;  nuclear magnetic resonance;  priority journal;  protein binding;  protein function;  protein interaction;  protein phosphorylation;  protein processing, Acetylation;  Autoantigens;  Binding Sites;  Chromatin;  DNA Helicases;  Histone Acetyltransferases;  Histone-Lysine N-Methyltransferase;  Histones;  Homeodomain Proteins;  Humans;  Hydrophobic and Hydrophilic Interactions;  Methylation;  Mi-2 Nucleosome Remodeling and Deacetylase Complex;  Models, Biological;  Protein Binding;  Protein Structure, Tertiary;  Substrate Specificity},\ncorrespondence_address1={Kutateladze, T.G.; Department of Pharmacology, , Aurora, CO 80045, United States; email: tatiana.kutateladze@ucdenver.edu},\nissn={02646021},\ncoden={BIJOA},\npubmed_id={19624289},\nlanguage={English},\nabbrev_source_title={Biochem. J.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Conformational Stability and DNA Binding Specificity of the Cardiac T-Box Transcription Factor Tbx20.\n \n \n \n \n\n\n \n Macindoe, I.; Glockner, L.; Vukašin, P.; Stennard, F.; Costa, M.; Harvey, R.; Mackay, J.; and Sunde, M.\n\n\n \n\n\n\n Journal of Molecular Biology, 389(3): 606-618. 2009.\n cited By 22\n\n\n\n
\n\n\n\n \n \n $\"Conformational$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Macindoe2009606,\nauthor={Macindoe, I. and Glockner, L. and Vukašin, P. and Stennard, F.A. and Costa, M.W. and Harvey, R.P. and Mackay, J.P. and Sunde, M.},\ntitle={Conformational Stability and DNA Binding Specificity of the Cardiac T-Box Transcription Factor Tbx20},\njournal={Journal of Molecular Biology},\nyear={2009},\nvolume={389},\nnumber={3},\npages={606-618},\ndoi={10.1016/j.jmb.2009.04.056},\nnote={cited By 22},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-65649111564&doi=10.1016%2fj.jmb.2009.04.056&partnerID=40&md5=1162c2c4b4224777ee5cfa53503447e6},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculties of Medicine and Science, University of New South Wales, Kensington, NSW 2026, Australia},\nabstract={The transcription factor Tbx20 acts within a hierarchy of T-box factors in lineage specification and morphogenesis in the mammalian heart and is mutated in congenital heart disease. T-box family members share a ∼ 20-kDa DNA-binding domain termed the T-box. The question of how highly homologous T-box proteins achieve differential transcriptional control in heart development, while apparently binding to the same DNA sequence, remains unresolved. Here we show that the optimal DNA recognition sequence for the T-box of Tbx20 corresponds to a T-half-site. Furthermore, we demonstrate using purified recombinant domains that distinct T-boxes show significant differences in the affinity and kinetics of binding and in conformational stability, with the T-box of Tbx20 displaying molten globule character. Our data highlight unique features of Tbx20 and suggest mechanistic ways in which cardiac T-box factors might interact synergistically and/or competitively within the cardiac regulatory network. © 2009 Elsevier Ltd. All rights reserved.},\nauthor_keywords={DNA binding;  T-box;  T-site;  Tbx proteins;  transcription factor},\nkeywords={T box transcription factor;  transcription factor;  transcription factor TBX2;  transcription factor tbx20;  transcription factor TBX3;  transcription factor TBX5;  unclassified drug, article;  binding affinity;  binding competition;  congenital heart disease;  crystal structure;  DNA sequence;  gene mutation;  heart development;  molecular recognition;  priority journal;  protein conformation;  protein DNA binding;  protein domain;  protein secondary structure;  protein stability;  transcription regulation, Mammalia},\ncorrespondence_address1={Sunde, M.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: m.sunde@usyd.edu.au},\npublisher={Academic Press},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={19414016},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences.\n \n \n \n \n\n\n \n Loughlin, F.; Mansfield, R.; Vaz, P.; McGrath, A.; Setiyaputra, S.; Gamsjaeger, R.; Chen, E.; Morris, B.; Guss, J.; and Mackay, J.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 106(14): 5581-5586. 2009.\n cited By 57\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Loughlin20095581,\nauthor={Loughlin, F.E. and Mansfield, R.E. and Vaz, P.M. and McGrath, A.P. and Setiyaputra, S. and Gamsjaeger, R. and Chen, E.S. and Morris, B.J. and Guss, J.M. and Mackay, J.P.},\ntitle={The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2009},\nvolume={106},\nnumber={14},\npages={5581-5586},\ndoi={10.1073/pnas.0802466106},\nnote={cited By 57},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-65249133459&doi=10.1073%2fpnas.0802466106&partnerID=40&md5=698a9f6211fe20c6f2747b49bef7afc3},\naffiliation={School of Molecular and Microbial Biosciences, School of Medical Sciences, University of Sydney, Sydney NSW 2006, Australia},\nabstract={The alternative splicing of mRNA is a critical process in higher eukaryotes that generates substantial proteomic diversity. Many of the proteins that are essential to this process contain arginine/serine-rich (RS) domains. ZRANB2 is a widely-expressed and highly-conserved RS-domain protein that can regulate alternative splicing but lacks canonical RNA-binding domains. Instead, it contains 2 RanBP2-type zinc finger (ZnF) domains. We demonstrate that these ZnFs recognize ssRNA with high affinity and specificity. Each ZnF binds to a single AGGUAA motif and the 2 domains combine to recognize AGGUAA (Nx) AGGUAA double sites, suggesting that ZRANB2 regulates alternative splicing via a direct interaction with pre-mRNA at sites that resemble the consensus 5' splice site. We show using X-ray crystallography that recognition of an AGGUAA motif by a single ZnF is dominated by side-chain hydrogen bonds to the bases and formation of a guanine-tryptophan-guanine ''ladder.'' A number of other human proteins that function in RNA processing also contain RanBP2 ZnFs in which the RNA-binding residues of ZRANB2 are conserved. The ZnFs of ZRANB2 therefore define another class of RNA-binding domain, advancing our understanding of RNA recognition and emphasizing the versatility of domains in molecular recognition.},\nauthor_keywords={Protein structure;  RanBP2 zinc fingers;  RNA-binding proteins;  Splicing},\nkeywords={adenine;  guanine;  protein zranb2;  single stranded RNA;  tryptophan;  unclassified drug;  zinc finger protein, alternative RNA splicing;  article;  hydrogen bond;  priority journal;  protein binding;  protein domain;  protein motif;  protein RNA binding;  protein structure;  RNA binding;  RNA processing;  X ray crystallography, Amino Acid Sequence;  Binding Sites;  Humans;  Protein Structure, Tertiary;  RNA;  RNA Splice Sites;  RNA-Binding Proteins;  Zinc Fingers, Eukaryota},\ncorrespondence_address1={Mackay, J. P.; School of Molecular and Microbial Biosciences, , Sydney NSW 2006, Australia; email: j.mackay@usyd.edu.au},\nissn={00278424},\ncoden={PNASA},\npubmed_id={19304800},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Erratum: Structure and inhibition of orotidine 5#-Monophosphate decarboxylase from plasmodium falciparum (Biochemistry (2009) 48:11 (2570-2570) 10.1021/bi900043p).\n \n \n \n \n\n\n \n Langley, D.; Shojaei, M.; Chan, C.; Lok, H.; Mackay, J.; Traut, T.; Guss, J.; and Christopherson, R.\n\n\n \n\n\n\n Biochemistry, 48(11): 2570. 2009.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Erratum:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Langley20092570,\nauthor={Langley, D.B. and Shojaei, M. and Chan, C. and Lok, H.C. and Mackay, J.P. and Traut, T.W. and Guss, J.M. and Christopherson, R.I.},\ntitle={Erratum: Structure and inhibition of orotidine 5#-Monophosphate decarboxylase from plasmodium falciparum (Biochemistry (2009) 48:11 (2570-2570) 10.1021/bi900043p)},\njournal={Biochemistry},\nyear={2009},\nvolume={48},\nnumber={11},\npages={2570},\ndoi={10.1021/bi900043p},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-64849102261&doi=10.1021%2fbi900043p&partnerID=40&md5=59c1f16d2ad9d71e89d1902fdccfc5d8},\nkeywords={erratum;  error;  priority journal, Plasmodium falciparum},\nissn={00062960},\ncoden={BICHA},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Erratum},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structural analysis of MED-1 reveals unexpected diversity in the mechanism of DNA recognition by GATA-type zinc finger domains.\n \n \n \n \n\n\n \n Lowry, J.; Gamsjaeger, R.; Thong, S.; Hung, W.; Kwan, A.; Broitman-Maduro, G.; Matthews, J.; Maduro, M.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 284(9): 5827-5835. 2009.\n cited By 17\n\n\n\n
\n\n\n\n \n \n $\"Structural$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Lowry20095827,\nauthor={Lowry, J.A. and Gamsjaeger, R. and Thong, S.Y. and Hung, W. and Kwan, A.H. and Broitman-Maduro, G. and Matthews, J.M. and Maduro, M. and Mackay, J.P.},\ntitle={Structural analysis of MED-1 reveals unexpected diversity in the mechanism of DNA recognition by GATA-type zinc finger domains},\njournal={Journal of Biological Chemistry},\nyear={2009},\nvolume={284},\nnumber={9},\npages={5827-5835},\ndoi={10.1074/jbc.M808712200},\nnote={cited By 17},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-65549120319&doi=10.1074%2fjbc.M808712200&partnerID=40&md5=8c2a9f192f52f609c7e6a55967f01cb8},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Department of Biology, University of California, Riverside, CA 92521, United States},\nabstract={MED-1 is a member of a group of divergent GATA-type zinc finger proteins recently identified in several species of Caenorhabditis. The med genes are transcriptional regulators that are involved in the specification of the mesoderm and endoderm precursor cells in nematodes. Unlike other GATA-type zinc fingers that recognize the consensus sequence (A/C/ T)GATA(A/G), the MED-1 zinc finger (MED1zf) binds the larger and atypical site GTATACT(T/C)3. We have examined the basis for this unusual DNA specificity using a range of biochemical and biophysical approaches. Most strikingly, we show that although the core of the MED1zf structure is similar to that of GATA-1, the basic tail C-terminal to the zinc finger unexpectedly adopts an α-helical structure upon binding DNA. This additional helix appears to contact the major groove of the DNA, making contacts that explain the extended DNA consensus sequence observed for MED1zf. Our data expand the versatility of DNA recognition by GATA-type zinc fingers and perhaps shed new light on the DNA-binding properties of mammalian GATA factors. © 2009 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Caenorhabditis;  Consensus sequence;  DNA consensus sequence;  DNA recognition;  DNA-binding properties;  Helical structures;  Precursor cells;  Transcriptional regulator;  Zinc finger;  Zinc finger domains;  Zinc finger protein, Binding energy;  DNA;  Mammals;  Nucleic acids;  Structural analysis;  Zinc, Genes, palindromic DNA;  transcription factor GATA;  transcription factor MED 1;  unclassified drug;  zinc finger protein;  Caenorhabditis elegans protein;  DNA;  MED 1 protein, C elegans;  MED-1 protein, C elegans;  primer DNA;  transcription factor GATA 1;  zinc finger protein, alpha helix;  article;  binding affinity;  carboxy terminal sequence;  consensus sequence;  molecular recognition;  nonhuman;  priority journal;  protein DNA binding;  protein domain;  protein expression;  protein function;  protein structure;  structure analysis;  amino acid sequence;  animal;  calorimetry;  chemistry;  gel mobility shift assay;  genetics;  metabolism;  molecular genetics;  nuclear magnetic resonance spectroscopy;  sequence homology;  site directed mutagenesis;  surface plasmon resonance, Caenorhabditis;  Mammalia;  Nematoda, Amino Acid Sequence;  Animals;  Caenorhabditis elegans Proteins;  Calorimetry;  DNA;  DNA Primers;  Electrophoretic Mobility Shift Assay;  GATA Transcription Factors;  GATA1 Transcription Factor;  Magnetic Resonance Spectroscopy;  Molecular Sequence Data;  Mutagenesis, Site-Directed;  Sequence Homology, Amino Acid;  Surface Plasmon Resonance;  Zinc Fingers},\ncorrespondence_address1={Mackay, J.P.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.mackay@usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={19095651},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n A mass spectrometric investigation of the ability of metal complexes to modulate transcription factor activity.\n \n \n \n \n\n\n \n Talib, J.; Beck, J.; Urathamakul, T.; Nguyen, C.; Aldrich-Wright, J.; MacKay, J.; and Ralph, S.\n\n\n \n\n\n\n Chemical Communications, (37): 5546-5548. 2009.\n cited By 16\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Talib20095546,\nauthor={Talib, J. and Beck, J.L. and Urathamakul, T. and Nguyen, C.D. and Aldrich-Wright, J.R. and MacKay, J.P. and Ralph, S.F.},\ntitle={A mass spectrometric investigation of the ability of metal complexes to modulate transcription factor activity},\njournal={Chemical Communications},\nyear={2009},\nnumber={37},\npages={5546-5548},\ndoi={10.1039/b904751d},\nnote={cited By 16},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-70349267679&doi=10.1039%2fb904751d&partnerID=40&md5=5d6a3066741adcd7fef02f1b23d523a4},\naffiliation={School of Chemistry, University of Wollongong, Wollongong, NSW 2522, Australia; School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; School of Biomedical and Health Sciences, University of Western Sydney, Locked Bag 1797, Penrith South DC, NSW 1797, Australia},\nabstract={ESI mass spectrometry was used to assess the ability of metal complexes to inhibit binding of a transcription factor to a DNA molecule containing its recognition sequence. © 2009 The Royal Society of Chemistry.},\nkeywords={metal complex;  transcription factor, article;  complex formation;  electrospray mass spectrometry;  ionization;  molecular recognition;  protein DNA binding;  protein function},\ncorrespondence_address1={Ralph, S. F.; School of Chemistry, , Wollongong, NSW 2522, Australia; email: sralph@uow.edu.au},\npublisher={Royal Society of Chemistry},\nissn={13597345},\ncoden={CHCOF},\npubmed_id={19753352},\nlanguage={English},\nabbrev_source_title={Chem. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2008\n \n \n (11)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Crystallization of a ZRANB2-RNA complex.\n \n \n \n \n\n\n \n Loughlin, F.; Lee, M.; Guss, J.; and Mackay, J.\n\n\n \n\n\n\n Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 64(12): 1175-1177. 2008.\n cited By 2\n\n\n\n
\n\n\n\n \n \n $\"Crystallization$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Loughlin20081175,\nauthor={Loughlin, F.E. and Lee, M. and Guss, J.M. and Mackay, J.P.},\ntitle={Crystallization of a ZRANB2-RNA complex},\njournal={Acta Crystallographica Section F: Structural Biology and Crystallization Communications},\nyear={2008},\nvolume={64},\nnumber={12},\npages={1175-1177},\ndoi={10.1107/S1744309108036993},\nnote={cited By 2},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-57349100022&doi=10.1107%2fS1744309108036993&partnerID=40&md5=b9afecc28d908f4e2245b2f7837b60ce},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW, Australia},\nabstract={ZRANB2 is a zinc-finger protein that has been shown to influence alternative splice-site selection. The protein comprises a C-terminal arginine/serine-rich domain that interacts with spliceosomal proteins and two N-terminal RanBP2-type zinc fingers that have been implicated in RNA recognition. The second zinc finger bound to a six-nucleotide single-stranded RNA target sequence crystallized in the hexagonal space group P6522 or P6122, with unit-cell parameters a = 54.52, b = 54.52, c = 48.07 Å; the crystal contains one monomeric complex per asymmetric unit. This crystal form has a solvent content of 39% and diffracted to 1.4 Å resolution using synchrotron radiation. © International Union of Crystallography 2008.},\nauthor_keywords={RanBP2-type zinc fingers;  RNA-binding proteins;  Splicing factors},\nkeywords={RNA;  RNA binding protein;  ZRANB2 protein, human, article;  binding site;  chemistry;  crystallization;  genetics;  human;  metabolism;  molecular cloning;  X ray crystallography, Binding Sites;  Cloning, Molecular;  Crystallization;  Crystallography, X-Ray;  Humans;  RNA;  RNA-Binding Proteins},\ncorrespondence_address1={Mackay, J. P.; School of Molecular and Microbial Biosciences, , Sydney, NSW, Australia; email: j.mackay@usyd.edu.au},\nissn={17443091},\npubmed_id={19052380},\nlanguage={English},\nabbrev_source_title={Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The Cys3-Cys4 Loop of the Hydrophobin EAS Is Not Required for Rodlet Formation and Surface Activity.\n \n \n \n \n\n\n \n Kwan, A.; Macindoe, I.; Vukašin, P.; Morris, V.; Kass, I.; Gupte, R.; Mark, A.; Templeton, M.; Mackay, J.; and Sunde, M.\n\n\n \n\n\n\n Journal of Molecular Biology, 382(3): 708-720. 2008.\n cited By 55\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Kwan2008708,\nauthor={Kwan, A.H. and Macindoe, I. and Vukašin, P.V. and Morris, V.K. and Kass, I. and Gupte, R. and Mark, A.E. and Templeton, M.D. and Mackay, J.P. and Sunde, M.},\ntitle={The Cys3-Cys4 Loop of the Hydrophobin EAS Is Not Required for Rodlet Formation and Surface Activity},\njournal={Journal of Molecular Biology},\nyear={2008},\nvolume={382},\nnumber={3},\npages={708-720},\ndoi={10.1016/j.jmb.2008.07.034},\nnote={cited By 55},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-50149110926&doi=10.1016%2fj.jmb.2008.07.034&partnerID=40&md5=62ef7202e70f78be0e6f1db85719ff72},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; School of Molecular and Microbial Sciences, University of Queensland, St. Lucia, QLD 4072, Australia; The Horticulture and Food Research Institute of New Zealand, Mt. Albert Research Centre, Auckland, 1025, New Zealand},\nabstract={Class I hydrophobins are fungal proteins that self-assemble into robust amphipathic rodlet monolayers on the surface of aerial structures such as spores and fruiting bodies. These layers share many structural characteristics with amyloid fibrils and belong to the growing family of functional amyloid-like materials produced by microorganisms. Although the three-dimensional structure of the soluble monomeric form of a class I hydrophobin has been determined, little is known about the molecular structure of the rodlets or their assembly mechanism. Several models have been proposed, some of which suggest that the Cys3-Cys4 loop has a critical role in the initiation of assembly or in the polymeric structure. In order to provide insight into the relationship between hydrophobin sequence and rodlet assembly, we investigated the role of the Cys3-Cys4 loop in EAS, a class I hydrophobin from Neurospora crassa. Remarkably, deletion of up to 15 residues from this 25-residue loop does not impair rodlet formation or reduce the surface activity of the protein, and the physicochemical properties of rodlets formed by this mutant are indistinguishable from those of its full-length counterpart. In addition, the core structure of the truncation mutant is essentially unchanged. Molecular dynamics simulations carried out on the full-length protein and this truncation mutant binding to an air-water interface show that, although it is hydrophobic, the loop does not play a role in positioning the protein at the surface. These results demonstrate that the Cys3-Cys4 loop does not have an integral role in the formation or structure of the rodlets and that the major determinant of the unique properties of these proteins is the amphipathic core structure, which is likely to be preserved in all hydrophobins despite the high degree of sequence variation across the family. © 2008 Elsevier Ltd. All rights reserved.},\nauthor_keywords={amyloid;  assembly;  EAS;  hydrophobin;  rodlets},\nkeywords={cysteine;  hydrophobin;  protein eas;  unclassified drug, amino acid sequence;  article;  controlled study;  Neurospora crassa;  nonhuman;  nucleotide sequence;  priority journal;  protein assembly;  protein binding;  protein structure, Neurospora crassa},\ncorrespondence_address1={Sunde, M.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: m.sunde@mmb.usyd.edu.au},\npublisher={Academic Press},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={18674544},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structural analysis of hydrophobins.\n \n \n \n \n\n\n \n Sunde, M.; Kwan, A.; Templeton, M.; Beever, R.; and Mackay, J.\n\n\n \n\n\n\n Micron, 39(7): 773-784. 2008.\n cited By 172\n\n\n\n
\n\n\n\n \n \n $\"Structural$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Sunde2008773,\nauthor={Sunde, M. and Kwan, A.H.Y. and Templeton, M.D. and Beever, R.E. and Mackay, J.P.},\ntitle={Structural analysis of hydrophobins},\njournal={Micron},\nyear={2008},\nvolume={39},\nnumber={7},\npages={773-784},\ndoi={10.1016/j.micron.2007.08.003},\nnote={cited By 172},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-48749113989&doi=10.1016%2fj.micron.2007.08.003&partnerID=40&md5=2611fb5358515f43c0490587cec3ba81},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, 2006, Australia; The Horticultural and Food Research Institute of New Zealand, Mt Albert Research Centre, Auckland, New Zealand; Landcare Research, Tamaki Campus, Auckland, New Zealand},\nabstract={Hydrophobins are a remarkable class of small cysteine-rich proteins found exclusively in fungi. They self-assemble to form robust polymeric monolayers that are highly amphipathic and play numerous roles in fungal biology, such as in the formation and dispersal of aerial spores and in pathogenic and mutualistic interactions. The polymeric form can be reversibly disassembled and is able to reverse the wettability of a surface, leading to many proposals for nanotechnological applications over recent years. The surprising properties of hydrophobins and their potential for commercialization have led to substantial efforts to delineate their morphology and molecular structure. In this review, we summarize the progress that has been made using a variety of spectroscopic and microscopic approaches towards understanding the molecular mechanisms underlying hydrophobin structure. © 2007 Elsevier Ltd. All rights reserved.},\nauthor_keywords={Amphipathic;  Biofilm;  Hydrophobin;  Monolayer;  NMR;  Rodlet;  Self-assembly;  X-ray diffraction},\nkeywords={Photoresists;  Structural analysis, Amphipathic;  Biofilm;  Hydrophobin;  Hydrophobins;  Molecular mechanisms;  Monolayer;  NMR;  Polymeric monolayers;  Rodlet;  Self assembling;  Self-assembly;  To many;  X-ray diffraction, Quantum chemistry, fungal protein;  hydrophobin protein, fungal, chemistry;  fungus;  genetics;  growth, development and aging;  metabolism;  physiology;  protein conformation;  review, Fungal Proteins;  Fungi;  Protein Conformation, Bacteria (microorganisms);  Fungi},\ncorrespondence_address1={Mackay, J.P.; School of Molecular and Microbial Biosciences, , Sydney, 2006, Australia; email: j.mackay@mmb.usyd.edu.au},\nissn={09684328},\ncoden={MCONE},\npubmed_id={17875392},\nlanguage={English},\nabbrev_source_title={Micron},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n NMR spectroscopy as a tool for the rapid assessment of the conformation of GST-fusion proteins.\n \n \n \n \n\n\n \n Chu, K.; Gamsjaeger, R.; Mansfield, R.; and Mackay, J.\n\n\n \n\n\n\n Protein Science, 17(9): 1630-1635. 2008.\n cited By 9\n\n\n\n
\n\n\n\n \n \n $\"NMR$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Chu20081630,\nauthor={Chu, K.L. and Gamsjaeger, R. and Mansfield, R.E. and Mackay, J.P.},\ntitle={NMR spectroscopy as a tool for the rapid assessment of the conformation of GST-fusion proteins},\njournal={Protein Science},\nyear={2008},\nvolume={17},\nnumber={9},\npages={1630-1635},\ndoi={10.1110/ps.034983.108},\nnote={cited By 9},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-50049088243&doi=10.1110%2fps.034983.108&partnerID=40&md5=a3583ec1f45c3ba84371ae9424183663},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; School of Molecular and Microbial Biosciences, Building G08, University of Sydney, Maze Crescent, Sydney, NSW 2006, Australia},\nabstract={Glutathione-S-transferase (GST)-fusion proteins are used extensively for structural, biochemical, and functional analyses. Although the conformation of the target protein is of critical importance, confirmation of the folded state of the target is often not undertaken or is cumbersome because of the requirement to first remove the GST tag. Here, we demonstrate that it is possible to record conventional 15N-HSQC NMR spectra of small GST-fusion proteins and that the observed signals arise almost exclusively from the target protein. This approach constitutes a rapid and straightforward means of assessing the conformation of a GST-fusion protein without having to cleave the GST and should prove valuable, both to biochemists seeking to check the conformation of their proteins prior to functional studies and to structural biologists screening protein constructs for suitability as targets for structural studies. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 The Protein Society.},\nauthor_keywords={GST fusion;  GST pulldown;  NMR spectroscopy;  Protein conformation},\nkeywords={glutathione transferase;  hybrid protein, article;  chemical analysis;  nitrogen nuclear magnetic resonance;  nuclear magnetic resonance spectroscopy;  priority journal;  protein analysis;  protein conformation;  protein expression;  protein purification;  protein structure;  screening, Animals;  Buffers;  Caenorhabditis elegans Proteins;  Dimerization;  Evaluation Studies as Topic;  Glutathione Transferase;  Molecular Weight;  Nuclear Magnetic Resonance, Biomolecular;  Protein Conformation;  Protein Structure, Tertiary;  Recombinant Fusion Proteins;  Time Factors},\ncorrespondence_address1={Chu, K. L.; School of Molecular and Microbial Biosciences, Maze Crescent, Sydney, NSW 2006, Australia; email: ckliew@mmb.usyd.edu.au},\nissn={09618368},\ncoden={PRCIE},\npubmed_id={18556474},\nlanguage={English},\nabbrev_source_title={Protein Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Designed metal-binding sites in biomolecular and bioinorganic interactions.\n \n \n \n \n\n\n \n Matthews, J.; Loughlin, F.; and Mackay, J.\n\n\n \n\n\n\n Current Opinion in Structural Biology, 18(4): 484-490. 2008.\n cited By 26\n\n\n\n
\n\n\n\n \n \n $\"Designed$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Matthews2008484,\nauthor={Matthews, J.M. and Loughlin, F.E. and Mackay, J.P.},\ntitle={Designed metal-binding sites in biomolecular and bioinorganic interactions},\njournal={Current Opinion in Structural Biology},\nyear={2008},\nvolume={18},\nnumber={4},\npages={484-490},\ndoi={10.1016/j.sbi.2008.04.009},\nnote={cited By 26},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-49549085951&doi=10.1016%2fj.sbi.2008.04.009&partnerID=40&md5=8b9db32a28900e07dc27a30c69cc3f28},\naffiliation={School of Molecular and Microbial Biosciences, The University of Sydney, NSW 2006, Australia},\nabstract={The design of metal-binding functionality in proteins is expanding into many different areas with a wide range of practical and research applications. Here we review several developing areas of metal-related protein design, including the use of metals to induce protein-protein interactions or facilitate the assembly of extended nanostructures; the design of metallopeptides that bind metal and other inorganic surfaces, an area with potential in diverse applications ranging from nanoelectronics and photonics to biotechnology and biomedicine; and, the creation of sensitive and selective metal sensors for use both in vivo and in vitro. © 2008 Elsevier Ltd. All rights reserved.},\nkeywords={cupric ion;  inorganic compound;  metal;  metal ion;  nanomaterial;  zinc, biomedicine;  biosensor;  biotechnology;  in vitro study;  in vivo study;  metal binding;  molecular interaction;  nonhuman;  priority journal;  protein assembly;  protein function;  protein protein interaction;  protein structure;  review, Binding Sites;  Metals;  Models, Molecular;  Proteins},\ncorrespondence_address1={Matthews, J.M.; School of Molecular and Microbial Biosciences, , NSW 2006, Australia; email: j.matthews@usyd.edu.au},\nissn={0959440X},\ncoden={COSBE},\npubmed_id={18554898},\nlanguage={English},\nabbrev_source_title={Curr. Opin. Struct. Biol.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Implementing the LIM code: The structural basis for cell type-specific assembly of LIM-homeodomain complexes.\n \n \n \n \n\n\n \n Bhati, M.; Lee, C.; Nancarrow, A.; Lee, M.; Craig, V.; Bach, I.; Guss, J.; Mackay, J.; and Matthews, J.\n\n\n \n\n\n\n EMBO Journal, 27(14): 2018-2029. 2008.\n cited By 62\n\n\n\n
\n\n\n\n \n \n $\"Implementing$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Bhati20082018,\nauthor={Bhati, M. and Lee, C. and Nancarrow, A.L. and Lee, M. and Craig, V.J. and Bach, I. and Guss, J.M. and Mackay, J.P. and Matthews, J.M.},\ntitle={Implementing the LIM code: The structural basis for cell type-specific assembly of LIM-homeodomain complexes},\njournal={EMBO Journal},\nyear={2008},\nvolume={27},\nnumber={14},\npages={2018-2029},\ndoi={10.1038/emboj.2008.123},\nnote={cited By 62},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-47949099570&doi=10.1038%2femboj.2008.123&partnerID=40&md5=ffc6a986d0bc3cb909bcf9d16e78eb13},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW, Australia; Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States; School of Molecular and Microbial Biosciences, University of Sydney, Darlinghurst, NSW 2006, Australia},\nabstract={LIM-homeodomain (LIM-HD) transcription factors form a combinatorial 'LIM code' that contributes to the specification of cell types. In the ventral spinal cord, the binary LIM homeobox protein 3 (Lhx3)/LIM domain-binding protein 1 (Ldb1) complex specifies the formation of V2 interneurons. The additional expression of islet-1 (Isl1) in adjacent cells instead specifies the formation of motor neurons through assembly of a ternary complex in which Isl1 contacts both Lhx3 and Ldb1, displacing Lhx3 as the binding partner of Ldb1. However, little is known about how this molecular switch occurs. Here, we have identified the 30-residue Lhx3-binding domain on Isl1 (Isl1LBD). Although the LIM interaction domain of Ldb1 (Ldb1LID) and Isl1LBD share low levels of sequence homology, X-ray and NMR structures reveal that they bind Lhx3 in an identical manner, that is, Isl1LBD mimics Ldb1 LID. These data provide a structural basis for the formation of cell type-specific protein-protein interactions in which unstructured linear motifs with diverse sequences compete to bind protein partners. The resulting alternate protein complexes can target different genes to regulate key biological events. ©2008 European Molecular Biology Organization.},\nauthor_keywords={Cell specification;  Competitive binding;  LIM code;  LIM homeodomain proteins;  Protein complexes},\nkeywords={transcription factor LHX3, article;  cell structure;  cell type;  interneuron;  motoneuron;  nuclear magnetic resonance;  priority journal;  protein binding;  protein protein interaction;  sequence homology;  X ray analysis, Crystallography, X-Ray;  DNA-Binding Proteins;  Homeodomain Proteins;  Humans;  Models, Molecular;  Mutagenesis;  Nuclear Magnetic Resonance, Biomolecular;  Protein Interaction Domains and Motifs;  Thermodynamics;  Two-Hybrid System Techniques},\ncorrespondence_address1={Matthews, J. M.; School of Molecular and Microbial Biosciences, , Darlinghurst, NSW 2006, Australia; email: j.matthews@usyd.edu.au},\nissn={02614189},\ncoden={EMJOD},\npubmed_id={18583962},\nlanguage={English},\nabbrev_source_title={EMBO J.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Evolution of Quaternary Structure in a Homotetrameric Enzyme.\n \n \n \n \n\n\n \n Griffin, M.; Dobson, R.; Pearce, F.; Antonio, L.; Whitten, A.; Liew, C.; Mackay, J.; Trewhella, J.; Jameson, G.; Perugini, M.; and Gerrard, J.\n\n\n \n\n\n\n Journal of Molecular Biology, 380(4): 691-703. 2008.\n cited By 67\n\n\n\n
\n\n\n\n \n \n $\"Evolution$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Griffin2008691,\nauthor={Griffin, M.D.W. and Dobson, R.C.J. and Pearce, F.G. and Antonio, L. and Whitten, A.E. and Liew, C.K. and Mackay, J.P. and Trewhella, J. and Jameson, G.B. and Perugini, M.A. and Gerrard, J.A.},\ntitle={Evolution of Quaternary Structure in a Homotetrameric Enzyme},\njournal={Journal of Molecular Biology},\nyear={2008},\nvolume={380},\nnumber={4},\npages={691-703},\ndoi={10.1016/j.jmb.2008.05.038},\nnote={cited By 67},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-45549122274&doi=10.1016%2fj.jmb.2008.05.038&partnerID=40&md5=856f55c7914b27d6f5fcfca0b9ce7b65},\naffiliation={School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand; Department of Biochemistry, Molecular Biology Department, Bio21 Molecular Science and Biotechnology Institute, Parkville, Vic. 3010, Australia; Bragg Institute, Australian Nuclear Science and Technology Organisation, NSW 2234, Australia; School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia; Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand},\nabstract={Dihydrodipicolinate synthase (DHDPS) is an essential enzyme in (S)-lysine biosynthesis and an important antibiotic target. All X-ray crystal structures solved to date reveal a homotetrameric enzyme. In order to explore the role of this quaternary structure, dimeric variants of Escherichia coli DHDPS were engineered and their properties were compared to those of the wild-type tetrameric form. X-ray crystallography reveals that the active site is not disturbed when the quaternary structure is disrupted. However, the activity of the dimeric enzymes in solution is substantially reduced, and a tetrahedral adduct of a substrate analogue is observed to be trapped at the active site in the crystal form. Remarkably, heating the dimeric enzymes increases activity. We propose that the homotetrameric structure of DHDPS reduces dynamic fluctuations present in the dimeric forms and increases specificity for the first substrate, pyruvate. By restricting motion in a key catalytic motif, a competing, non-productive reaction with a substrate analogue is avoided. Small-angle X-ray scattering and mutagenesis data, together with a B-factor analysis of the crystal structures, support this hypothesis and lead to the suggestion that in at least some cases, the evolution of quaternary enzyme structures might serve to optimise the dynamic properties of the protein subunits. © 2008 Elsevier Ltd. All rights reserved.},\nauthor_keywords={DHDPS;  dihydrodipicolinate synthase;  enzyme dynamics;  quaternary structure},\nkeywords={dihydrodipicolinate synthase;  enzyme;  pyruvic acid, article;  crystal structure;  enzyme activity;  enzyme engineering;  factorial analysis;  heating;  mutagenesis;  nonhuman;  nucleotide sequence;  priority journal;  protein quaternary structure;  radiation scattering;  X ray crystallography, Escherichia coli},\ncorrespondence_address1={Gerrard, J.A.; School of Biological Sciences, , Christchurch, 8140, New Zealand; email: juliet.gerrard@canterbury.ac.nz},\npublisher={Academic Press},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={18556019},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Response to Chatr-aryamontri et al.: Protein interactions: to believe or not to believe?.\n \n \n \n \n\n\n \n Mackay, J.; Sunde, M.; Lowry, J.; Crossley, M.; and Matthews, J.\n\n\n \n\n\n\n Trends in Biochemical Sciences, 33(6): 242-243. 2008.\n cited By 9\n\n\n\n
\n\n\n\n \n \n $\"Response$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mackay2008242,\nauthor={Mackay, J.P. and Sunde, M. and Lowry, J.A. and Crossley, M. and Matthews, J.M.},\ntitle={Response to Chatr-aryamontri et al.: Protein interactions: to believe or not to believe?},\njournal={Trends in Biochemical Sciences},\nyear={2008},\nvolume={33},\nnumber={6},\npages={242-243},\ndoi={10.1016/j.tibs.2008.04.003},\nnote={cited By 9},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-44749093208&doi=10.1016%2fj.tibs.2008.04.003&partnerID=40&md5=4b964d56dc1a36bb79f20d8cf979b5b2},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia},\nkeywords={amino acid sequence;  cell lysate;  data base;  filtration;  human;  immunoprecipitation;  letter;  molecular interaction;  priority journal;  protein interaction},\ncorrespondence_address1={Mackay, J.P.; School of Molecular and Microbial Biosciences, , NSW 2006, Australia; email: j.mackay@mmb.usyd.edu.au},\nissn={09680004},\ncoden={TBSCD},\nlanguage={English},\nabbrev_source_title={Trends Biochem. Sci.},\ndocument_type={Letter},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Escherichia coli glucuronylsynthase: An engineered enzyme for the synthesis of β-glucuronides.\n \n \n \n \n\n\n \n Wilkinson, S.; Liew, C.; Mackay, J.; Salleh, H.; Withers, S.; and McLeod, M.\n\n\n \n\n\n\n Organic Letters, 10(8): 1585-1588. 2008.\n cited By 30\n\n\n\n
\n\n\n\n \n \n $\"Escherichia$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Wilkinson20081585,\nauthor={Wilkinson, S.M. and Liew, C.W. and Mackay, J.P. and Salleh, H.M. and Withers, S.G. and McLeod, M.D.},\ntitle={Escherichia coli glucuronylsynthase: An engineered enzyme for the synthesis of β-glucuronides},\njournal={Organic Letters},\nyear={2008},\nvolume={10},\nnumber={8},\npages={1585-1588},\ndoi={10.1021/ol8002767},\nnote={cited By 30},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-44449175733&doi=10.1021%2fol8002767&partnerID=40&md5=ecc5e94d95cd07261dbe3f07751e87c7},\naffiliation={School of Chemistry, University of Sydney, NSW 2006, Australia; Australian National University, Canberra, ACT 0200, Australia; School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia; Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; Department of Biotechnology Engineering, International Islamic University Malaysia, Kuala Lumpur, 53100, Malaysia},\nabstract={The glycosynthase derived from E. coli β-glucuronidase catalyzes the glucuronylation of a range of primary, secondary, and aryl alcohols with moderate to excellent yields. The procedure provides an efficient, stereoselective, and scalable single-step synthesis of β-glucuronides under mild conditions. © 2008 American Chemical Society.},\nkeywords={glucuronide;  glucuronosyltransferase, article;  biosynthesis;  chemistry;  enzymology;  Escherichia coli;  metabolism;  protein engineering, Escherichia coli;  Glucuronides;  Glucuronosyltransferase;  Protein Engineering},\ncorrespondence_address1={McLeod, M. D.; School of Chemistry, , NSW 2006, Australia; email: m.mcleod@rsc.anu.edu.au},\nissn={15237060},\npubmed_id={18345681},\nlanguage={English},\nabbrev_source_title={Org. Lett.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structure and inhibition of orotidine 5′-monophosphate decarboxylase from Plasmodium falciparum.\n \n \n \n \n\n\n \n Langley, D.; Shojaei, M.; Chan, C.; Hiu, C.; Mackay, J.; Traut, T.; Guss, J.; and Christopherson, R.\n\n\n \n\n\n\n Biochemistry, 47(12): 3842-3854. 2008.\n cited By 18\n\n\n\n
\n\n\n\n \n \n $\"Structure$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Langley20083842,\nauthor={Langley, D.B. and Shojaei, M. and Chan, C. and Hiu, C.L. and Mackay, J.P. and Traut, T.W. and Guss, J.M. and Christopherson, R.I.},\ntitle={Structure and inhibition of orotidine 5′-monophosphate decarboxylase from Plasmodium falciparum},\njournal={Biochemistry},\nyear={2008},\nvolume={47},\nnumber={12},\npages={3842-3854},\ndoi={10.1021/bi702390k},\nnote={cited By 18},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-41149088218&doi=10.1021%2fbi702390k&partnerID=40&md5=348de5c6236f102d5821be25d8a12c9d},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260, United States; Natural Sciences Department, Tabriz University, Tabriz, Iran},\nabstract={Orotidine 5′-monophosphate (OMP) decarboxylase from Plasmodium falciparum (PfODCase, EC 4.1.1.23) has been overexpressed, purified, subjected to kinetic and biochemical analysis, and crystallized. The native enzyme is a homodimer with a subunit molecular mass of 38 kDa. The saturation curve for OMP as a substrate conformed to Michaelis-Menten kinetics with Km = 350 ± 60 nM and Vmax = 2.70 ± 0.10 μmol/min/mg protein. Inhibition patterns for nucleoside 5′-monophosphate analogues were linear competitive with respect to OMP with a decreasing potency of inhibition of PfODCase in the order: pyrazofurin 5′-monophosphate (Ki = 3.6 ± 0.7 nM) &gt; xanthosine 5′-monophosphate (XMP, Ki = 4.4 ± 0.7 nM) &gt; 6-azauridine 5′-monophosphate (AzaUMP, K i = 12 ±3 nM) &gt; allopurinol-3-riboside 5′- monophosphate (Ki = 240 ± 20 nM). XMP is an ∼150-fold more potent inhibitor of PfODCase compared with the human enzyme. The structure of PfODCase was solved in the absence of ligand and displays a classic TIM-barrel fold characteristic of the enzyme. Both the phosphate-binding loop and the βα5-loop have conformational flexibility, which may be associated with substrate capture and product release along the reaction pathway. © 2008 American Chemical Society.},\nkeywords={Biochemistry;  Biodiversity;  Chemical analysis;  Conformations, Inhibition patterns;  Michaelis-Menten kinetics;  Plasmodium falciparum, Enzyme inhibition, orotidine 5' phosphate decarboxylase, article;  controlled study;  enzyme conformation;  enzyme inhibition;  enzyme structure;  enzyme substrate;  gene overexpression;  Michaelis Menten kinetics;  molecular weight;  nonhuman;  Plasmodium falciparum;  priority journal;  protein analysis;  protein folding;  protein purification, Animals;  Binding Sites;  Crystallization;  Crystallography, X-Ray;  Dimerization;  Escherichia coli;  Humans;  Kinetics;  Models, Molecular;  Molecular Weight;  Orotidine-5'-Phosphate Decarboxylase;  Plasmodium falciparum;  Recombinant Proteins;  Ribonucleotides;  Species Specificity;  Uridine Monophosphate, Plasmodium falciparum},\ncorrespondence_address1={Christopherson, R. I.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: ric@mmb.usyd.edu.au},\nissn={00062960},\ncoden={BICHA},\npubmed_id={18303855},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structural and biophysical analysis of the DNA binding properties of myelin transcription factor 1.\n \n \n \n \n\n\n \n Gamsjaeger, R.; Swanton, M.; Kobus, F.; Lehtomaki, E.; Lowry, J.; Kwan, A.; Matthews, J.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 283(8): 5158-5167. 2008.\n cited By 27\n\n\n\n
\n\n\n\n \n \n $\"Structural$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Gamsjaeger20085158,\nauthor={Gamsjaeger, R. and Swanton, M.K. and Kobus, F.J. and Lehtomaki, E. and Lowry, J.A. and Kwan, A.H. and Matthews, J.M. and Mackay, J.P.},\ntitle={Structural and biophysical analysis of the DNA binding properties of myelin transcription factor 1},\njournal={Journal of Biological Chemistry},\nyear={2008},\nvolume={283},\nnumber={8},\npages={5158-5167},\ndoi={10.1074/jbc.M703772200},\nnote={cited By 27},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-41949138538&doi=10.1074%2fjbc.M703772200&partnerID=40&md5=daab15a0bf3a50a896c89930c61db02d},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Building G08, Sydney, NSW 2006, Australia},\nabstract={Zinc binding domains, or zinc fingers (ZnFs), form one of the most numerous and most diverse superclasses of protein structural motifs in eukaryotes. Although our understanding of the functions of several classes of these domains is relatively well developed, we know much less about the molecular mechanisms of action of many others. Myelin transcription factor 1 (MyT1) type ZnFs are found in organisms as diverse as nematodes and mammals and are found in a range of sequence contexts. MyT1, one of the early transcription factors expressed in the developing central nervous system, contains seven MyT1 ZnFs that are very highly conserved both within the protein and between species. We have used a range of biophysical techniques, including NMR spectroscopy and data-driven macromolecular docking, to investigate the structural basis for the interaction between MyT1 ZnFs and DNA. Our data indicate that MyT1 ZnFs recognize the major groove of DNA in a way that appears to differ from other known zinc binding domains. © 2008 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Binding energy;  DNA;  Genes;  Mammals;  Nuclear magnetic resonance;  Nuclear magnetic resonance spectroscopy;  Nucleic acids;  Organic acids;  Proteins;  Transcription factors;  Zinc, Biophysical analyses;  Biophysical techniques;  Central nervous systems;  Dna bindings;  Do-mains;  Major grooves;  Molecular mechanisms;  Nmr spectroscopies;  Protein structural motifs;  Structural bases;  Zinc bindings;  Zinc fingers, Transcription, double stranded DNA;  myelin transcription factor 1;  unclassified drug;  zinc finger protein;  DNA;  DNA binding protein;  Myt1 protein, mouse;  transcription factor, article;  binding affinity;  DNA binding;  hydrophobicity;  isothermal titration calorimetry;  nuclear magnetic resonance;  priority journal;  protein analysis;  protein domain;  protein interaction;  protein structure;  surface plasmon resonance;  zinc finger motif;  animal;  central nervous system;  chemical structure;  chemistry;  metabolism;  mouse;  nematode;  physiology;  prenatal development;  protein binding;  structure activity relation, Eukaryota;  Mammalia;  Nematoda, Animals;  Central Nervous System;  DNA;  DNA-Binding Proteins;  Mice;  Models, Molecular;  Nematoda;  Nuclear Magnetic Resonance, Biomolecular;  Protein Binding;  Structure-Activity Relationship;  Transcription Factors;  Zinc Fingers},\ncorrespondence_address1={Mackay, J. P.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.mackay@mmb.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={18073212},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2007\n \n \n (7)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation.\n \n \n \n \n\n\n \n Porter, C.; Matthews, J.; Mackay, J.; Pursglove, S.; Schmidberger, J.; Leedman, P.; Pero, S.; Krag, D.; Wilce, M.; and Wilce, J.\n\n\n \n\n\n\n BMC Structural Biology, 7. 2007.\n cited By 40\n\n\n\n
\n\n\n\n \n \n $\"Grb7$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Porter2007,\nauthor={Porter, C.J. and Matthews, J.M. and Mackay, J.P. and Pursglove, S.E. and Schmidberger, J.W. and Leedman, P.J. and Pero, S.C. and Krag, D.N. and Wilce, M.C.J. and Wilce, J.A.},\ntitle={Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation},\njournal={BMC Structural Biology},\nyear={2007},\nvolume={7},\ndoi={10.1186/1472-6807-7-58},\nart_number={58},\nnote={cited By 40},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-37449002863&doi=10.1186%2f1472-6807-7-58&partnerID=40&md5=89564d6657b26abf735883aa35af0edc},\naffiliation={School of Biomedical and Chemical Sciences, University of Western Australia, WA 6009, Australia; Department of Biochemistry and Microbiology, University of Sydney, NSW 2006, Australia; Western Australian Institute of Medical Research, WA 6000, Australia; Department of Surgery, Vermont Cancer Center, University of Vermont, Burlington, VT, United States; Department of Biochemistry and Molecular Biology, Monash University, Vic. 3800, Australia},\nabstract={Background. Human growth factor receptor bound protein 7 (Grb7) is an adapter protein that mediates the coupling of tyrosine kinases with their downstream signaling pathways. Grb7 is frequently overexpressed in invasive and metastatic human cancers and is implicated in cancer progression via its interaction with the ErbB2 receptor and focal adhesion kinase (FAK) that play critical roles in cell proliferation and migration. It is thus a prime target for the development of novel anti-cancer therapies. Recently, an inhibitory peptide (G7-18NATE) has been developed which binds specifically to the Grb7 SH2 domain and is able to attenuate cancer cell proliferation and migration in various cancer cell lines. Results. As a first step towards understanding how Grb7 may be inhibited by G7-18NATE, we solved the crystal structure of the Grb7 SH2 domain to 2.1 Å resolution. We describe the details of the peptide binding site underlying target specificity, as well as the dimer interface of Grb 7 SH2. Dimer formation of Grb7 was determined to be in the μM range using analytical ultracentrifugation for both full-length Grb7 and the SH2 domain alone, suggesting the SH2 domain forms the basis of a physiological dimer. ITC measurements of the interaction of the G7-18NATE peptide with the Grb7 SH2 domain revealed that it binds with a binding affinity of Kd= ∼35.7 μM and NMR spectroscopy titration experiments revealed that peptide binding causes perturbations to both the ligand binding surface of the Grb7 SH2 domain as well as to the dimer interface, suggesting that dimerisation of Grb7 is impacted on by peptide binding. Conclusion. Together the data allow us to propose a model of the Grb7 SH2 domain/G7-18NATE interaction and to rationalize the basis for the observed binding specificity and affinity. We propose that the current study will assist with the development of second generation Grb7 SH2 domain inhibitors, potentially leading to novel inhibitors of cancer cell migration and invasion. © 2007 Porter et al; licensee BioMed Central Ltd.},\nkeywords={cyclopeptide;  dimer;  growth factor receptor bound protein 7;  protein inhibitor;  protein SH2;  cyclopeptide;  GRB7 protein, human;  growth factor receptor bound protein 7;  ligand;  unclassified drug, article;  binding affinity;  binding site;  cancer cell;  cancer growth;  cancer invasion;  cell migration;  cell proliferation;  crystal structure;  dimerization;  drug specificity;  human;  human cell;  ligand binding;  molecular model;  nuclear magnetic resonance spectroscopy;  protein binding;  protein domain;  protein interaction;  protein structure;  ultracentrifugation;  amino acid sequence;  cell motion;  cell proliferation;  chemical structure;  chemistry;  drug antagonism;  drug effect;  molecular genetics;  neoplasm;  nuclear magnetic resonance;  pathology;  protein conformation;  sequence homology;  Src homology domain;  X ray crystallography, Amino Acid Sequence;  Cell Movement;  Cell Proliferation;  Crystallography, X-Ray;  Dimerization;  GRB7 Adaptor Protein;  Ligands;  Models, Molecular;  Molecular Sequence Data;  Neoplasms;  Nuclear Magnetic Resonance, Biomolecular;  Peptides, Cyclic;  Protein Conformation;  Sequence Homology, Amino Acid;  src Homology Domains},\ncorrespondence_address1={Wilce, J.A.; Department of Biochemistry and Molecular Biology, , Vic. 3800, Australia; email: jackie.wilce@med.monash.edu.au},\nissn={14726807},\npubmed_id={17894853},\nlanguage={English},\nabbrev_source_title={BMC Struct. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n

\n Background. Human growth factor receptor bound protein 7 (Grb7) is an adapter protein that mediates the coupling of tyrosine kinases with their downstream signaling pathways. Grb7 is frequently overexpressed in invasive and metastatic human cancers and is implicated in cancer progression via its interaction with the ErbB2 receptor and focal adhesion kinase (FAK) that play critical roles in cell proliferation and migration. It is thus a prime target for the development of novel anti-cancer therapies. Recently, an inhibitory peptide (G7-18NATE) has been developed which binds specifically to the Grb7 SH2 domain and is able to attenuate cancer cell proliferation and migration in various cancer cell lines. Results. As a first step towards understanding how Grb7 may be inhibited by G7-18NATE, we solved the crystal structure of the Grb7 SH2 domain to 2.1 Å resolution. We describe the details of the peptide binding site underlying target specificity, as well as the dimer interface of Grb 7 SH2. Dimer formation of Grb7 was determined to be in the μM range using analytical ultracentrifugation for both full-length Grb7 and the SH2 domain alone, suggesting the SH2 domain forms the basis of a physiological dimer. ITC measurements of the interaction of the G7-18NATE peptide with the Grb7 SH2 domain revealed that it binds with a binding affinity of Kd= ∼35.7 μM and NMR spectroscopy titration experiments revealed that peptide binding causes perturbations to both the ligand binding surface of the Grb7 SH2 domain as well as to the dimer interface, suggesting that dimerisation of Grb7 is impacted on by peptide binding. Conclusion. Together the data allow us to propose a model of the Grb7 SH2 domain/G7-18NATE interaction and to rationalize the basis for the observed binding specificity and affinity. We propose that the current study will assist with the development of second generation Grb7 SH2 domain inhibitors, potentially leading to novel inhibitors of cancer cell migration and invasion. © 2007 Porter et al; licensee BioMed Central Ltd.\n

\n\n\n

\n \n\n \n \n \n \n \n \n Protein interactions: is seeing believing?.\n \n \n \n \n\n\n \n Mackay, J.; Sunde, M.; Lowry, J.; Crossley, M.; and Matthews, J.\n\n\n \n\n\n\n Trends in Biochemical Sciences, 32(12): 530-531. 2007.\n cited By 58\n\n\n\n
\n\n\n\n \n \n $\"Protein$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mackay2007530,\nauthor={Mackay, J.P. and Sunde, M. and Lowry, J.A. and Crossley, M. and Matthews, J.M.},\ntitle={Protein interactions: is seeing believing?},\njournal={Trends in Biochemical Sciences},\nyear={2007},\nvolume={32},\nnumber={12},\npages={530-531},\ndoi={10.1016/j.tibs.2007.09.006},\nnote={cited By 58},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-36249019164&doi=10.1016%2fj.tibs.2007.09.006&partnerID=40&md5=fc7ecc452d325a4ac1755f4669ab18df},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Building G08, NSW 2006, Australia},\nkeywords={gene deletion;  gene mutation;  isothermal titration calorimetry;  letter;  nuclear magnetic resonance spectroscopy;  priority journal;  protein analysis;  protein domain;  protein expression;  protein folding;  protein protein interaction;  protein purification;  protein structure;  protein targeting, Calorimetry;  Nuclear Magnetic Resonance, Biomolecular;  Protein Binding;  Proteins},\ncorrespondence_address1={Mackay, J.P.; School of Molecular and Microbial Biosciences, Building G08, NSW 2006, Australia; email: j.mackay@mmb.usyd.edu.au},\nissn={09680004},\ncoden={TBSCD},\npubmed_id={17980603},\nlanguage={English},\nabbrev_source_title={Trends Biochem. Sci.},\ndocument_type={Letter},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n An erythroid chaperone that facilitates folding of α-globin subunits for hemoglobin synthesis.\n \n \n \n \n\n\n \n Yu, X.; Kong, Y.; Dore, L.; Abdulmalik, O.; Katein, A.; Zhou, S.; Choi, J.; Gell, D.; Mackay, J.; Gow, A.; and Weiss, M.\n\n\n \n\n\n\n Journal of Clinical Investigation, 117(7): 1856-1865. 2007.\n cited By 92\n\n\n\n
\n\n\n\n \n \n $\"An$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Yu20071856,\nauthor={Yu, X. and Kong, Y. and Dore, L.C. and Abdulmalik, O. and Katein, A.M. and Zhou, S. and Choi, J.K. and Gell, D. and Mackay, J.P. and Gow, A.J. and Weiss, M.J.},\ntitle={An erythroid chaperone that facilitates folding of α-globin subunits for hemoglobin synthesis},\njournal={Journal of Clinical Investigation},\nyear={2007},\nvolume={117},\nnumber={7},\npages={1856-1865},\ndoi={10.1172/JCI31664},\nnote={cited By 92},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34447121854&doi=10.1172%2fJCI31664&partnerID=40&md5=5c77d5e619e84bb548e097d34f2ebf3b},\naffiliation={Cell and Molecular Biology Graduate Program, University of Pennsylvania School of Medicine, Philadelphia, PA, United States; GlaxoSmithKline, King of Prussia, PA, United States; Children's Hospital of Philadelphia, Philadelphia, PA, United States; Safety Assessment, AstraZeneca Pharmaceuticals LP, Wilmington, DE, United States; School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW, Australia; Department of Pharmacology, Rutgers University, Piscataway, NJ, United States; Children's Hospital of Philadelphia, Abramson Research Building, 3615 Civic Center Blvd., Philadelphia, PA 19104, United States},\nabstract={Erythrocyte precursors produce abundant α- and β-globin proteins, which assemble with each other to form hemoglobin A (HbA), the major blood oxygen carrier. αHb-stabilizing protein (AHSP) binds free α subunits reversibly to maintain their structure and limit their ability to generate reactive oxygen species. Accordingly, loss of AHSP aggravates the toxicity of excessive free α-globin caused by β-globin gene disruption in mice. Surprisingly, we found that AHSP also has important functions when free α-globin is limited. Thus, compound mutants lacking both Ahsp and 1 of 4 α-globin genes (genotype Ahsp-/-α-globin -/-α/αα) exhibited more severe anemia and Hb instability than mice with either mutation alone. In vitro, recombinant AHSP promoted folding of newly translated α-globin, enhanced its refolding after denaturation, and facilitated its incorporation into HbA. Moreover, in erythroid precursors, newly formed free α-globin was destabilized by loss of AHSP. Therefore, in addition to its previously defined role in detoxification of excess α-globin, AHSP also acts as a molecular chaperone to stabilize nascent α-globin for HbA assembly. Our findings illustrate what we believe to be a novel adaptive mechanism by which a specialized cell coordinates high-level production of a multisubunit protein and protects against various synthetic imbalances.},\nkeywords={alpha globin;  beta globin;  chaperone;  hemoglobin A;  hemoglobin alpha stabilizing protein;  reactive oxygen metabolite;  recombinant hemoglobin;  unclassified drug, anemia;  animal cell;  animal model;  article;  controlled study;  denaturation;  detoxification;  erythrocyte;  erythroid precursor cell;  gene disruption;  gene mutation;  genotype;  hemoglobin synthesis;  in vitro study;  mouse;  nonhuman;  priority journal;  protein binding;  toxicity, Animals;  Apoproteins;  Blood Proteins;  Cell Differentiation;  Cell Shape;  Erythroid Cells;  Hemoglobins;  Mice;  Mice, Knockout;  Mice, Transgenic;  Molecular Chaperones;  Mutation;  Protein Folding;  Protein Subunits;  Reticulocytes},\ncorrespondence_address1={Weiss, M.J.; Children's Hospital of Philadelphia, 3615 Civic Center Blvd., Philadelphia, PA 19104, United States; email: weissmi@email.chop.edu},\nissn={00219738},\ncoden={JCINA},\npubmed_id={17607360},\nlanguage={English},\nabbrev_source_title={J. Clin. Invest.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Solution Structure of the THAP Domain from Caenorhabditis elegans C-terminal Binding Protein (CtBP).\n \n \n \n \n\n\n \n Liew, C.; Crossley, M.; Mackay, J.; and Nicholas, H.\n\n\n \n\n\n\n Journal of Molecular Biology, 366(2): 382-390. 2007.\n cited By 14\n\n\n\n
\n\n\n\n \n \n $\"Solution$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Liew2007382,\nauthor={Liew, C.K. and Crossley, M. and Mackay, J.P. and Nicholas, H.R.},\ntitle={Solution Structure of the THAP Domain from Caenorhabditis elegans C-terminal Binding Protein (CtBP)},\njournal={Journal of Molecular Biology},\nyear={2007},\nvolume={366},\nnumber={2},\npages={382-390},\ndoi={10.1016/j.jmb.2006.11.058},\nnote={cited By 14},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33846336737&doi=10.1016%2fj.jmb.2006.11.058&partnerID=40&md5=7b01ecb1237725abf39c552e2db4d727},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={The THAP (Thanatos-associated protein) domain is a recently discovered zinc-binding domain found in proteins involved in transcriptional regulation, cell-cycle control, apoptosis and chromatin modification. It contains a single zinc atom ligated by cysteine and histidine residues within a Cys-X2-4-Cys-X35-53-Cys-X2-His consensus. We have determined the NMR solution structure of the THAP domain from Caenorhabditis elegans C-terminal binding protein (CtBP) and show that it adopts a fold containing a treble clef motif, bearing similarity to the zinc finger-associated domain (ZAD) from Drosophila Grauzone. The CtBP THAP domain contains a large, positively charged surface patch and we demonstrate that this domain can bind to double-stranded DNA in an electrophoretic mobility-shift assay. These data, together with existing reports, indicate that THAP domains might exhibit a functional diversity similar to that observed for classical and GATA-type zinc fingers. © 2006 Elsevier Ltd. All rights reserved.},\nauthor_keywords={Caenorhabditis elegans;  CtBP;  NMR structure;  THAP domain;  zinc finger},\nkeywords={binding protein;  C terminal binding protein;  double stranded DNA;  unclassified drug;  zinc finger protein, article;  Caenorhabditis elegans;  carboxy terminal sequence;  Drosophila;  electrophoresis;  gel mobility shift assay;  nuclear magnetic resonance;  priority journal;  protein DNA binding;  protein domain;  protein folding;  protein structure;  sequence homology;  zinc finger motif, Caenorhabditis elegans},\ncorrespondence_address1={Liew, C.K.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: ckliew@mmb.usyd.edu.au},\npublisher={Academic Press},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={17174978},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Sticky fingers: zinc-fingers as protein-recognition motifs.\n \n \n \n \n\n\n \n Gamsjaeger, R.; Liew, C.; Loughlin, F.; Crossley, M.; and Mackay, J.\n\n\n \n\n\n\n Trends in Biochemical Sciences, 32(2): 63-70. 2007.\n cited By 327\n\n\n\n
\n\n\n\n \n \n $\"Sticky$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Gamsjaeger200763,\nauthor={Gamsjaeger, R. and Liew, C.K. and Loughlin, F.E. and Crossley, M. and Mackay, J.P.},\ntitle={Sticky fingers: zinc-fingers as protein-recognition motifs},\njournal={Trends in Biochemical Sciences},\nyear={2007},\nvolume={32},\nnumber={2},\npages={63-70},\ndoi={10.1016/j.tibs.2006.12.007},\nnote={cited By 327},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33846707892&doi=10.1016%2fj.tibs.2006.12.007&partnerID=40&md5=098e0411829a0b9ebdd8ad531c8b2796},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia},\nabstract={Zinc-fingers (ZnFs) are extremely abundant in higher eukaryotes. Once considered to function exclusively as sequence-specific DNA-binding motifs, ZnFs are now known to have additional activities such as the recognition of RNA and other proteins. Here we discuss recent advances in our understanding of ZnFs as specific modules for protein recognition. Structural studies of ZnF complexes reveal considerable diversity in terms of protein partners, binding modes and affinities, and highlight the often underestimated versatility of ZnF structure and function. An appreciation of the structural features of ZnF-protein interactions will contribute to our ability to engineer and to use ZnFs with tailored protein-binding properties. © 2006 Elsevier Ltd. All rights reserved.},\nkeywords={RNA;  zinc finger protein, binding affinity;  binding site;  DNA binding;  eukaryote;  genetic engineering;  molecular interaction;  molecular recognition;  nonhuman;  priority journal;  protein binding;  review;  sequence analysis;  zinc finger motif, Amino Acid Motifs;  Animals;  DNA-Binding Proteins;  Humans;  Ligands;  Models, Molecular;  Protein Binding;  Protein Structure, Tertiary;  Zinc Fingers, Eukaryota},\ncorrespondence_address1={Gamsjaeger, R.; School of Molecular and Microbial Biosciences, , NSW 2006, Australia},\nissn={09680004},\ncoden={TBSCD},\npubmed_id={17210253},\nlanguage={English},\nabbrev_source_title={Trends Biochem. Sci.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Crystal structures of flax rust avirulence proteins AvrL567-A and -D reveal details of the structural basis for flax disease resistance specificity.\n \n \n \n \n\n\n \n Wang, C.; Gunčar, G.; Forwood, J.; Teh, T.; Catanzariti, A.; Lawrence, G.; Loughlin, F.; Mackay, J.; Schirra, H.; Anderson, P.; Ellis, J.; Dodds, P.; and Kobe, B.\n\n\n \n\n\n\n Plant Cell, 19(9): 2898-2912. 2007.\n cited By 112\n\n\n\n
\n\n\n\n \n \n $\"Crystal$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Wang20072898,\nauthor={Wang, C.-I.A. and Gunčar, G. and Forwood, J.K. and Teh, T. and Catanzariti, A.-M. and Lawrence, G.J. and Loughlin, F.E. and Mackay, J.P. and Schirra, H.J. and Anderson, P.A. and Ellis, J.G. and Dodds, P.N. and Kobe, B.},\ntitle={Crystal structures of flax rust avirulence proteins AvrL567-A and -D reveal details of the structural basis for flax disease resistance specificity},\njournal={Plant Cell},\nyear={2007},\nvolume={19},\nnumber={9},\npages={2898-2912},\ndoi={10.1105/tpc.107.053611},\nnote={cited By 112},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-35748972958&doi=10.1105%2ftpc.107.053611&partnerID=40&md5=53fe697653b1f5772836c135a1c2fe7a},\naffiliation={School of Molecular and Microbial Sciences, University of Queensland, Brisbane, QLD 4072, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia; Division of Plant Industry, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT 2601, Australia; School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; School of Biological Sciences, Flinders University of South Australia, Adelaide, SA 5001, Australia; Special Research Centre for Functional and Applied Genomics, University of Queensland, Brisbane, QLD 4072, Australia; Department of Biochemistry and Molecular Biology, Josef Stefan Institute, Ljubljana, Slovenia; Department of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, United States},\nabstract={The gene-for-gene mechanism of plant disease resistance involves direct or indirect recognition of pathogen avirulence (Avr) proteins by plant resistance (R) proteins. Flax rust (Melampsora lini) AvrL567 avirulence proteins and the corresponding flax (Linum usitatissimum) L5, L6, and L7 resistance proteins interact directly. We determined the three-dimensional structures of two members of the AvrL567 family, AvrL567-A and AvrL567-D, at 1.4- and 2.3-Å resolution, respectively. The structures of both proteins are very similar and reveal a β-sandwich fold with no close known structural homologs. The polymorphic residues in the AvrL567 family map to the surface of the protein, and polymorphisms in residues associated with recognition differences for the R proteins lead to significant changes in surface chemical properties. Analysis of single amino acid substitutions in AvrL567 proteins confirm the role of individual residues in conferring differences in recognition and suggest that the specificity results from the cumulative effects of multiple amino acid contacts. The structures also provide insights into possible pathogen-associated functions of AvrL567 proteins, with nucleic acid binding activity demonstrated in vitro. Our studies provide some of the first structural information on avirulence proteins that bind directly to the corresponding resistance proteins, allowing an examination of the molecular basis of the interaction with the resistance proteins as a step toward designing new resistance specificities. © 2007 American Society of Plant Biologists.},\nkeywords={Amino acids;  Crystal structure;  Disease control;  Genes;  Pathogens;  Plants (botany);  Polymorphism, Avirulence;  Flax rust;  Plant disease resistance, Proteins, Linum usitatissimum;  Melampsora lini},\ncorrespondence_address1={Dodds, P.N.; Division of Plant Industry, , Canberra, ACT 2601, Australia; email: peter.dodds@csiro.au},\npublisher={American Society of Plant Biologists},\nissn={10404651},\ncoden={PLCEE},\npubmed_id={17873095},\nlanguage={English},\nabbrev_source_title={Plant Cell},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Mutations in crdiac T-box factor gene TBX20 are associated with diverse cardiac pathologies, including defects of septation and valvulogenesis and cardiomyopathy.\n \n \n \n \n\n\n \n Kirk, E.; Sunde, M.; Costa, M.; Rankin, S.; Wolstein, O.; Castro, M.; Butler, T.; Hyun, C.; Guo, G.; Otway, R.; Mackay, J.; Waddell, L.; Cole, A.; Hayward, C.; Keogh, A.; Macdonald, P.; Griffiths, L.; Fatkin, D.; Sholler, G.; Zorn, A.; Feneley, M.; Winlaw, D.; and Harvey, R.\n\n\n \n\n\n\n American Journal of Human Genetics, 81(2): 280-291. 2007.\n cited By 254\n\n\n\n
\n\n\n\n \n \n $\"Mutations$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Kirk2007280,\nauthor={Kirk, E.P. and Sunde, M. and Costa, M.W. and Rankin, S.A. and Wolstein, O. and Castro, M.L. and Butler, T.L. and Hyun, C. and Guo, G. and Otway, R. and Mackay, J.P. and Waddell, L.B. and Cole, A.D. and Hayward, C. and Keogh, A. and Macdonald, P. and Griffiths, L. and Fatkin, D. and Sholler, G.F. and Zorn, A.M. and Feneley, M.P. and Winlaw, D.S. and Harvey, R.P.},\ntitle={Mutations in crdiac T-box factor gene TBX20 are associated with diverse cardiac pathologies, including defects of septation and valvulogenesis and cardiomyopathy},\njournal={American Journal of Human Genetics},\nyear={2007},\nvolume={81},\nnumber={2},\npages={280-291},\ndoi={10.1086/519530},\nnote={cited By 254},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34547738523&doi=10.1086%2f519530&partnerID=40&md5=f11d3a6f8fb7900b9076b9ef1b84d165},\naffiliation={Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; Cardiology Department, St. Vincent's Hospital, Darlinghurst, NSW, Australia; Department of Medical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia; School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Randwick, NSW, Australia; School of Molecular and Microbial Biosciences, Rio de Janeiro, Australia; Discipline of Paediatrics and Child Health, Faculty of Medicine, University of Sydney, Sydney, Australia; Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Division of Developmental Biology, Cincinnati Children's Research Foundation, Westmead, NSW, Australia; Department of Pediatrics, College of Medicine, University of Cincinnati, CT, United States; Kids Heart Research, Children's Hospital at Westmead, Westmead, NSW, Australia; Section of Small Animal Internal Medicine, School of Veterinary Medicine, Kangwon National University, Chuncheon, South Korea; Faculties of Medicine, University of New South Wales, Kensington, NSW, Australia; Life Science, University of New South Wales, Kensington, NSW, Australia; Genomics Research Center, School of Medical Science, Griffith University, Southport, QLD, Australia; Victor Chang Cardiac Research Institute, 384 Victoria Street, Darlinghurst, NSW 2010, Australia},\nabstract={The T-box family transcription factor gene TBX20 acts in a conserved regulatory network, guiding heart formation and patterning in diverse species. Mouse Tbx20 is expressed in cardiac progenitor cells, differentiating cardiomyocytes, and developing valvular tissue, and its deletion or RNA interference-mediated knockdown is catastrophic for heart development. TBX20 interacts physically, functionally, and genetically with other cardiac transcription factors, including NKX2-5, GATA4, and TBX5, mutations of which cause congenital heart disease (CHD). Here, we report nonsense (Q195X) and missense (I152M) germline mutations within the T-box DNA-binding domain of human TBX20 that were associated with a family history of CHD and a complex spectrum of developmental anomalies, including defects in septation, chamber growth, and valvulogenesis. Biophysical characterization of wild-type and mutant proteins indicated how the missense mutation disrupts the structure and function of the TBX20 T-box. Dilated cardiomyopathy was a feature of the TBX20 mutant phenotype in humans and mice, suggesting that mutations in developmental transcription factors can provide a sensitized template for adult-onset heart disease. Our findings are the first to link TBX20 mutations to human pathology. They provide insights into how mutation of different genes in an interactive regulatory circuit lead to diverse clinical phenotypes, with implications for diagnosis, genetic screening, and patient follow-up. © 2007 by The American Society of Human Genetics. All rights reserved.},\nkeywords={mutant protein;  protein TBX20;  T box transcription factor;  transcription factor GATA 4;  transcription factor Nkx2.5;  transcription factor TBX5;  unclassified drug;  T box transcription factor;  TBX20 protein, human, adolescent;  adult;  aged;  article;  cardiomyopathy;  cell differentiation;  child;  congenital heart disease;  family history;  female;  follow up;  gene;  gene expression;  gene mutation;  genetic association;  genetic conservation;  genetic screening;  germ line;  heart development;  heart muscle cell;  human;  major clinical study;  male;  missense mutation;  nonhuman;  nonsense mutation;  nucleotide sequence;  phenotype;  priority journal;  protein DNA binding;  protein domain;  protein protein interaction;  RNA interference;  stem cell;  TBX20 gene;  valvular heart disease;  wild type;  cardiomyopathy;  chemical structure;  congenital heart malformation;  congestive cardiomyopathy;  genetics;  heart;  heart septum defect;  infant;  middle aged;  molecular genetics;  mutation;  newborn;  pedigree;  preschool child;  stop codon, Mus, Adolescent;  Adult;  Aged;  Cardiomyopathies;  Cardiomyopathy, Dilated;  Child;  Child, Preschool;  Codon, Nonsense;  Female;  Heart;  Heart Defects, Congenital;  Heart Septal Defects;  Humans;  Infant;  Infant, Newborn;  Male;  Middle Aged;  Models, Molecular;  Molecular Sequence Data;  Mutation;  Mutation, Missense;  Pedigree;  T-Box Domain Proteins},\ncorrespondence_address1={Harvey, R.P.; Victor Chang Cardiac Research Institute, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; email: r.harvey@victorchang.edu.au},\npublisher={Cell Press},\nissn={00029297},\ncoden={AJHGA},\npubmed_id={17668378},\nlanguage={English},\nabbrev_source_title={Am. J. Hum. Genet.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2006\n \n \n (7)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Zinc fingers are known as domains for binding DNA and RNA. Do they also mediate protein-protein interactions?.\n \n \n \n \n\n\n \n Loughlin, F.; and Mackay, J.\n\n\n \n\n\n\n IUBMB Life, 58(12): 731-733. 2006.\n cited By 4\n\n\n\n
\n\n\n\n \n \n $\"Zinc$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Loughlin2006731,\nauthor={Loughlin, F.E. and Mackay, J.P.},\ntitle={Zinc fingers are known as domains for binding DNA and RNA. Do they also mediate protein-protein interactions?},\njournal={IUBMB Life},\nyear={2006},\nvolume={58},\nnumber={12},\npages={731-733},\ndoi={10.1080/15216540600868445},\nnote={cited By 4},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34250157355&doi=10.1080%2f15216540600868445&partnerID=40&md5=ab465561d124302cc0df4587b0eb7ce6},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Australia; School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia},\nkeywords={DNA;  RNA;  zinc finger protein, DNA binding;  DNA binding motif;  molecular interaction;  note;  protein function;  protein protein interaction;  RNA binding;  zinc finger motif, Protein Binding;  Protein Structure, Tertiary;  Transcription Factors;  Zinc Fingers},\ncorrespondence_address1={Mackay, J.P.; School of Molecular and Microbial Biosciences, , NSW 2006, Australia; email: j.mackay@mmb.usyd.edu.au},\nissn={15216543},\ncoden={IULIF},\npubmed_id={17424912},\nlanguage={English},\nabbrev_source_title={IUBMB Life},\ndocument_type={Note},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Molecular analysis of the interaction between the hematopoietic master transcription factors GATA-1 and PU.\n \n \n \n \n\n\n \n Chu, W.; Rand, K.; Simpson, R.; Yung, W.; Mansfield, R.; Crossley, M.; Prœtorius-Ibba, M.; Nerlov, C.; Poulsen, F.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 281(38): 28296-28306. 2006.\n cited By 47\n\n\n\n
\n\n\n\n \n \n $\"Molecular$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Chu200628296,\nauthor={Chu, W.L. and Rand, K.D. and Simpson, R.J.Y. and Yung, W.W. and Mansfield, R.E. and Crossley, M. and Prœtorius-Ibba, M. and Nerlov, C. and Poulsen, F.M. and Mackay, J.P.},\ntitle={Molecular analysis of the interaction between the hematopoietic master transcription factors GATA-1 and PU},\njournal={Journal of Biological Chemistry},\nyear={2006},\nvolume={281},\nnumber={38},\npages={28296-28306},\ndoi={10.1074/jbc.M602830200},\nnote={cited By 47},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33748793075&doi=10.1074%2fjbc.M602830200&partnerID=40&md5=dcdd35aef2aac6bf5a79462fcb50d8c7},\naffiliation={School of Molecular and Microbial Biosciences, G08, University of Sydney, Sydney, NSW 2006, Australia; Department of Protein Chemistry, Institute of Molecular Biology, University of Copenhagen, DK-1353 Copenhagen, Denmark; Laboratory of Gene Therapy Research, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark; Mouse Biology Unit, European Molecular Biology Laboratory, 00016 Monterotondo, Italy; Dept. of Protein Chemistry, Inst. of Molecular Biology, University of Copenhagen, Copenhagen, Denmark; School of MMB, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={GATA-1 and PU.1 are transcription factors that control erythroid and myeloid development, respectively. The two proteins have been shown to function in an antagonistic fashion, with GATA-1 repressing PU.1 activity during erythropoiesis and PU.1 repressing GATA-1 function during myelopoiesis. It has also become clear that this functional antagonism involves direct interactions between the two proteins. However, the molecular basis for these interactions is not known, and a number of inconsistencies exist in the literature. We have used a range of biophysical methods to define the molecular details of the GATA-1-PU.1 interaction. A combination of NMR titration data and extensive mutagenesis revealed that the PU.1-Ets domain and the GATA-1 C-terminal zinc finger (CF) form a low affinity interaction in which specific regions of each protein are implicated. Surprisingly, the interaction cannot be disrupted by single alanine substitution mutations, suggesting that binding is distributed over an extended interface. The C-terminal basic tail region of CF appears to be sufficient to mediate an interaction with PU.1-Ets, and neither acetylation nor phosphorylation of a peptide corresponding to this region disrupts binding, indicating that the interaction is not dominated by electrostatic interactions. The CF basic tail shares significant sequence homology with the PU.1 interacting motif from c-Jun, suggesting that GATA-1 and c-Jun might compete to bind PU.1. Taken together, our data provide a molecular perspective on the GATA-1-PU.1 interaction, resolving several issues in the existing data and providing insight into the mechanisms through which these two proteins combine to regulate blood development. © 2006 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Acetylation;  Amino acids;  Cells;  Molecular dynamics;  Nuclear magnetic resonance, Antagonistic fashion;  Biophysical methods;  Molecular analysis;  Mutations;  Phosphorylation, Proteins, transcription factor GATA 1;  transcription factor PU 1, amino acid substitution;  article;  binding affinity;  electricity;  erythropoiesis;  mutagenesis;  nuclear magnetic resonance;  priority journal;  protein analysis;  protein interaction;  sequence homology;  titrimetry, Acetylation;  Amino Acid Motifs;  Amino Acid Sequence;  Animals;  Binding Sites;  DNA;  GATA1 Transcription Factor;  Hematopoiesis;  Humans;  Mice;  Molecular Sequence Data;  Phosphorylation;  Proto-Oncogene Proteins;  Trans-Activators;  Zinc Fingers},\ncorrespondence_address1={Poulsen, F.M.; Dept. of Protein Chemistry, , Copenhagen, Denmark; email: fmp@apk.molbio.ku.dk},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={16861236},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n A Novel Haem-binding Interface in the 22 kDa Haem-binding Protein p22HBP.\n \n \n \n \n\n\n \n Gell, D.; Westman, B.; Gorman, D.; Liew, C.; Welch, J.; Weiss, M.; and Mackay, J.\n\n\n \n\n\n\n Journal of Molecular Biology, 362(2): 287-297. 2006.\n cited By 8\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Gell2006287,\nauthor={Gell, D.A. and Westman, B.J. and Gorman, D. and Liew, C. and Welch, J.J. and Weiss, M.J. and Mackay, J.P.},\ntitle={A Novel Haem-binding Interface in the 22 kDa Haem-binding Protein p22HBP},\njournal={Journal of Molecular Biology},\nyear={2006},\nvolume={362},\nnumber={2},\npages={287-297},\ndoi={10.1016/j.jmb.2006.07.010},\nnote={cited By 8},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33747806012&doi=10.1016%2fj.jmb.2006.07.010&partnerID=40&md5=b32d257ad995389a2802890fcf89df1a},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia; The Children's Hospital of Philadelphia, Division of Haematology, Philadelphia, PA 19104, United States},\nabstract={The 22 kDa haem-binding protein, p22HBP, is highly expressed in erythropoietic tissues and binds to a range of metallo- and non-metalloporphyrin molecules with similar affinities, suggesting a role in haem regulation or synthesis. We have determined the three-dimensional solution structure of p22HBP and mapped the porphyrin-binding site, which comprises a number of loops and a α-helix all located on a single face of the molecule. The structure of p22HBP is related to the bacterial multi-drug resistance protein BmrR, and is the first protein with this fold to be identified in eukaryotes. Strikingly, the porphyrin-binding site in p22HBP is located in a similar position to the drug-binding site of BmrR. These similarities suggest that the broad ligand specificity observed for both BmrR and p22HBP may result from a conserved ligand interaction mechanism. Taken together, these data suggest that the both the fold and its associated function, that of binding to a broad range of small hydrophobic molecules, are ancient, and have been adapted throughout evolution for a variety of purposes. © 2006 Elsevier Ltd. All rights reserved.},\nauthor_keywords={haem;  haem-binding protein;  NMR;  p22HBP;  protein structure},\nkeywords={binding protein;  multidrug resistance protein;  protein BmrR;  protoporphyrin binding protein;  unclassified drug, alpha helix;  article;  drug binding site;  hydrophobicity;  ligand binding;  molecular evolution;  molecular interaction;  molecular weight;  priority journal;  protein binding;  protein folding;  protein structure;  structure analysis;  three dimensional imaging, Bacteria (microorganisms);  Eukaryota},\ncorrespondence_address1={Gell, D.A.; School of Molecular and Microbial Biosciences, , NSW 2006, Australia; email: dagell@usyd.edu.au},\npublisher={Academic Press},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={16905148},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Analysis of the structure and function of the transcriptional coregulator HOP.\n \n \n \n \n\n\n \n Kook, H.; Yung, W.; Simpson, R.; Kee, H.; Shin, S.; Lowry, J.; Loughlin, F.; Yin, Z.; Epstein, J.; and Mackay, J.\n\n\n \n\n\n\n Biochemistry, 45(35): 10584-10590. 2006.\n cited By 31\n\n\n\n
\n\n\n\n \n \n $\"Analysis$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Kook200610584,\nauthor={Kook, H. and Yung, W.W. and Simpson, R.J. and Kee, H.J. and Shin, S. and Lowry, J.A. and Loughlin, F.E. and Yin, Z. and Epstein, J.A. and Mackay, J.P.},\ntitle={Analysis of the structure and function of the transcriptional coregulator HOP},\njournal={Biochemistry},\nyear={2006},\nvolume={45},\nnumber={35},\npages={10584-10590},\ndoi={10.1021/bi060641s},\nnote={cited By 31},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33748369871&doi=10.1021%2fbi060641s&partnerID=40&md5=442f2e13cb95316b8be48ba3f284cb96},\naffiliation={Medical Research Center for Gene Regulation, Chonnam National University Medical School, Gwangju, 501-746, South Korea; School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Cardiovascular Division, University of Pennsylvania Health System, Philadelphia, PA 19104, United States},\nabstract={Homeodomain-only protein (HOP) is an 8-kDa transcriptional corepressor that is essential for the normal development of the mammalian heart. Previous studies have shown that HOP, which consists entirely of a putative homeodomain, acts downstream of Nkx2.5 and associates with the serum response factor (SRF), repressing transcription from SRF-responsive genes. HOP is also able to recruit histone deacetylase (HDAC) activity, consistent with its ability to repress transcription. Unlike other classic homeodomain proteins, HOP does not appear to interact with DNA, although it has been unclear if this is because of an overall divergent structure or because of specific amino acid differences between HOP and other homeodomains. To work toward an understanding of HOP function, we have determined the 3D structure of full-length HOP and used a range of biochemical assays to define the parts of the protein that are functionally important for its repression activity. We show that HOP forms a classical homeodomain fold but that it cannot recognize double stranded DNA, a result that emphasizes the importance of caution in predicting protein function from sequence homology alone. We also demonstrate that two distinct regions on the surface of HOP are required for its ability to repress an SRF-driven reporter gene, and it is likely that these motifs direct interactions between HOP and partner proteins such as SRF- and HDAC-containing complexes. Our results demonstrate that the homeodomain fold has been co-opted during evolution for functions other than sequence-specific DNA binding and suggest that HOP functions as an adaptor protein to mediate transcriptional repression. © 2006 American Chemical Society.},\nkeywords={Bioassay;  Biochemistry;  Biodiversity;  Biological organs;  DNA;  Genes, Homeodomain-only protein (HOP);  Mammalian heart;  Putative homeodomain, Proteins, adaptor protein;  double stranded DNA;  histone deacetylase;  homeodomain only protein;  homeodomain protein;  protein hop;  repressor protein;  serum response factor;  unclassified drug, amino acid sequence;  article;  heart development;  human;  molecular evolution;  nonhuman;  nucleotide sequence;  priority journal;  protein analysis;  protein DNA binding;  protein folding;  protein function;  protein motif;  protein structure;  reporter gene;  sequence homology;  structure analysis;  transcription regulation, Amino Acid Motifs;  Amino Acid Sequence;  Animals;  Cercopithecus aethiops;  Conserved Sequence;  COS Cells;  Gene Expression Regulation;  Genes, Regulator;  Homeodomain Proteins;  Molecular Sequence Data;  Mutation;  Protein Structure, Tertiary;  Sequence Homology, Amino Acid;  Serum Response Factor;  Solutions;  Structure-Activity Relationship;  Transcription, Genetic;  Transfection, Mammalia},\ncorrespondence_address1={Mackay, J.P.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.mackay@mmb.usyd.edu.au},\nissn={00062960},\ncoden={BICHA},\npubmed_id={16939210},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Identification of the Key LMO2-binding Determinants on Ldb1.\n \n \n \n \n\n\n \n Ryan, D.; Sunde, M.; Kwan, A.; Marianayagam, N.; Nancarrow, A.; vanden Hoven, R.; Thompson, L.; Baca, M.; Mackay, J.; Visvader, J.; and Matthews, J.\n\n\n \n\n\n\n Journal of Molecular Biology, 359(1): 66-75. 2006.\n cited By 31\n\n\n\n
\n\n\n\n \n \n $\"Identification$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Ryan200666,\nauthor={Ryan, D.P. and Sunde, M. and Kwan, A.H.-Y. and Marianayagam, N.J. and Nancarrow, A.L. and vanden Hoven, R.N. and Thompson, L.S. and Baca, M. and Mackay, J.P. and Visvader, J.E. and Matthews, J.M.},\ntitle={Identification of the Key LMO2-binding Determinants on Ldb1},\njournal={Journal of Molecular Biology},\nyear={2006},\nvolume={359},\nnumber={1},\npages={66-75},\ndoi={10.1016/j.jmb.2006.02.074},\nnote={cited By 31},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33646174873&doi=10.1016%2fj.jmb.2006.02.074&partnerID=40&md5=5891a3d49f024b8f92345f6ab5e7c512},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia; Zenyth Therapeutics Limited, Richmond, Vic. 3121, Australia; Institute of Medical Research, Walter and Eliza Hall, Parkville, Vic. 3050, Australia},\nabstract={The overexpression of LIM-only protein 2 (LMO2) in T-cells, as a result of chromosomal translocations, retroviral insertion during gene therapy, or in transgenic mice models, leads to the onset of T-cell leukemias. LMO2 comprises two protein-binding LIM domains that allow LMO2 to interact with multiple protein partners, including LIM domain-binding protein 1 (Ldb1, also known as CLIM2 and NLI), an essential cofactor for LMO proteins. Sequestration of Ldb1 by LMO2 in T-cells may prevent it binding other key partners, such as LMO4. Here, we show using protein engineering and enzyme-linked immunosorbent assay (ELISA) methodologies that LMO2 binds Ldb1 with a twofold lower affinity than does LMO4. Thus, excess LMO2 rather than an intrinsically higher binding affinity would lead to sequestration of Ldb1. Both LIM domains of LMO2 are required for high-affinity binding to Ldb1 (KD=2.0×10-8 M). However, the first LIM domain of LMO2 is primarily responsible for binding to Ldb1 (KD=2.3×10-7 M), whereas the second LIM domain increases binding by an order of magnitude. We used mutagenesis in combination with yeast two-hybrid analysis, and phage display selection to identify LMO2-binding "hot spots" within Ldb1 that locate to the LIM1-binding region. The delineation of this region reveals some specific differences when compared to the equivalent LMO4:Ldb1 interaction that hold promise for the development of reagents to specifically bind LMO2 in the treatment of leukemia. © 2006 Elsevier Ltd. All rights reserved.},\nauthor_keywords={binding hot spots;  Ldb1;  LMO2;  protein-protein interactions;  T-cell leukemia},\nkeywords={binding protein;  LIM domain binding protein 1;  LIM only protein 2;  LIM only protein 4;  LIM protein;  reagent;  unclassified drug, article;  binding affinity;  binding assay;  binding site;  comparative study;  drug targeting;  enzyme linked immunosorbent assay;  leukemia;  mutagenesis;  phage display;  priority journal;  protein analysis;  protein domain;  protein engineering;  protein protein interaction;  two hybrid system;  yeast, Mus musculus},\ncorrespondence_address1={Matthews, J.M.; School of Molecular and Microbial Biosciences, , NSW 2006, Australia; email: j.matthews@mmb.usyd.edu.au},\npublisher={Academic Press},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={16616188},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structural basis for rodlet assembly in fungal hydrophobins.\n \n \n \n \n\n\n \n Kwan, A.; Winefield, R.; Sunde, M.; Matthews, J.; Haverkamp, R.; Templeton, M.; and Mackay, J.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 103(10): 3621-3626. 2006.\n cited By 205\n\n\n\n
\n\n\n\n \n \n $\"Structural$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Kwan20063621,\nauthor={Kwan, A.H.Y. and Winefield, R.D. and Sunde, M. and Matthews, J.M. and Haverkamp, R.G. and Templeton, M.D. and Mackay, J.P.},\ntitle={Structural basis for rodlet assembly in fungal hydrophobins},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2006},\nvolume={103},\nnumber={10},\npages={3621-3626},\ndoi={10.1073/pnas.0505704103},\nnote={cited By 205},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33644864861&doi=10.1073%2fpnas.0505704103&partnerID=40&md5=3ba4f01a3750d49aac64c7f7f51b9c93},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Horticultural and Food Research Institute of New Zealand, Mount Albert Research Centre, Auckland, New Zealand; Institute of Technology and Engineering, Massey University, Palmerston North, New Zealand; Bioprotection Group, Horticulture and Food Research Institute of New Zealand, Private Bag 92-169, Auckland, New Zealand},\nabstract={Class I hydrophobins are a unique family of fungal proteins that form a polymeric, water-repellent monolayer on the surface of structures such as spores and fruiting bodies. Similar monolayers are being discovered on an increasing range of important microorganisms. Hydrophobin monolayers are amphipathic and particularly robust, and they reverse the wettability of the surface on which they are formed. There are also significant similarities between these polymers and amyloid-like fibrils. However, structural information on these proteins and the rodlets they form has been elusive. Here, we describe the three-dimensional structure of the monomeric form of the class I hydrophobin EAS. EAS forms a β-barrel structure punctuated by several disordered regions and displays a complete segregation of charged and hydrophobic residues on its surface. This structure is consistent with its ability to form an amphipathic polymer. By using this structure, together with data from mutagenesis and previous biophysical studies, we have been able to propose a model for the polymeric rodlet structure adopted by these proteins. X-ray fiber diffraction data from EAS rodlets are consistent with our model. Our data provide molecular insight into the nature of hydrophobin rodlet films and extend our understanding of the fibrillar β-structures that continue to be discovered in the protein world. © 2006 by The National Academy of Sciences of the USA.},\nauthor_keywords={Amyloid;  NMR;  Polymer},\nkeywords={amyloid;  fungal protein;  hydrophobin;  polymer, article;  fungus;  hydrophobicity;  molecular model;  mutagenesis;  Neospora;  nonhuman;  nuclear magnetic resonance spectroscopy;  polymerization;  priority journal;  protein assembly;  protein structure;  structure analysis;  X ray diffraction, Amino Acid Sequence;  Biophysics;  Electrostatics;  Fungal Proteins;  Models, Molecular;  Molecular Sequence Data;  Neurospora crassa;  Nuclear Magnetic Resonance, Biomolecular;  Protein Conformation;  Protein Structure, Secondary;  Recombinant Proteins;  Sequence Deletion;  X-Ray Diffraction, Fungi;  Neospora},\ncorrespondence_address1={Templeton, M.D.; Bioprotection Group, Private Bag 92-169, Auckland, New Zealand; email: mtempleton@hortresearch.co.nz},\nissn={00278424},\ncoden={PNASA},\npubmed_id={16537446},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n GATA-1: One protein, many partners.\n \n \n \n \n\n\n \n Lowry, J.; and MacKay, J.\n\n\n \n\n\n\n International Journal of Biochemistry and Cell Biology, 38(1): 6-11. 2006.\n cited By 43\n\n\n\n
\n\n\n\n \n \n $\"GATA-1:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Lowry20066,\nauthor={Lowry, J.A. and MacKay, J.P.},\ntitle={GATA-1: One protein, many partners},\njournal={International Journal of Biochemistry and Cell Biology},\nyear={2006},\nvolume={38},\nnumber={1},\npages={6-11},\ndoi={10.1016/j.biocel.2005.06.017},\nnote={cited By 43},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-27544483178&doi=10.1016%2fj.biocel.2005.06.017&partnerID=40&md5=ef25d289135ad73c55499598f31dd559},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={GATA-1, the founding member of the GATA transcription factor family, is essential for cell maturation and differentiation within the erythroid and megakaryocytic lineages. GATA-1 regulates the expression of many genes within these lineages and its functionality depends upon its ability to bind both DNA and protein partners. Disruption of either of these functions causes severe hematopoietic dysfunction and results in blood disorders, such as thrombocytopenia and anemia. Within this review, we will focus on the structural aspects of GATA-1 with regard to interactions with its many partners and the identification of several mutations that disrupt these interactions. © 2005 Elsevier Ltd. All rights reserved.},\nauthor_keywords={Factor;  Finger;  Hematopoiesis;  Transcription;  Zinc},\nkeywords={transcription factor GATA 1;  zinc, anemia;  blood disease;  cell damage;  cell differentiation;  cell lineage;  cell maturation;  DNA binding;  erythroid cell;  gene expression;  gene identification;  gene mutation;  hematopoiesis;  hematopoietic cell;  human;  megakaryocyte;  nonhuman;  nucleotide sequence;  protein function;  protein interaction;  protein protein interaction;  review;  thrombocytopenia},\ncorrespondence_address1={Lowry, J.A.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.lowry@mmb.usyd.edu.au},\npublisher={Elsevier Ltd},\nissn={13572725},\ncoden={IJBBF},\npubmed_id={16095949},\nlanguage={English},\nabbrev_source_title={Int. J. Biochem. Cell Biol.},\ndocument_type={Short Survey},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2005\n \n \n (10)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n 1H, 15N and 13C assignments of an intramolecular Lhx3:ldb1 complex [4].\n \n \n \n \n\n\n \n Lee, C.; Nancarrow, A.; Bach, I.; Mackay, J.; and Matthews, J.\n\n\n \n\n\n\n Journal of Biomolecular NMR, 33(3): 198. 2005.\n cited By 7\n\n\n\n
\n\n\n\n \n \n $\"1H,$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Lee2005198,\nauthor={Lee, C. and Nancarrow, A.L. and Bach, I. and Mackay, J.P. and Matthews, J.M.},\ntitle={1H, 15N and 13C assignments of an intramolecular Lhx3:ldb1 complex [4]},\njournal={Journal of Biomolecular NMR},\nyear={2005},\nvolume={33},\nnumber={3},\npages={198},\ndoi={10.1007/s10858-005-3209-7},\nnote={cited By 7},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-31444453206&doi=10.1007%2fs10858-005-3209-7&partnerID=40&md5=7a6e15f00f7ebfba4bbbe833be357100},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; University of Massachusetts Medical School, Worcester, MA 01605, United States},\nkeywords={homeodomain protein;  transcription factor;  transcription factor LHX3;  unclassified drug;  carbon;  DNA binding protein;  homeodomain protein;  LDB1 protein, human;  nitrogen;  proton;  transcription factor LHX3, binding affinity;  carbon nuclear magnetic resonance;  complex formation;  homeostasis;  hypophysis function;  letter;  nerve growth;  nitrogen nuclear magnetic resonance;  nonhuman;  priority journal;  protein analysis;  protein binding;  protein engineering;  protein function;  proton nuclear magnetic resonance;  chemistry;  human;  metabolism;  nuclear magnetic resonance spectroscopy, Carbon Isotopes;  DNA-Binding Proteins;  Homeodomain Proteins;  Humans;  Magnetic Resonance Spectroscopy;  Nitrogen Isotopes;  Protons},\ncorrespondence_address1={Matthews, J.M.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.matthews@mmb.usyd.edu.au},\nissn={09252738},\ncoden={JBNME},\npubmed_id={16331426},\nlanguage={English},\nabbrev_source_title={J. Biomol. NMR},\ndocument_type={Letter},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Grb7-SH2 domain dimerisation is affected by a single point mutation.\n \n \n \n \n\n\n \n Porter, C.; Wilce, M.; Mackay, J.; Leedman, P.; and Wilce, J.\n\n\n \n\n\n\n European Biophysics Journal, 34(5): 454-460. 2005.\n cited By 24\n\n\n\n
\n\n\n\n \n \n $\"Grb7-SH2$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Porter2005454,\nauthor={Porter, C.J. and Wilce, M.C.J. and Mackay, J.P. and Leedman, P. and Wilce, J.A.},\ntitle={Grb7-SH2 domain dimerisation is affected by a single point mutation},\njournal={European Biophysics Journal},\nyear={2005},\nvolume={34},\nnumber={5},\npages={454-460},\ndoi={10.1007/s00249-005-0480-1},\nnote={cited By 24},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-22844435175&doi=10.1007%2fs00249-005-0480-1&partnerID=40&md5=80176ab821b1958b0ba96861c0a7da52},\naffiliation={School of Biomedical and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia; School of Medicine and Pharmacology, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia; Western Australian Institute for Medical Research, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia; School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Growth factor receptor bound protein 7 (Grb7) is an adaptor protein that is co-overexpressed and forms a tight complex with the ErbB2 receptor in a number of breast tumours and breast cancer cell lines. The interaction of Grb7 with the ErbB2 receptor is mediated via its Src homology 2 (SH2) domain. Whilst most SH2 domains exist as monomers, recently reported studies have suggested that the Grb7-SH2 domain exists as a homodimer. The self-association properties of the Grb7-SH2 domain were therefore studied using sedimentation equilibrium ultracentrifugation. Analysis of the data demonstrated that the Grb7-SH2 domain is dimeric with a dissociation constant of approximately 11 μM. We also demonstrate, using size-exclusion chromatography, that mutation of phenylalanine 511 to an arginine produces a monomeric form of the Grb7-SH2 domain. This mutation represents the first step in the engineering of a Grb7-SH2 domain with good solution properties for further biophysical and structural investigation. © EBSA 2005.},\nauthor_keywords={Analytical ultracentrifugation;  Growth factor receptor bound protein 7;  Protein engineering;  Size-exclusion chromatography;  Src homology 2 domain},\nkeywords={adaptor protein;  arginine;  dimer;  growth factor receptor;  growth factor receptor bound protein 7;  monomer;  phenylalanine;  unclassified drug, article;  breast cancer;  cancer cell culture;  gel permeation chromatography;  protein domain;  protein engineering;  protein expression;  protein interaction;  sedimentation;  Src homology domain;  ultracentrifugation, Arginine;  Biophysics;  Cell Line, Tumor;  Chromatography;  Dimerization;  Dose-Response Relationship, Drug;  Escherichia coli;  Humans;  Hydrogen-Ion Concentration;  Models, Statistical;  Molecular Conformation;  Mutagenesis, Site-Directed;  Mutation;  Phenylalanine;  Plasmids;  Point Mutation;  Protein Binding;  Protein Engineering;  Protein Structure, Tertiary;  src Homology Domains;  Ultracentrifugation},\ncorrespondence_address1={Wilce, J.A.; School of Biomedical and Chemical Sciences, 35 Stirling Highway, Perth, WA 6009, Australia; email: Jackie.wilce@med.monash.edu.au},\nissn={01757571},\ncoden={EBJOE},\npubmed_id={15841400},\nlanguage={English},\nabbrev_source_title={Eur. Biophys. J.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structure of oxidized α-haemoglobin bound to AHSP reveals a protective mechanism for haem.\n \n \n \n \n\n\n \n Feng, L.; Zhou, S.; Gu, L.; Gell, D.; Mackay, J.; Weiss, M.; Gow, A.; and Shi, Y.\n\n\n \n\n\n\n Nature, 435(7042): 697-701. 2005.\n cited By 94\n\n\n\n
\n\n\n\n \n \n $\"Structure$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Feng2005697,\nauthor={Feng, L. and Zhou, S. and Gu, L. and Gell, D.A. and Mackay, J.P. and Weiss, M.J. and Gow, A.J. and Shi, Y.},\ntitle={Structure of oxidized α-haemoglobin bound to AHSP reveals a protective mechanism for haem},\njournal={Nature},\nyear={2005},\nvolume={435},\nnumber={7042},\npages={697-701},\ndoi={10.1038/nature03609},\nnote={cited By 94},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-20444445134&doi=10.1038%2fnature03609&partnerID=40&md5=ddfe830aa3d3ef98f1482394e95b7302},\naffiliation={Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, United States; Children's Hospital of Philadelphia and the University of Pennsylvania, Philadelphia, PA 19104, United States; School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={The synthesis of haemoglobin A (HbA) is exquisitely coordinated during erythrocyte development to prevent damaging effects from individual α- and β-subunits. The α-haemoglobin-stabilizing protein (AHSP) binds α-haemoglobin (αHb), inhibits the ability of αHb to generate reactive oxygen species and prevents its precipitation on exposure to oxidant stress. The structure of AHSP bound to ferrous αHb is thought to represent a transitional complex through which αHb is converted to a non-reactive, hexacoordinate ferric form. Here we report the crystal structure of this ferric αHb-AHSP complex at 2.4 A resolution. Our findings reveal a striking bis-histidyl configuration in which both the proximal and the distal histidines coordinate the haem iron atom. To attain this unusual conformation, segments of αHb undergo drastic structural rearrangements, including the repositioning of several α-helices. Moreover, conversion to the ferric bishistidine configuration strongly and specifically inhibits redox chemistry catalysis and haem loss from αHb. The observed structural changes, which impair the chemical reactivity of haem iron, explain how AHSP stabilizes αHb and prevents its damaging effects in cells.},\nkeywords={Catalysis;  Crystal structure;  Iron;  Oxidation;  Oxygen;  Precipitation (chemical);  Redox reactions;  Stress analysis;  Structure (composition);  Synthesis (chemical), Chemical reactivity;  Ferric bihistidine;  Oxidant stress;  Structural changes, Hemoglobin, alpha hemoglobin stabilizing protein;  binding protein;  ferric ion;  ferrous ion;  heme;  hemoglobin A;  histidine;  oxidized hemoglobin A;  reactive oxygen metabolite;  unclassified drug;  chaperone;  oxyhemoglobin;  plasma protein, medicine, alpha helix;  article;  chemoreactivity;  complex formation;  crystal structure;  erythrocyte;  oxidation reduction reaction;  oxidative stress;  priority journal;  protection;  protein conformation;  protein stability;  protein structure;  protein synthesis;  chemical structure;  chemistry;  metabolism;  protein binding;  X ray crystallography, Blood Proteins;  Crystallography, X-Ray;  Heme;  Hemoglobin A;  Models, Molecular;  Molecular Chaperones;  Oxidation-Reduction;  Oxyhemoglobins;  Protein Binding;  Protein Conformation;  Reactive Oxygen Species},\ncorrespondence_address1={Gow, A.J.; Children's Hospital of Philadelphia and the University of Pennsylvania, Philadelphia, PA 19104, United States; email: gow@email.chop.edu},\nissn={00280836},\ncoden={NATUA},\npubmed_id={15931225},\nlanguage={English},\nabbrev_source_title={Nature},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n A complex mechanism determines polarity of DNA replication fork arrest by the replication terminator complex of Bacillus subtilis.\n \n \n \n \n\n\n \n Duggin, I.; Matthews, J.; Dixon, N.; Wake, R.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 280(13): 13105-13113. 2005.\n cited By 9\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Duggin200513105,\nauthor={Duggin, I.G. and Matthews, J.M. and Dixon, N.E. and Wake, R.G. and Mackay, J.P.},\ntitle={A complex mechanism determines polarity of DNA replication fork arrest by the replication terminator complex of Bacillus subtilis},\njournal={Journal of Biological Chemistry},\nyear={2005},\nvolume={280},\nnumber={13},\npages={13105-13113},\ndoi={10.1074/jbc.M414187200},\nnote={cited By 9},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-16844380010&doi=10.1074%2fjbc.M414187200&partnerID=40&md5=71adecac2ffbfae5b39e65dd5330c470},\naffiliation={Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW 2006, Australia; Research School of Chemistry, Australian National University, ACT 0200, Australia; Hutchinson/MRC Research Centre, Hills Rd., Cambridge, CB2 2XZ, United Kingdom},\nabstract={Two dimers of the replication terminator protein (RTP) of Bacillus subtilis bind to a chromosomal DNA terminator site to effect polar replication fork arrest. Cooperative binding of the dimers to overlapping half-sites within the terminator is essential for arrest. It was suggested previously that polarity of fork arrest is the result of the RTP dimer at the blocking (proximal) side within the complex binding very tightly and the permissive-side RTP dimer binding relatively weakly. In order to investigate this "differential binding affinity" model, we have constructed a series of mutant terminators that contain half-sites of widely different RTP binding affinities in various combinations. Although there appeared to be a correlation between binding affinity at the proximal half-site and fork arrest efficiency in vivo for some terminators, several deviated significantly from this correlation. Some terminators exhibited greatly reduced binding cooperativity (and therefore have reduced affinity at each half-site) but were highly efficient in fork arrest, whereas one terminator had normal affinity over the proximal half-site, yet had low fork arrest efficiency. The results show clearly that there is no direct correlation between the RTP binding affinity (either within the full complex or at the proximal half-site within the full complex) and the efficiency of replication fork arrest in vivo. Thus, the differential binding affinity over the proximal and distal half-sites cannot be solely responsible for functional polarity of fork arrest. Furthermore, efficient fork arrest relies on features in addition to the tight binding of RTP to terminator DNA. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Binding energy;  Chromosomes;  Correlation methods;  Microorganisms, Bacillus subtilis;  Cooperative binding;  Differential binding;  Replication terminator proteins (RTP), DNA, bacterial protein;  dimer, article;  Bacillus subtilis;  binding affinity;  controlled study;  correlation analysis;  DNA replication;  molecular model;  nonhuman;  polarization;  priority journal;  stop codon},\ncorrespondence_address1={Duggin, I.G.; Hutchinson/MRC Research Centre, Hills Rd., Cambridge, CB2 2XZ, United Kingdom; email: iduggin@gmail.com},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={15657033},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Solution structure of a recombinant type I sculpin antifreeze protein.\n \n \n \n \n\n\n \n Kwan, A.; Fairley, K.; Anderberg, P.; Liew, C.; Harding, M.; and Mackay, J.\n\n\n \n\n\n\n Biochemistry, 44(6): 1980-1988. 2005.\n cited By 26\n\n\n\n
\n\n\n\n \n \n $\"Solution$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Kwan20051980,\nauthor={Kwan, A.H.-Y. and Fairley, K. and Anderberg, P.I. and Liew, C.W. and Harding, M.M. and Mackay, J.P.},\ntitle={Solution structure of a recombinant type I sculpin antifreeze protein},\njournal={Biochemistry},\nyear={2005},\nvolume={44},\nnumber={6},\npages={1980-1988},\ndoi={10.1021/bi047782j},\nnote={cited By 26},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-13544268362&doi=10.1021%2fbi047782j&partnerID=40&md5=1786209627caf7fe4a68dc2d7b77a1e3},\naffiliation={School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia; Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW 2006, Australia},\nabstract={We have determined the solution structure of rSS3, a recombinant form of the type I shorthorn sculpin antifreeze protein (AFP), at 278 and 268 K. This AFP contains an unusual sequence of N-terminal residues, together with two of the 11-residue repeats that are characteristic of the type I winter flounder AFP. The solution conformation of the N-terminal region of the sculpin AFP has been assumed to be the critical factor that results in recognition of different ice planes by the sculpin and flounder AFPs. At 278 K, the two repeats units (residues 11-20 and 21-32) in rSS3 form a continuous α-helix, with the residues 30-33 in the second repeat somewhat less well defined. Within the N-terminal region, residues 2-6 are well defined and helical and linked to the main helix by a more flexible region comprising residues A7-T11. At 268 K the AFP is overall more helical but retains the apparent hinge region. The helical conformation of the two repeats units is almost identical to the corresponding repeats in the type I winter flounder AFP. We also show that while tetracetylated rSS3 has antifreeze activity comparable to the natural AFP, its overall structure is the same as that of the unacetylated peptide. These data provide some insight into the structural determinants of antifreeze activity and should assist in the development of models that explain the recognition of different ice interfaces by the sculpin and flounder type I AFPs.},\nkeywords={Antifreeze solutions;  Hinges;  Ice;  Mathematical models;  Structural design;  Tetrodes, Residues;  Sculpin antifreeze protein (AFP);  Solution structure;  Terminal region, Proteins, antifreeze protein;  ice;  peptide derivative;  protein rSS3;  recombinant protein;  sculpin 1;  unclassified drug, acylation;  alpha helix;  amino terminal sequence;  article;  priority journal;  protein conformation;  protein structure;  structure analysis, Acetylation;  Amino Acid Sequence;  Animals;  Antifreeze Proteins, Type I;  Chromatography, High Pressure Liquid;  Crystallography, X-Ray;  Fishes;  Flounder;  Molecular Sequence Data;  Nuclear Magnetic Resonance, Biomolecular;  Protein Conformation;  Protein Structure, Secondary;  Recombinant Proteins;  Solutions;  Structural Homology, Protein;  Temperature;  Thermodynamics, Myoxocephalus scorpius;  Pleuronectoidei;  Pseudopleuronectes americanus},\ncorrespondence_address1={Harding, M.M.; Sch. of Molec. and Microbial Biosci., , Sydney, NSW 2006, Australia; email: harding@chem.usyd.edu.au},\nissn={00062960},\ncoden={BICHA},\npubmed_id={15697223},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Zinc fingers as protein recognition motifs: Structural basis for the GATA-1/friend of GATA interaction.\n \n \n \n \n\n\n \n Liew, C.; Simpson, R.; Kwan, A.; Crofts, L.; Loughlin, F.; Matthews, J.; Crossley, M.; and Mackay, J.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 102(3): 583-588. 2005.\n cited By 80\n\n\n\n
\n\n\n\n \n \n $\"Zinc$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Liew2005583,\nauthor={Liew, C.K. and Simpson, R.J.Y. and Kwan, A.H.Y. and Crofts, L.A. and Loughlin, F.E. and Matthews, J.M. and Crossley, M. and Mackay, J.P.},\ntitle={Zinc fingers as protein recognition motifs: Structural basis for the GATA-1/friend of GATA interaction},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2005},\nvolume={102},\nnumber={3},\npages={583-588},\ndoi={10.1073/pnas.0407511102},\nnote={cited By 80},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-14144252920&doi=10.1073%2fpnas.0407511102&partnerID=40&md5=718bd14e3ed99c6753b5d12ba1bd6f2e},\naffiliation={Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW 2006, Australia},\nabstract={GATA-1 and friend of GATA (FOG) are zinc-finger transcription factors that physically interact to play essential roles in erythroid and megakaryocytic development. Several naturally occurring mutations in the GATA-1 gene that alter the FOG-binding domain have been reported. The mutations are associated with familial anemias and thrombocytopenias of differing severity. To elucidate the molecular basis for the GATA-1/FOG interaction, we have determined the three-dimensional structure of a complex comprising the interaction domains of these proteins. The structure reveals how zinc fingers can act as protein recognition motifs. Details of the architecture of the contact domains and their physical properties provide a molecular explanation for how the GATA-1 mutations contribute to distinct but related genetic diseases.},\nauthor_keywords={Factor;  Gene expression;  Transcription},\nkeywords={friend of gata 1 protein;  transcription factor GATA 1;  unclassified drug;  zinc finger protein, anemia;  article;  controlled study;  disease association;  disease severity;  erythroid cell;  familial disease;  gene mutation;  genetic disorder;  human;  human cell;  megakaryocyte;  molecular interaction;  priority journal;  protein binding;  protein domain;  protein interaction;  protein motif;  protein structure;  structure analysis;  three dimensional imaging;  thrombocytopenia;  transcription regulation;  zinc finger motif, Binding Sites;  Carrier Proteins;  DNA-Binding Proteins;  Erythroid-Specific DNA-Binding Factors;  GATA1 Transcription Factor;  Hematologic Diseases;  Humans;  Models, Molecular;  Molecular Structure;  Mutation;  Nuclear Proteins;  Protein Binding;  Protein Conformation;  Transcription Factors;  Zinc Fingers},\ncorrespondence_address1={Mackay, J.P.; Sch. of Molec. and Microbial Biosci., , Sydney, NSW 2006, Australia; email: j.mackay@mmb.usyd.edu.au},\nissn={00278424},\ncoden={PNASA},\npubmed_id={15644435},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Role of alpha hemoglobin-stabilizing protein in normal erythropoiesis and β-thalassemia.\n \n \n \n \n\n\n \n Weiss, M.; Zhou, S.; Feng, L.; Gell, D.; Mackay, J.; Shi, Y.; and Gow, A.\n\n\n \n\n\n\n Annals of the New York Academy of Sciences, 1054: 103-117. 2005.\n cited By 41\n\n\n\n
\n\n\n\n \n \n $\"Role$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Weiss2005103,\nauthor={Weiss, M.J. and Zhou, S. and Feng, L. and Gell, D.A. and Mackay, J.P. and Shi, Y. and Gow, A.J.},\ntitle={Role of alpha hemoglobin-stabilizing protein in normal erythropoiesis and β-thalassemia},\njournal={Annals of the New York Academy of Sciences},\nyear={2005},\nvolume={1054},\npages={103-117},\ndoi={10.1196/annals.1345.013},\nnote={cited By 41},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-29744437673&doi=10.1196%2fannals.1345.013&partnerID=40&md5=98e453e74b11fc157fb81cb4803f4b48},\naffiliation={Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, United States; Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, United States; School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Children's Hospital of Philadelphia, ARC, 3615 Civic Center Blvd., Philadelphia, PA 19104, United States},\nabstract={Hemoglobin (Hb) synthesis is coordinated by homeostatic mechanisms to limit the accumulation of free α or β subunits, which are cytotoxic. Alpha hemoglobin-stabilizing protein (AHSP) is an abundant erythroid protein that specifically binds free αHb, stabilizes its structure, and limits its ability to participate in chemical reactions that generate reactive oxygen species. Gene ablation studies in mice demonstrate that AHSP is required for normal erythropoiesis. AHSP-null erythrocytes are short-lived, contain Hb precipitates, and exhibit signs of oxidative damage. Loss of AHSP exacerbates β-thalassemia in mice, indicating that altered AHSP expression or function could modify thalassemia phenotypes in humans, a topic that is beginning to be explored in clinical studies. We used biochemical, spectroscopic, and crystallographic methods to examine how AHSP stabilizes αHb. AHSP binds the G and H helices of αHb on a surface that largely overlaps with the α1-β1 interface of HbA. This result explains previous findings that βHb can competitively displace AHSP from αHb to form HbA tetramer. Remarkably, binding of AHSP to oxygenated αHb induces dramatic conformational changes and converts the heme-bound iron to an oxidized hemichrome state in which all six coordinate positions are occupied. This structure limits the reactivity of heme iron, providing a mechanism by which AHSP stabilizes αHb. These findings suggest a biochemical pathway through which AHSP might participate in normal Hb synthesis and modulate the severity of thalassemias. Moreover, understanding how AHSP stabilizes αHb provides a theoretical basis for new strategies to inhibit the damaging effects of free αHb that accumulates in β-thalassemia. © 2005 New York Academy of Sciences.},\nauthor_keywords={Erythropoiesis;  GATA-1;  Hemoglobinopathy;  Reactive oxygen species},\nkeywords={alpha hemoglobin stabilizing protein;  heme;  hemoglobin;  hemoglobin A;  iron;  protein subunit;  reactive oxygen metabolite;  tetramer;  unclassified drug, beta thalassemia;  binding competition;  chemical reaction;  conference paper;  conformational transition;  crystallography;  disease exacerbation;  disease severity;  erythrocyte;  erythroid cell;  erythropoiesis;  gene loss;  hemoglobin synthesis;  homeostasis;  nonhuman;  oxidative stress;  phenotype;  protein protein interaction;  protein stability;  spectroscopy},\ncorrespondence_address1={Weiss, M.J.; Children's Hospital of Philadelphia, 3615 Civic Center Blvd., Philadelphia, PA 19104, United States; email: weissmi@email.chop.edu},\npublisher={New York Academy of Sciences},\nissn={00778923},\ncoden={ANYAA},\npubmed_id={16339656},\nlanguage={English},\nabbrev_source_title={Ann. New York Acad. Sci.},\ndocument_type={Conference Paper},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n CSL: A notch above the rest.\n \n \n \n \n\n\n \n Pursglove, S.; and Mackay, J.\n\n\n \n\n\n\n International Journal of Biochemistry and Cell Biology, 37(12): 2472-2477. 2005.\n cited By 28\n\n\n\n
\n\n\n\n \n \n $\"CSL:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Pursglove20052472,\nauthor={Pursglove, S.E. and Mackay, J.P.},\ntitle={CSL: A notch above the rest},\njournal={International Journal of Biochemistry and Cell Biology},\nyear={2005},\nvolume={37},\nnumber={12},\npages={2472-2477},\ndoi={10.1016/j.biocel.2005.06.013},\nnote={cited By 28},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-25844489960&doi=10.1016%2fj.biocel.2005.06.013&partnerID=40&md5=5acd13aaf52f87227ea36e147dd1b6e6},\naffiliation={School of Molecular and Microbial Biosciences, Building G08, University of Sydney, NSW 2006, Australia},\nabstract={CSL (CBF1, Suppressor of Hairless, Lag-1) is a transcription factor that is responsible for activating the genes downstream of the Notch signalling pathway, a pathway that is essential for the development of the nervous system and the differentiation of the haematopoietic system among others. In the absence of Notch signalling, CSL represses transcription of Notch target genes, and following activation by Notch, CSL is converted into a transcriptional activator and activates transcription of the same genes. These two opposing functions of CSL are mediated through interactions with distinct protein complexes. The Notch signalling pathway and its crucial cofactor CSL can maintain cells in an undifferentiated state, and have therefore been associated with a growing list of cancers. In addition, CSL has been co-opted by Epstein-Barr virus to mediate viral and host gene transcription following infection. © 2005 Elsevier Ltd. All rights reserved.},\nauthor_keywords={CSL;  Epstein-Barr virus;  Notch;  Suppressor of Hairless;  Transcription},\nkeywords={Notch receptor;  transcription factor;  transcription factor CSL;  unclassified drug, cancer growth;  cell differentiation;  Epstein Barr virus;  gene activation;  gene repression;  gene targeting;  genetic transcription;  hematopoietic system;  human;  immune response;  nervous system development;  nonhuman;  nucleotide sequence;  protein interaction;  review;  signal transduction;  transcription initiation;  virus infection;  virus transcription, Human herpesvirus 4},\npublisher={Elsevier Ltd},\nissn={13572725},\ncoden={IJBBF},\npubmed_id={16095948},\nlanguage={English},\nabbrev_source_title={Int. J. Biochem. Cell Biol.},\ndocument_type={Short Survey},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The hydrophobic domain 26 of human tropoelastin is unstructured in solution.\n \n \n \n \n\n\n \n MacKay, J.; Muiznieks, L.; Toonkool, P.; and Weiss, A.\n\n\n \n\n\n\n Journal of Structural Biology, 150(2): 154-162. 2005.\n cited By 16\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{MacKay2005154,\nauthor={MacKay, J.P. and Muiznieks, L.D. and Toonkool, P. and Weiss, A.S.},\ntitle={The hydrophobic domain 26 of human tropoelastin is unstructured in solution},\njournal={Journal of Structural Biology},\nyear={2005},\nvolume={150},\nnumber={2},\npages={154-162},\ndoi={10.1016/j.jsb.2005.02.005},\nnote={cited By 16},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-18144374871&doi=10.1016%2fj.jsb.2005.02.005&partnerID=40&md5=60f19a5b70aa13f3c56fa67668e36be0},\naffiliation={Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW 2006, Australia; Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand},\nabstract={Elastin is the protein responsible for the elastic properties of vertebrate tissue. Very little is currently known about the structure of elastin or of its soluble precursor tropoelastin. We have used high-resolution solution NMR methods to probe the conformational preferences of a conserved hydrophobic region in tropoelastin, domain 26 (D26). Using a combination of homonuclear, 15N-separated and triple resonance experiments, we have obtained essentially full chemical shift assignments for D26 at 278 K. An analysis of secondary chemical shift changes, as well as NOE and 15N relaxation data, leads us to conclude that this domain is essentially unstructured in solution and does not interact with intact tropoelastin. D26 does not display exposed hydrophobic clusters, as expected for a fully unfolded protein and commensurate with an absence of flexible structural motifs, as identified by lack of binding of the fluorescent probe 4,4′-dianilino-1,1′- binaphthyl-5,5′-disulfonic acid. Sedimentation equilibrium data establish that this domain is strictly monomeric in solution. NMR spectra recorded at 278 and 308 K indicate that no significant structural changes occur for this domain over the temperature range 278-308 K, in contrast to the characteristic coacervation behavior that is observed for the full-length protein. © 2005 Elsevier Inc. All rights reserved.},\nauthor_keywords={NMR spectroscopy;  Protein structure;  Tropoelastin},\nkeywords={fluorescent dye;  sulfonic acid derivative;  tropoelastin, article;  data analysis;  hydrophobicity;  nuclear magnetic resonance;  nuclear Overhauser effect;  priority journal;  protein analysis;  protein binding;  protein conformation;  protein domain;  protein folding;  protein motif;  protein structure;  temperature dependence, Vertebrata},\ncorrespondence_address1={Weiss, A.S.; Sch. of Molec. and Microbial Biosci., , Sydney, NSW 2006, Australia; email: a.weiss@mmb.usyd.edu.au},\npublisher={Academic Press Inc.},\nissn={10478477},\ncoden={JSBIE},\npubmed_id={15866738},\nlanguage={English},\nabbrev_source_title={J. Struct. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Assessment of the robustness of a serendipitous zinc binding fold: Mutagenesis and protein grafting.\n \n \n \n \n\n\n \n Sharpe, B.; Liew, C.; Kwan, A.; Wilce, J.; Crossley, M.; Matthews, J.; and Mackay, J.\n\n\n \n\n\n\n Structure, 13(2): 257-266. 2005.\n cited By 8\n\n\n\n
\n\n\n\n \n \n $\"Assessment$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Sharpe2005257,\nauthor={Sharpe, B.K. and Liew, C.K. and Kwan, A.H. and Wilce, J.A. and Crossley, M. and Matthews, J.M. and Mackay, J.P.},\ntitle={Assessment of the robustness of a serendipitous zinc binding fold: Mutagenesis and protein grafting},\njournal={Structure},\nyear={2005},\nvolume={13},\nnumber={2},\npages={257-266},\ndoi={10.1016/j.str.2004.12.007},\nnote={cited By 8},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-13844272073&doi=10.1016%2fj.str.2004.12.007&partnerID=40&md5=813056e419f1726286f40cff0d95f691},\naffiliation={Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW 2006, Australia; Sch. of Biomed. and Chem. Sciences, University of Western Australia, Perth, WA 6009, Australia},\nabstract={Zinc binding motifs have received much attention in the area of protein design. Here, we have tested the suitability of a recently discovered nonnative zinc binding structure as a protein design scaffold. A series of multiple alanine mutants was created to investigate the minimal requirements for folding, and solution structures of these mutants showed that the original fold was maintained, despite changes in 50% of the sequence. We next attempted to transplant binding faces from chosen bimolecular interactions onto one of these mutants, and many of the resulting "chimeras" were shown to adopt a native-like fold. These results both highlight the robust nature of small zinc binding domains and underscore the complexity of designing functional proteins, even using such small, highly ordered scaffolds as templates.},\nkeywords={alanine;  mutant protein;  zinc, amino acid sequence;  article;  chimera;  complex formation;  molecular interaction;  mutagenesis;  priority journal;  protein binding;  protein domain;  protein folding;  protein function;  structure analysis},\ncorrespondence_address1={Mackay, J.P.; Sch. of Molec. and Microbial Biosci., , Sydney, NSW 2006, Australia; email: j.mackay@mmb.usyd.edu.au},\npublisher={Cell Press},\nissn={09692126},\ncoden={STRUE},\npubmed_id={15698569},\nlanguage={English},\nabbrev_source_title={Structure},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2004\n \n \n (8)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Molecular mechanism of AHSP-mediated stabilization of α-hemoglobin.\n \n \n \n \n\n\n \n Feng, L.; Gell, D.; Zhou, S.; Gu, L.; Kong, Y.; Li, J.; Hu, M.; Yan, N.; Lee, C.; Rich, A.; Armstrong, R.; Lay, P.; Gow, A.; Weiss, M.; MacKay, J.; and Shi, Y.\n\n\n \n\n\n\n Cell, 119(5): 629-640. 2004.\n cited By 134\n\n\n\n
\n\n\n\n \n \n $\"Molecular$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Feng2004629,\nauthor={Feng, L. and Gell, D.A. and Zhou, S. and Gu, L. and Kong, Y. and Li, J. and Hu, M. and Yan, N. and Lee, C. and Rich, A.M. and Armstrong, R.S. and Lay, P.A. and Gow, A.J. and Weiss, M.J. and MacKay, J.P. and Shi, Y.},\ntitle={Molecular mechanism of AHSP-mediated stabilization of α-hemoglobin},\njournal={Cell},\nyear={2004},\nvolume={119},\nnumber={5},\npages={629-640},\ndoi={10.1016/j.cell.2004.11.025},\nnote={cited By 134},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-8844285199&doi=10.1016%2fj.cell.2004.11.025&partnerID=40&md5=27f288dcb2581a94812fe009ea36514c},\naffiliation={Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, 08544, Princeton, NJ, United States; Sch. of Molec. and Microbial Biosci., University of Sydney, NSW 2006, Sydney, Australia; Children's Hosp. Philadelphia U., Philadelphia, PA, United States; Ctr. Heavy Met. Res. Ctr. Struct. B., School of Chemistry, University of Sydney, NSW 2006, Sydney, Australia},\nabstract={Hemoglobin A (HbA), the oxygen delivery system in humans, comprises two α and two β subunits. Free α-hemoglobin (αHb) is unstable, and its precipitation contributes to the pathophysiology of β thalassemia. In erythrocytes, the α-hemoglobin stabilizing protein (AHSP) binds αHb and inhibits its precipitation. The crystal structure of AHSP bound to Fe(II)-αHb reveals that AHSP specifically recognizes the G and H helices of αHb through a hydrophobic interface that largely recapitulates the α1-β1 interface of hemoglobin. The AHSP-αHb interactions are extensive but suboptimal, explaining why β-hemoglobin can competitively displace AHSP to form HbA. Remarkably, the Fe(II)-heme group in AHSP bound αHb is coordinated by the distal but not the proximal histidine. Importantly, binding to AHSP facilitates the conversion of oxy-αHb to a deoxygenated, oxidized [Fe(III)], nonreactive form in which all six coordinate positions are occupied. These observations reveal the molecular mechanisms by which AHSP stabilizes free αHb.},\nkeywords={alpha hemoglobin;  alpha hemoglobin stabilizing protein;  heme;  hemoglobin;  histidine;  iron;  protein;  unclassified drug, article;  crystal structure;  deoxygenation;  erythrocyte;  hydrophobicity;  oxidation;  precipitation;  priority journal;  protein binding;  protein stability, Oxy},\ncorrespondence_address1={Weiss, M.J.; Children's Hosp. Philadelphia U., Philadelphia, PA, United States; email: yshi@molbio.princeton.edu},\npublisher={Elsevier B.V.},\nissn={00928674},\ncoden={CELLB},\npubmed_id={15550245},\nlanguage={English},\nabbrev_source_title={Cell},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structural studies on a protein-binding zinc-finger domain of eos reveal both similarities and differences to classical zinc fingers.\n \n \n \n \n\n\n \n Westman, B.; Perdomo, J.; Matthews, J.; Crossley, M.; and Mackay, J.\n\n\n \n\n\n\n Biochemistry, 43(42): 13318-13327. 2004.\n cited By 11\n\n\n\n
\n\n\n\n \n \n $\"Structural$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Westman200413318,\nauthor={Westman, B.J. and Perdomo, J. and Matthews, J.M. and Crossley, M. and Mackay, J.P.},\ntitle={Structural studies on a protein-binding zinc-finger domain of eos reveal both similarities and differences to classical zinc fingers},\njournal={Biochemistry},\nyear={2004},\nvolume={43},\nnumber={42},\npages={13318-13327},\ndoi={10.1021/bi049506a},\nnote={cited By 11},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-6344254942&doi=10.1021%2fbi049506a&partnerID=40&md5=a8f51141fecd870e37eb93d60604a94d},\naffiliation={Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW 2006, Australia; Sch. of Molec. and Microbial Biosci., Building G08, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={The oligomerization domain that is present at the C terminus of Ikaros-family proteins and the protein Trps-1 is important for the proper regulation of developmental processes such as hematopoiesis. Remarkably, this domain is predicted to contain two classical zinc fingers (ZnFs), domains normally associated with the recognition of nucleic acids. The preference for protein binding by these predicted ZnFs is not well-understood. We have used a range of methods to gain insight into the structure of this domain. Circular dichroism, UV - vis, and NMR experiments carried out on the C-terminal domain of Eos (EosC) revealed that the two putative ZnFs (C1 and C2) are separable, i.e., capable of folding independently in the presence of ZnII. We next determined the structure of EosC2 using NMR spectroscopy, revealing that, although the overall fold of EosC2 is similar to other classical ZnFs, a number of differences exist. For example, the conformation of the C terminus of EosC2 appears to be flexible and may result in a major rearrangement of the zinc ligands. Finally, alanine-scanning mutagenesis was used to identify the residues that are involved in the homo- and hetero-oligomerization of Eos, and these results are discussed in the context of the structure of EosC. These studies provide the first structural insights into how EosC mediates protein - protein interactions and contributes to our understanding of why it does not exhibit high-affinity DNA binding.},\nkeywords={Biochemistry;  DNA;  Mutagenesis;  Nuclear magnetic resonance spectroscopy;  Oligomers;  Zinc, Hematopoiesis;  Oligomerization;  Protein interactions;  Protein-binding zinc-finger domains, Proteins, alanine;  ligand;  nucleic acid;  zinc;  zinc finger protein, article;  carboxy terminal sequence;  circular dichroism;  DNA binding;  hematopoiesis;  mutagenesis;  nuclear magnetic resonance spectroscopy;  oligomerization;  priority journal;  protein binding;  protein domain;  protein protein interaction;  zinc finger motif, Eos;  Homo},\ncorrespondence_address1={Mackay, J.P.; Sch. of Molec. and Microbial Biosci., , Sydney, NSW 2006, Australia; email: j.mackay@mmb.usyd.edu.au},\npublisher={American Chemical Society},\nissn={00062960},\ncoden={BICHA},\npubmed_id={15491138},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structural and functional analysis of the Josephin domain of the polyglutamine protein ataxin-3.\n \n \n \n \n\n\n \n Chow, M.; MacKay, J.; Whisstock, J.; Scanlon, M.; and Bottomley, S.\n\n\n \n\n\n\n Biochemical and Biophysical Research Communications, 322(2): 387-394. 2004.\n cited By 53\n\n\n\n
\n\n\n\n \n \n $\"Structural$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Chow2004387,\nauthor={Chow, M.K.M. and MacKay, J.P. and Whisstock, J.C. and Scanlon, M.J. and Bottomley, S.P.},\ntitle={Structural and functional analysis of the Josephin domain of the polyglutamine protein ataxin-3},\njournal={Biochemical and Biophysical Research Communications},\nyear={2004},\nvolume={322},\nnumber={2},\npages={387-394},\ndoi={10.1016/j.bbrc.2004.07.131},\nnote={cited By 53},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-6044269458&doi=10.1016%2fj.bbrc.2004.07.131&partnerID=40&md5=7e16a2c3dfd0b77f0901f2d4af8bcb40},\naffiliation={Dept. of Biochem. and Molec. Biology, P.O. Box 13D, Monash Univ., Vic. 3800, Australia, Australia; Sch. of Molec. and Microbial Biosci., University of Sydney, NSW 2006, Australia, Australia; Department of Medicinal Chemistry, Victorian College of Pharmacy, Monash Univ., Vic. 3800, Australia, Australia},\nabstract={Ataxin-3 belongs to the family of polyglutamine proteins, which are associated with nine different neurodegenerative disorders. Relatively little is known about the structural and functional properties of ataxin-3, and only recently have these aspects of the protein begun to be explored. We have performed a preliminary investigation into the conserved N-terminal domain of ataxin-3, termed Josephin. We show that Josephin is a monomeric domain which folds into a globular conformation and possesses ubiquitin protease activity. In addition, we demonstrate that the presence of the polyglutamine region of the protein does not alter the structure of the protein. However, its presence destabilizes the Josephin domain. The implications of these data in the pathogenesis of polyglutamine repeat proteins are discussed. © 2004 Elsevier Inc. All rights reserved.},\nauthor_keywords={Ataxin-3;  Conformational disease;  Fibril;  Polyglutamine repeat;  Protein folding;  Protein misfolding},\nkeywords={ataxin 3;  polyglutamine;  protein;  proteinase;  ubiquitin;  unclassified drug;  ATXN3 protein, human;  nerve protein;  nuclear protein;  peptide;  polyglutamine;  repressor protein, amino terminal sequence;  article;  controlled study;  enzyme activity;  nonhuman;  nucleotide sequence;  priority journal;  protein analysis;  protein conformation;  protein domain;  protein structure;  structure analysis;  chemistry;  genetics;  human;  isolation and purification;  Machado Joseph disease;  metabolism;  nuclear magnetic resonance spectroscopy;  physiology;  protein tertiary structure;  thermodynamics, Endopeptidases;  Humans;  Machado-Joseph Disease;  Magnetic Resonance Spectroscopy;  Nerve Tissue Proteins;  Nuclear Proteins;  Peptides;  Protein Structure, Tertiary;  Repressor Proteins;  Thermodynamics;  Ubiquitin},\ncorrespondence_address1={Dept. of Biochem. and Molec. Biology, Australia; email: steve.bottomley@med.monash.edu.au},\nissn={0006291X},\ncoden={BBRCA},\npubmed_id={15325242},\nlanguage={English},\nabbrev_source_title={Biochem. Biophys. Res. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Classic zinc finger from friend of GATA mediates an interaction with the coiled-coil of transforming acidic coiled-coil 3.\n \n \n \n \n\n\n \n Simpson, R.; Lee, S.; Bartle, N.; Sum, E.; Visvader, J.; Matthews, J.; Mackay, J.; and Crossley, M.\n\n\n \n\n\n\n Journal of Biological Chemistry, 279(38): 39789-39797. 2004.\n cited By 28\n\n\n\n
\n\n\n\n \n \n $\"Classic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Simpson200439789,\nauthor={Simpson, R.J.Y. and Lee, S.H.Y. and Bartle, N. and Sum, E.Y. and Visvader, J.E. and Matthews, J.M. and Mackay, J.P. and Crossley, M.},\ntitle={Classic zinc finger from friend of GATA mediates an interaction with the coiled-coil of transforming acidic coiled-coil 3},\njournal={Journal of Biological Chemistry},\nyear={2004},\nvolume={279},\nnumber={38},\npages={39789-39797},\ndoi={10.1074/jbc.M404130200},\nnote={cited By 28},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-4544366535&doi=10.1074%2fjbc.M404130200&partnerID=40&md5=0f131222a132dcba70daed2a4487b34a},\naffiliation={Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW 2006, Australia; Walter/Eliza Hall Inst. of Med. Res., Bone Marrow Research Laboratories, Royal Melbourne Hospital, 1G Royal Parade, Parkville, Vic. 3050, Australia},\nabstract={Classic zinc finger domains (cZFs) consist of a β-hairpin followed by an α-helix. They are among the most abundant of all protein domains and are often found in tandem arrays in DNA-binding proteins, with each finger contributing an α-helix to effect sequence-specific DNA recognition. Lone cZFs, not found in tandem arrays, have been postulated to function in protein interactions. We have studied the transcriptional co-regulator Friend of GATA (FOG), which contains nine zinc fingers. We have discovered that the third cZF of FOG contacts a coiled-coil domain in the centrosomal protein transforming acidic coiled-coil 3 (TACC3). Although FOG-ZF3 exhibited low solubility, we have used a combination of mutational mapping and protein engineering to generate a derivative that was suitable for in vitro and structural analysis. We report that the α-helix of FOG-ZF3 recognizes a C-terminal portion of the TACC3 coiled-coil. Remarkably, the α-helical surface utilized by FOG-ZF3 is the same surface responsible for the well established sequence-specific DNA-binding properties of many other cZFs. Our data demonstrate the versatility of cZFs and have implications for the analysis of many as yet uncharacterized cZF proteins.},\nkeywords={Derivatives;  DNA;  Surface phenomena;  Zinc, Classic zinc finger domains;  Mutational mapping;  Protein domains;  Tandem arrays, Proteins, cell protein;  friend of GATA transcription factor;  transcription factor;  transforming acidic coiled coil 3 protein;  unclassified drug, alpha helix;  article;  carboxy terminal sequence;  centrosome;  controlled study;  DNA binding;  gene mapping;  in vitro study;  nonhuman;  priority journal;  protein analysis;  protein domain;  protein engineering;  protein function;  protein protein interaction;  protein structure;  solubility;  structure analysis;  zinc finger motif, Amino Acid Sequence;  Animals;  Binding Sites;  Carrier Proteins;  Cells, Cultured;  Dimerization;  Fetal Proteins;  Humans;  Mice;  Molecular Sequence Data;  Nuclear Proteins;  Protein Structure, Quaternary;  Protein Structure, Secondary;  Protein Structure, Tertiary;  Solubility;  Transcription Factors;  Zinc Fingers},\ncorrespondence_address1={Mackay, J.P.; Sch. of Molec. and Microbial Biosci., , Sydney, NSW 2006, Australia; email: j.mackay@mmb.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={15234987},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Presence of transient helical segments in the galanin-like peptide evident from 1H NMR, circular dichroism, and prediction studies.\n \n \n \n \n\n\n \n Dastmalchi, S.; Church, W.; Morris, M.; Iismaa, T.; and Mackay, J.\n\n\n \n\n\n\n Journal of Structural Biology, 146(3): 261-271. 2004.\n cited By 7\n\n\n\n
\n\n\n\n \n \n $\"Presence$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Dastmalchi2004261,\nauthor={Dastmalchi, S. and Church, W.B. and Morris, M.B. and Iismaa, T.P. and Mackay, J.P.},\ntitle={Presence of transient helical segments in the galanin-like peptide evident from 1H NMR, circular dichroism, and prediction studies},\njournal={Journal of Structural Biology},\nyear={2004},\nvolume={146},\nnumber={3},\npages={261-271},\ndoi={10.1016/j.jsb.2004.01.004},\nnote={cited By 7},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-1942521630&doi=10.1016%2fj.jsb.2004.01.004&partnerID=40&md5=f3300e8d75ec6dd489baf1a2f7c0a082},\naffiliation={School of Pharmacy, Tabriz Univ. of Medical Sciences, Tabriz 51664, Iran; Sch. of Molec. and Microbial Biosci., Building G08, University of Sydney, Sydney, NSW 2006, Australia; Sch. of Molec. and Biomed. Science, University of Adelaide, Adelaide, SA 5005, Australia; Neurobiology Program, Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia},\nabstract={Galanin and its newly discovered relative galanin-like peptide (GALP) are neuropeptides that are implicated in the neuroendocrine regulation of body weight and reproduction. GALP encompasses within its sequence the first 13 residues of galanin, known to be crucial to binding and activation of galanin receptor (GalR) subtypes. Using 2D-NMR and circular dichroism spectroscopy we demonstrated that GALP does not adopt a preferred conformation in pure water alone. However, it shows characteristics of transient turn-like structures in two distinct regions of its sequence, 11-23 and 41-49. These transient ordered structures, nascent helices, probably form stable helical structures upon addition of the helix-inducing solvent, trifluoroethanol, as determined by circular dichroism studies. Secondary structure prediction methods also predict the presence of two helical regions in the sequence of GALP overlapping reasonably with those regions identified as nascent helical structures by experimental methods. © 2004 Elsevier Inc. All rights reserved.},\nauthor_keywords={Circular dichroism;  Galanin-like peptide;  Nascent helix;  NMR spectroscopy;  Secondary structure prediction},\nkeywords={galanin like peptide;  galanin receptor;  neuropeptide;  trifluoroethanol;  water, amino acid sequence;  article;  body weight;  circular dichroism;  experimental test;  macromolecule;  neuroendocrine system;  prediction;  priority journal;  protein binding;  protein conformation;  protein function;  protein structure;  proton nuclear magnetic resonance;  receptor binding;  reproduction, Animals;  Circular Dichroism;  Galanin-Like Peptide;  Magnetic Resonance Spectroscopy;  Models, Molecular;  Protein Conformation;  Protein Structure, Secondary;  Swine;  Trifluoroethanol;  Water},\ncorrespondence_address1={Dastmalchi, S.; School of Pharmacy, , Tabriz 51664, Iran; email: dastmalchi.s@tbzmed.ac.ir},\nissn={10478477},\ncoden={JSBIE},\npubmed_id={15099568},\nlanguage={English},\nabbrev_source_title={J. Struct. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n TC-1 Is a Novel Tumorigenic and Natively Disordered Protein Associated with Thyroid Cancer.\n \n \n \n \n\n\n \n Sunde, M.; McGrath, K.; Young, L.; Matthews, J.; Chua, E.; Mackay, J.; and Death, A.\n\n\n \n\n\n\n Cancer Research, 64(8): 2766-2773. 2004.\n cited By 64\n\n\n\n
\n\n\n\n \n \n $\"TC-1$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Sunde20042766,\nauthor={Sunde, M. and McGrath, K.C.Y. and Young, L. and Matthews, J.M. and Chua, E.L. and Mackay, J.P. and Death, A.K.},\ntitle={TC-1 Is a Novel Tumorigenic and Natively Disordered Protein Associated with Thyroid Cancer},\njournal={Cancer Research},\nyear={2004},\nvolume={64},\nnumber={8},\npages={2766-2773},\ndoi={10.1158/0008-5472.CAN-03-2093},\nnote={cited By 64},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-13844261745&doi=10.1158%2f0008-5472.CAN-03-2093&partnerID=40&md5=5dd3acbe7ff6a0a080df2e9bf045816a},\naffiliation={Sch. of Molec. and Microbial Biosci., University of Sydney, Australia; Discipline of Medicine, University of Sydney, Australia; Department of Endocrinology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; Heart Research Institute, 145 Missenden Road, Camperdown, NSW 2050, Australia},\nabstract={A novel gene, thyroid cancer 1 (TC-1), was found recently to be overexpressed in thyroid cancer. TC-1 shows no homology to any of the known thyroid cancer-associated genes. We have produced stable transformants of normal thyroid cells that express the TC-1 gene, and these cells show increased proliferation rates and anchorage-independent growth in soft agar. Apoptosis rates also are decreased in the transformed cells. We also have expressed recombinant TC-1 protein and have undertaken a structural and functional characterization of the protein. The protein is monomeric and predominantly unstructured under conditions of physiologic salt and pH. This places it in the category of natively disordered proteins, a rapidly expanding group of proteins, many members of which play critical roles in cell regulation processes. We show that the protein can be phosphorylated by cyclic AMP-dependent protein kinase and protein kinase C, and the activity of both of these kinases is up-regulated when cells are stably transfected with TC-1. These results suggest that overexpression of TC-1 may be important in thyroid carcinogenesis.},\nkeywords={agar;  cyclic AMP;  protein kinase;  protein kinase C;  sodium chloride, article;  carcinogenesis;  cell anchorage;  cell growth;  cell proliferation;  controlled study;  disease association;  gene;  gene expression;  genetic transfection;  human;  human cell;  pH;  priority journal;  protein phosphorylation;  protein structure;  regulatory mechanism;  structure activity relation;  tc 1 gene;  thyroid cancer;  thyroid cell;  upregulation, Apoptosis;  Cell Adhesion;  Cell Division;  Cell Line, Tumor;  Cyclic AMP-Dependent Protein Kinases;  Humans;  Neoplasm Proteins;  Nuclear Magnetic Resonance, Biomolecular;  Phosphorylation;  Protein Conformation;  Protein Kinase C;  Signal Transduction;  Thyroid Neoplasms;  Transfection},\ncorrespondence_address1={Death, A.K.; Heart Research Institute, 145 Missenden Road, Camperdown, NSW 2050, Australia; email: deatha@hri.org.au},\nissn={00085472},\ncoden={CNREA},\npubmed_id={15087392},\nlanguage={English},\nabbrev_source_title={Cancer Res.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Loss of α-hemoglobin-stabilizing protein impairs erythropoiesis and exacerbates β-thalassemia.\n \n \n \n \n\n\n \n Kong, Y.; Zhou, S.; Kihm, A.; Katein, A.; Yu, X.; Gell, D.; Mackay, J.; Adachi, K.; Foster-Brown, L.; Louden, C.; Gow, A.; and Weiss, M.\n\n\n \n\n\n\n Journal of Clinical Investigation, 114(10): 1457-1466. 2004.\n cited By 138\n\n\n\n
\n\n\n\n \n \n $\"Loss$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Kong20041457,\nauthor={Kong, Y. and Zhou, S. and Kihm, A.J. and Katein, A.M. and Yu, X. and Gell, D.A. and Mackay, J.P. and Adachi, K. and Foster-Brown, L. and Louden, C.S. and Gow, A.J. and Weiss, M.J.},\ntitle={Loss of α-hemoglobin-stabilizing protein impairs erythropoiesis and exacerbates β-thalassemia},\njournal={Journal of Clinical Investigation},\nyear={2004},\nvolume={114},\nnumber={10},\npages={1457-1466},\ndoi={10.1172/JCI21982},\nnote={cited By 138},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85047690518&doi=10.1172%2fJCI21982&partnerID=40&md5=16b2fe2d1ae75290544e946c9b3ac78f},\naffiliation={Cell and Molec. Biol. Grad. Program, Univ. of Pennsylvania Sch. of Med., Philadelphia, PA, United States; Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States; Safety Assessment, Astra-Zeneca Pharmaceuticals, L.P., Wilmington, DE, United States; Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW, Australia; Children's Hospital of Philadelphia, Univ. of Pennsylvania Sch. of Med., Philadelphia, PA 19104, United States; Johnson and Johnson, Somerville, NJ, United States},\nabstract={Hemoglobin (Hb) A production during red blood cell development is coordinated to minimize the deleterious effects of free α- and β-Hb subunits, which are unstable and cytotoxic. The α-Hb-stabilizing protein (AHSP) is an erythroid protein that specifically binds α-Hb and prevents its precipitation in vitro, which suggests that it may function to limit free α-Hb toxicities in vivo. We investigated this possibility through gene ablation and biochemical studies. AHSP-/- erythrocytes contained hemoglobin precipitates and were short-lived. In hematopoietic tissues, erythroid precursors were elevated in number but exhibited increased apoptosis. Consistent with unstable α-Hb, AHSP-/- erythrocytes contained increased ROS and evidence of oxidative damage. Moreover, purified recombinant AHSP inhibited ROS production by α-Hb in solution. Finally, loss of AHSP worsened the phenotype of β-thalassemia, a common inherited anemia characterized by excess free α-Hb. Together, the data support a model in which AHSP binds α-Hb transiently to stabilize its conformation and render it biochemically inert prior to Hb A assembly. This function is essential for normal erythropoiesis and, to a greater extent, in β-thalassemia. Our findings raise the possibility that altered AHSP expression levels could modulate the severity of β-thalassemia in humans.},\nkeywords={alpha hemoglobin stabilizing protein;  cell protein;  hemoglobin A;  hemoglobin alpha chain;  hemoglobin beta chain;  protein subunit;  reactive oxygen metabolite;  recombinant protein;  unclassified drug;  hemoglobin;  reactive oxygen metabolite, animal cell;  animal experiment;  animal model;  animal tissue;  apoptosis;  article;  beta thalassemia;  biosynthesis;  cell damage;  controlled study;  cytopathogenic effect;  disease severity;  erythroid precursor cell;  erythropoiesis;  hemoglobin synthesis;  mouse;  nonhuman;  oxidative stress;  phenotype;  precipitation;  priority journal;  protein assembly;  protein binding;  protein conformation;  protein depletion;  protein expression;  protein function;  protein protein interaction;  protein stability;  animal;  biological model;  chemistry;  comparative study;  erythrocyte;  genetics;  Heinz body;  heterozygote;  isolation and purification;  kinetics;  metabolism;  mouse mutant;  pathology;  physiology, Animals;  Apoptosis;  beta-Thalassemia;  Erythrocytes;  Erythropoiesis;  Heinz Bodies;  Hemoglobins;  Heterozygote;  Kinetics;  Mice;  Mice, Knockout;  Models, Biological;  Protein Conformation;  Reactive Oxygen Species;  Recombinant Proteins},\ncorrespondence_address1={Weiss, M.J.; Children's Hospital of Philadelphia, , Philadelphia, PA 19104, United States; email: weissmi@email.chop.edu},\npublisher={The American Society for Clinical Investigation},\nissn={00219738},\ncoden={JCINA},\npubmed_id={15545996},\nlanguage={English},\nabbrev_source_title={J. Clin. Invest.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Crystal and Solution Structures of a Superantigen from Yersinia pseudotuberculosis Reveal a Yelly-Roll Fold.\n \n \n \n \n\n\n \n Donadini, R.; Liew, C.; Kwan, A.; Mackay, J.; and Fields, B.\n\n\n \n\n\n\n Structure, 12(1): 145-156. 2004.\n cited By 24\n\n\n\n
\n\n\n\n \n \n $\"Crystal$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Donadini2004145,\nauthor={Donadini, R. and Liew, C.W. and Kwan, A.H.Y. and Mackay, J.P. and Fields, B.A.},\ntitle={Crystal and Solution Structures of a Superantigen from Yersinia pseudotuberculosis Reveal a Yelly-Roll Fold},\njournal={Structure},\nyear={2004},\nvolume={12},\nnumber={1},\npages={145-156},\ndoi={10.1016/j.str.2003.12.002},\nnote={cited By 24},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-1642493665&doi=10.1016%2fj.str.2003.12.002&partnerID=40&md5=93b528cbdc75c8811b32e600f3c781ed},\naffiliation={Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW 2006, Australia; Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Private Bag 92019, New Zealand; Therapeutic Goods Administration, PO Box 100, Woden, ACT 2606, Australia},\nabstract={Superantigens are a class of microbial proteins with the ability to excessively activate T cells by binding to the T cell receptor. The staphylococcal and streptococcal superantigens are closely related in structure and possess an N-terminal domain that resembles an OB fold and a C-terminal domain similar to a β-grasp fold. Yersinia pseudotuberculosis produces superantigens, YPMa, YPMb, and YPMc, which have no significant amino acid similarity to other proteins. We have determined the crystal and solution structures of YPMa, which show that the protein has a jelly-roll fold. The closest structural neighbors to YPMa are viral capsid proteins and members of the tumor necrosis factor superfamily. In the crystal structure, YPMa packs as a trimer, another feature shared with viral capsid proteins and TNF superfamily proteins. However, in solution YPMa behaves as a monomer, and any functional relevance of the trimer observed in the crystals is yet to be established.},\nkeywords={bacterial antigen;  bacterial protein;  capsid protein;  monomer;  superantigen;  tumor necrosis factor;  unclassified drug;  yersinia pseudotuberculosis derived mitogen a, antigen structure;  article;  crystal structure;  nonhuman;  nuclear magnetic resonance;  priority journal;  protein cross linking;  protein determination;  protein family;  protein folding;  protein function;  sequence homology;  structural homology;  virus capsid;  X ray crystallography;  Yersinia pseudotuberculosis, Bacteria (microorganisms);  Negibacteria;  Yersinia;  Yersinia pseudotuberculosis},\ncorrespondence_address1={Fields, B.A.; Therapeutic Goods Administration, PO Box 100, Woden, ACT 2606, Australia; email: barry.fields@health.gov.au},\npublisher={Cell Press},\nissn={09692126},\ncoden={STRUE},\npubmed_id={14725774},\nlanguage={English},\nabbrev_source_title={Structure},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2003\n \n \n (8)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n The C-terminal Domain of Eos Forms a High Order Complex in Solution.\n \n \n \n \n\n\n \n Westman, B.; Perdomo, J.; Sunde, M.; Crossley, M.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 278(43): 42419-42426. 2003.\n cited By 11\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Westman200342419,\nauthor={Westman, B.J. and Perdomo, J. and Sunde, M. and Crossley, M. and Mackay, J.P.},\ntitle={The C-terminal Domain of Eos Forms a High Order Complex in Solution},\njournal={Journal of Biological Chemistry},\nyear={2003},\nvolume={278},\nnumber={43},\npages={42419-42426},\ndoi={10.1074/jbc.M306817200},\nnote={cited By 11},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0142149099&doi=10.1074%2fjbc.M306817200&partnerID=40&md5=70880073f5f14af6098e59240413c461},\nabstract={Ikaros family transcription factors play important roles in the control of hematopoiesis. Family members are predicted to contain up to six classic zinc fingers that are arranged into N- and C-terminal domains. The N-terminal domain is responsible for site-specific DNA binding, whereas the C-terminal domain primarily mediates the homo- and hetero-oligomerization between family members. Although the mechanisms of action of these proteins are not completely understood, the zinc finger domains are known to play a central role. In the current study, we have sought to understand the physical and functional properties of these domains, in particular the C-terminal domain. We show that the N-terminal domain from Eos, and not its C-terminal region, is required to recognize GGGA consensus sequences. Surprisingly, in contrast to the behavior exhibited by Ikaros, the C-terminal domain of Eos inhibits the DNA-binding activity of the full-length protein. In addition, we have used a range of biophysical techniques to demonstrate that the C-terminal domain of Eos mediates the formation of complexes that consist of nine or ten molecules. These results constitute the first direct demonstration that Ikaros family proteins can form higher order complexes in solution, and we discuss this unexpected result in the context of what is currently known about the family members and their possible mechanism of action.},\nkeywords={Complexation;  DNA;  Isomerization;  Molecules, Transcription factors, Biochemistry, adenine;  amino acid;  guanine;  Ikaros transcription factor;  protein eos;  transcription factor;  unclassified drug;  zinc finger protein, amino acid sequence;  amino terminal sequence;  animal cell;  article;  biophysics;  carboxy terminal sequence;  complex formation;  consensus sequence;  hematopoiesis;  molecular recognition;  nonhuman;  priority journal;  protein DNA binding;  protein domain;  protein function;  sequence analysis;  zinc finger motif, Amino Acid Sequence;  Animals;  Carrier Proteins;  Consensus Sequence;  Dimerization;  DNA-Binding Proteins;  Ikaros Transcription Factor;  Nerve Tissue Proteins;  Protein Binding;  Protein Structure, Tertiary;  Sequence Alignment;  Solutions;  Transcription Factors;  Zinc Fingers, Animalia;  Eos;  Homo},\ncorrespondence_address1={email: j.mackay@mmb.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={12917396},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions.\n \n \n \n \n\n\n \n Simpson, R.; Cram, E.; Czolij, R.; Matthews, J.; Crossley, M.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 278(30): 28011-28018. 2003.\n cited By 45\n\n\n\n
\n\n\n\n \n \n $\"CCHX$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Simpson200328011,\nauthor={Simpson, R.J.Y. and Cram, E.D. and Czolij, R. and Matthews, J.M. and Crossley, M. and Mackay, J.P.},\ntitle={CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions},\njournal={Journal of Biological Chemistry},\nyear={2003},\nvolume={278},\nnumber={30},\npages={28011-28018},\ndoi={10.1074/jbc.M211146200},\nnote={cited By 45},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0042346328&doi=10.1074%2fjbc.M211146200&partnerID=40&md5=807368322eccb378e28b8c571df2472a},\naffiliation={Sch. of Molec./Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Classical (CCHH) zinc fingers are among the most common protein domains found in eukaryotes. They function as molecular recognition elements that mediate specific contact with DNA, RNA, or other proteins and are composed of a ββα fold surrounding a single zinc ion that is ligated by two cysteine and two histidine residues. In a number of variant zinc fingers, the final histidine is not conserved, and in other unrelated zinc binding domains, residues such as aspartate can function as zinc ligands. To test whether the final histidine is required for normal folding and the DNA-binding function of classical zinc fingers, we focused on finger 3 of basic Krüppel-like factor. The structure of this domain was determined using NMR spectroscopy and found to constitute a typical classical zinc finger. We generated a panel of substitution mutants at the final histidine in this finger and found that several of the mutants retained some ability to fold in the presence of zinc. Consistent with this result, we showed that mutation of the final histidine had only a modest effect on DNA binding in the context of the full three-finger DNA-binding domain of basic Krüppel-like factor. Further, the zinc binding ability of one of the point mutants was tested and found to be indistinguishable from the wild-type domain. These results suggest that the final zinc chelating histidine is not an essential feature of classical zinc fingers and have implications for zinc finger evolution, regulation, and the design of experiments testing the functional roles of these domains.},\nkeywords={Derivatives;  DNA;  Nuclear magnetic resonance spectroscopy;  Proteins;  Zinc, Eukaryotes, Biochemistry, cysteine;  DNA;  histidine;  ligand;  RNA;  zinc finger protein;  zinc ion, amino acid substitution;  article;  controlled study;  eukaryote;  human;  nonhuman;  nuclear magnetic resonance spectroscopy;  point mutation;  priority journal;  protein DNA binding;  protein DNA interaction;  protein domain;  protein folding;  protein function;  protein structure;  rat;  regulatory mechanism;  structure analysis;  wild type, Amino Acid Sequence;  Animals;  Aspartic Acid;  Circular Dichroism;  Cysteine;  DNA;  DNA-Binding Proteins;  Dose-Response Relationship, Drug;  Histidine;  Humans;  Kinetics;  Magnetic Resonance Spectroscopy;  Models, Molecular;  Molecular Sequence Data;  Mutation;  Plasmids;  Protein Binding;  Protein Conformation;  Protein Folding;  Protein Structure, Tertiary;  Sequence Homology, Amino Acid;  Spectrophotometry, Atomic;  Ultracentrifugation;  Ultraviolet Rays;  Zinc;  Zinc Fingers, Eukaryota},\ncorrespondence_address1={Mackay, J.P.; Sch. of Molec./Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.mackay@mmb.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={12736264},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Engineering a protein scaffold from a PHD finger.\n \n \n \n \n\n\n \n Kwan, A.; Gell, D.; Verger, A.; Crossley, M.; Matthews, J.; and Mackay, J.\n\n\n \n\n\n\n Structure, 11(7): 803-813. 2003.\n cited By 53\n\n\n\n
\n\n\n\n \n \n $\"Engineering$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Kwan2003803,\nauthor={Kwan, A.H.Y. and Gell, D.A. and Verger, A. and Crossley, M. and Matthews, J.M. and Mackay, J.P.},\ntitle={Engineering a protein scaffold from a PHD finger},\njournal={Structure},\nyear={2003},\nvolume={11},\nnumber={7},\npages={803-813},\ndoi={10.1016/S0969-2126(03)00122-9},\nnote={cited By 53},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0038646892&doi=10.1016%2fS0969-2126%2803%2900122-9&partnerID=40&md5=6d1c1fb990a83c548dd185a73422031e},\naffiliation={Sch. of Molec./Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={The design of proteins with tailored functions remains a relatively elusive goal. Small size, a well-defined structure, and the ability to maintain structural integrity despite multiple mutations are all desirable properties for such designer proteins. Many zinc binding domains fit this description. We determined the structure of a PHD finger from the transcriptional cofactor Mi2β and investigated the suitability of this domain as a scaffold for presenting selected binding functions. The two flexible loops in the structure were mutated extensively by either substitution or expansion, without affecting the overall fold of the domain. A binding site for the corepressor CtBP2 was also grafted onto the domain, creating a new PHD domain that can specifically bind CtBP2 both in vitro and in the context of a eukaryotic cell nucleus. These results represent a step toward designing new regulatory proteins for modulating aberrant gene expression in vivo.},\nkeywords={protein;  transcription factor;  zinc, amino acid substitution;  article;  binding site;  cell nucleus;  gene expression;  priority journal;  protein binding;  protein domain;  protein engineering;  protein function;  protein structure;  zinc finger motif, Eukaryota},\ncorrespondence_address1={Mackay, J.P.; Sch. of Molec./Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.mackay@mmb.usyd.edu.au},\npublisher={Cell Press},\nissn={09692126},\ncoden={STRUE},\npubmed_id={12842043},\nlanguage={English},\nabbrev_source_title={Structure},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The structure of the zinc finger domain from human splicing factor ZNF265 fold.\n \n \n \n \n\n\n \n Plambeck, C.; Kwan, A.; Adams, D.; Westman, B.; Van der Weyden, L.; Medcalf, R.; Morris, B.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 278(25): 22805-22811. 2003.\n cited By 30\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Plambeck200322805,\nauthor={Plambeck, C.A. and Kwan, A.H.Y. and Adams, D.J. and Westman, B.J. and Van der Weyden, L. and Medcalf, R.L. and Morris, B.J. and Mackay, J.P.},\ntitle={The structure of the zinc finger domain from human splicing factor ZNF265 fold},\njournal={Journal of Biological Chemistry},\nyear={2003},\nvolume={278},\nnumber={25},\npages={22805-22811},\ndoi={10.1074/jbc.M301896200},\nnote={cited By 30},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0038604103&doi=10.1074%2fjbc.M301896200&partnerID=40&md5=f737a4ca50081249ad11d327b4ac0cf3},\naffiliation={Monash University, Department of Medicine, Box Hill Hospital, Box Hill, Vic. 3128, Australia; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom},\nabstract={Identification of the protein domains that are responsible for RNA recognition has lagged behind the characterization of protein-DNA interactions. However, it is now becoming clear that a range of structural motifs bind to RNA and their structures and molecular mechanisms of action are beginning to be elucidated. In this report, we have expressed and purified one of the two putative RNA-binding domains from ZNF265, a protein that has been shown to bind to the spliceosomal components U1-70K and U2AF35 and to direct alternative splicing. We show that this domain, which contains four highly conserved cysteine residues, forms a stable, monomeric structure upon the addition of 1 molar eq of Zn(II). Determination of the solution structure of this domain reveals a conformation comprising two stacked β-hairpins oriented at ·80° to each other and sandwiching the zinc ion; the fold resembles the zinc ribbon class of zinc-binding domains, although with one less β-strand than most members of the class. Analysis of the structure reveals a striking resemblance to known RNA-binding motifs in terms of the distribution of key surface residues responsible for making RNA contacts, despite a complete lack of structural homology. Furthermore, we have used an RNA gel shift assay to demonstrate that a single crossed finger domain from ZNF265 is capable of binding to an RNA message. Taken together, these results define a new RNA-binding motif and should provide insight into the functions of the &gt;100 uncharacterized proteins in the sequence data bases that contain this domain.},\nkeywords={Biochemistry;  Chemical bonds;  Conformations;  Molecular structure;  RNA;  Zinc, Solution structure, Proteins, amino acid;  cysteine;  protein U1 70k;  protein U2AF35;  protein znf265;  regulator protein;  RNA;  RNA binding protein;  unclassified drug;  zinc ion, alternative RNA splicing;  amino acid sequence;  article;  beta sheet;  molecular recognition;  priority journal;  protein conformation;  protein expression;  protein function;  protein motif;  protein RNA binding;  protein structure;  sequence analysis;  spliceosome;  structure analysis;  zinc finger motif},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={12657633},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Structural basis for the recognition of Idb1 by the N-terminal LIM domains of LMO2 and LMO4.\n \n \n \n \n\n\n \n Deane, J.; Mackay, J.; Kwan, A.; Sum, E.; Visvader, J.; and Matthews, J.\n\n\n \n\n\n\n EMBO Journal, 22(9): 2224-2233. 2003.\n cited By 60\n\n\n\n
\n\n\n\n \n \n $\"Structural$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Deane20032224,\nauthor={Deane, J.E. and Mackay, J.P. and Kwan, A.H.Y. and Sum, E.Y.M. and Visvader, J.E. and Matthews, J.M.},\ntitle={Structural basis for the recognition of Idb1 by the N-terminal LIM domains of LMO2 and LMO4},\njournal={EMBO Journal},\nyear={2003},\nvolume={22},\nnumber={9},\npages={2224-2233},\ndoi={10.1093/emboj/cdg196},\nnote={cited By 60},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037543995&doi=10.1093%2femboj%2fcdg196&partnerID=40&md5=6cb8f920f435149333f628533dd6929a},\naffiliation={Sch. of Molec./Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Walter/Eliza Hall Inst. of Med. Res., 1G Royal Parade, Parkville, Vic. 3050, Australia},\nabstract={LMO2 and LMO4 are members of a small family of nuclear transcriptional regulators that are important for both normal development and disease processes. LMO2 is essential for hemopoiesis and angiogenesis, and inappropriate overexpression of this protein leads to T-cell leukemias. LMO4 is developmentally regulated in the mammary gland and has been implicated in breast oncogenesis. Both proteins comprise two tandemly repeated LIM domains. LMO2 and LMO4 interact with the ubiquitous nuclear adaptor protein Idb1/NLI/CLIM2, which associates with the LIM domains of LMO and LIM homeodomain proteins via its LIM interaction domain (Idb1-LID). We report the solution structures of two LMO:Idb1 complexes (PDB: 1M3V and 1J20) and show that Idb1-LID binds to the N-terminal LIM domain (LIM1) of LMO2 and LMO4 in an extended conformation, contributing a third strand to a β-hairpin in LIM1 domains. These findings constitute the first molecular definition of LIM-mediated protein-protein interactions and suggest a mechanism by which Idb1 can bind a variety of LIM domains that share low sequence homology.},\nauthor_keywords={Idb1;  LIM domains;  LMO2;  LMO4;  Protein complex},\nkeywords={adaptor protein;  homeodomain protein;  nuclear protein;  protein Idb1;  protein LMO2;  protein lmo4;  unclassified drug, amino terminal sequence;  angiogenesis;  article;  beta sheet;  breast carcinogenesis;  complex formation;  embryo;  hematopoiesis;  human;  human cell;  molecular recognition;  nucleotide sequence;  priority journal;  protein conformation;  protein domain;  protein expression;  protein protein interaction;  protein structure;  sequence homology;  T cell leukemia, Amino Acid Sequence;  Circular Dichroism;  DNA-Binding Proteins;  Homeodomain Proteins;  Inhibitor of Differentiation Protein 1;  Metalloproteins;  Models, Molecular;  Molecular Sequence Data;  Nuclear Magnetic Resonance, Biomolecular;  Protein Conformation;  Repressor Proteins;  Sequence Homology, Amino Acid;  Spectrophotometry, Ultraviolet;  Transcription Factors},\ncorrespondence_address1={Matthews, J.M.; Sch. of Molec./Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.matthews@mmb.usyd.edu.au},\nissn={02614189},\ncoden={EMJOD},\npubmed_id={12727888},\nlanguage={English},\nabbrev_source_title={EMBO J.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Solution structure and behaviour of Δ-m-α-[Ru(R,R- picchxnMe2)(phi)]2+ by NMR spectroscopy and molecular modelling.\n \n \n \n \n\n\n \n Proudfoot, E.; Mackay, J.; and Karuso, P.\n\n\n \n\n\n\n Dalton Transactions, (2): 165-170. 2003.\n cited By 11\n\n\n\n
\n\n\n\n \n \n $\"Solution$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Proudfoot2003165,\nauthor={Proudfoot, E.M. and Mackay, J.P. and Karuso, P.},\ntitle={Solution structure and behaviour of Δ-m-α-[Ru(R,R- picchxnMe2)(phi)]2+ by NMR spectroscopy and molecular modelling},\njournal={Dalton Transactions},\nyear={2003},\nnumber={2},\npages={165-170},\ndoi={10.1039/b208846k},\nnote={cited By 11},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-2942642705&doi=10.1039%2fb208846k&partnerID=40&md5=a6c5191d097829585fa3ee4981ec31e8},\naffiliation={Department of Chemistry, Macquarie University, NSW 2109, Australia; Department of Biochemistry, University of Sydney, NSW 2006, Australia},\nabstract={The self-association of the DNA metalloprobe Δ-cis-α-[Ru(R,R- picchxnMe2)(phi)]2+ (α-phi) in aqueous solution has been investigated using 1H NMR spectroscopy and molecular modelling. The concentration dependence of proton chemical shifts of the complex gave initial indications of a self-associated species, while its structural isomer Δ-cis-β-[Ru(R,R-picchxnMe2)(phi)]2+ (β-phi) showed no such dependence. 2D-COSY and 2D-ROESY experiments were used for the complete assignment of the proton resonances of both isomers and allowed a qualitative determination of the self-association of the a isomer through the detection of intermolecular ROEs. NMR spectroscopy can also be effectively used to differentiate Δ- and Λ-diastereomers. In addition, we show, by pulsed field gradient longitudinal eddy-current delay (PFGLED) NMR spectroscopy, that α-phi self-associates at higher concentrations with an effective molecular weight at 25 mM three times that at 2.5 mM. This apparent oligomerisation was not observed for the β-isomer. © The Royal Society of Chemistry 2003.},\nkeywords={Computer simulation;  DNA;  Eddy currents;  Isomers;  Mathematical models;  Molecular weight;  Nuclear magnetic resonance;  Oligomers;  Resonance;  Spectroscopic analysis, Chemical shifts;  Metalloprobes;  Molecular modeling;  Self-association, Association reactions},\ncorrespondence_address1={Department of Chemistry, , NSW 2109, Australia; email: Peter.Karuso@mq.edu.au},\nissn={14779226},\nlanguage={English},\nabbrev_source_title={Dalton Trans.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Cardiac hypertrophy and histone deacetylase-dependent transcriptional repression mediated by the atypical homeodomain protein Hop.\n \n \n \n \n\n\n \n Kook, H.; Lepore, J.; Gitler, A.; Lu, M.; Yung, W.; Mackay, J.; Zhou, R.; Ferrari, V.; Gruber, P.; and Epstein, J.\n\n\n \n\n\n\n Journal of Clinical Investigation, 112(6): 863-871. 2003.\n cited By 269\n\n\n\n
\n\n\n\n \n \n $\"Cardiac$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Kook2003863,\nauthor={Kook, H. and Lepore, J.J. and Gitler, A.D. and Lu, M.M. and Yung, W.W.-M. and Mackay, J. and Zhou, R. and Ferrari, V. and Gruber, P. and Epstein, J.A.},\ntitle={Cardiac hypertrophy and histone deacetylase-dependent transcriptional repression mediated by the atypical homeodomain protein Hop},\njournal={Journal of Clinical Investigation},\nyear={2003},\nvolume={112},\nnumber={6},\npages={863-871},\ndoi={10.1172/JCI19137},\nnote={cited By 269},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85047694248&doi=10.1172%2fJCI19137&partnerID=40&md5=87cb6c38850dfdcc95a85c5fd4cd0493},\naffiliation={Cardiovascular Division, Univ. of Pennsylvania Health System, Philadelphia, PA, United States; Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW, Australia; Department of Radiology, University of Pennsylvania, Philadelphia, PA, United States; Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA, United States; 954 Biomedical Research Building II, 421 Curie Boulevard, Philadelphia, PA 19104, United States},\nabstract={Activation of multiple pathways is associated with cardiac hypertrophy and heart failure. Repression of antihypertrophic pathways has rarely been demonstrated to cause cardiac hypertrophy in vivo. Hop is an unusual homeodomain protein that is expressed by embryonic and postnatal cardiac myocytes. Unlike other homeodomain proteins, Hop does not bind DNA. Rather, it modulates cardiac growth and proliferation by inhibiting the transcriptional activity of serum response factor (SRF) in cardiomyocytes. Here we show that Hop can inhibit SRF-dependent transcriptional activation by recruiting histone deacetylase (HDAC) activity and can form a complex that includes HDAC2. Transgenic mice that overexpress Hop develop severe cardiac hypertrophy, cardiac fibrosis, and premature death. A mutant form of Hop, which does not recruit HDAC activity, does not induce hypertrophy. Treatment of Hop transgenic mice with trichostatin A, an HDAC inhibitor, prevents hypertrophy. In addition trichostatin A also attenuates hypertrophy induced by infusion of isoproterenol. Thus, chromatin remodeling and repression of otherwise active transcriptional processes can result in hypertrophy and heart failure, and this process can be blocked with chemical HDAC inhibitors.},\nkeywords={histone deacetylase;  histone deacetylase 2;  histone deacetylase inhibitor;  homeodomain protein;  isoprenaline;  mutant protein;  protein hop;  serum response factor;  trichostatin A;  unclassified drug;  cardiotonic agent;  histone deacetylase;  Hop protein, mouse;  repressor protein;  serum response factor, adolescent;  animal cell;  animal model;  animal tissue;  article;  cell proliferation;  chromatin assembly and disassembly;  chromatin structure;  complex formation;  controlled study;  embryo cell;  enzyme activity;  gene overexpression;  gene repression;  heart development;  heart failure;  heart hypertrophy;  heart muscle cell;  heart muscle fibrosis;  mortality;  mouse;  nonhuman;  perinatal period;  priority journal;  protein expression;  protein function;  transcription regulation;  transgenic mouse;  animal;  cardiomegaly;  cell line;  gene expression regulation;  genetic transcription;  genetics;  heart muscle;  hemodynamics;  human;  metabolism;  pathology;  survival rate, Animals;  Cardiomegaly;  Cardiotonic Agents;  Cell Line;  Gene Expression Regulation;  Hemodynamic Processes;  Histone Deacetylases;  Homeodomain Proteins;  Humans;  Isoproterenol;  Mice;  Mice, Transgenic;  Myocardium;  Repressor Proteins;  Serum Response Factor;  Survival Rate;  Transcription, Genetic},\ncorrespondence_address1={Epstein, J.A.; 954 Biomedical Research Building II, 421 Curie Boulevard, Philadelphia, PA 19104, United States; email: epsteinj@mail.med.upenn.edu},\npublisher={The American Society for Clinical Investigation},\nissn={00219738},\ncoden={JCINA},\npubmed_id={12975471},\nlanguage={English},\nabbrev_source_title={J. Clin. Invest.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Pentaprobe: a comprehensive sequence for the one-step detection of DNA-binding activities.\n \n \n \n \n\n\n \n Kwan, A.; Czolij, R.; Mackay, J.; and Crossley, M.\n\n\n \n\n\n\n Nucleic acids research, 31(20): e124. 2003.\n cited By 24\n\n\n\n
\n\n\n\n \n \n $\"Pentaprobe:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Kwan2003,\nauthor={Kwan, A.H. and Czolij, R. and Mackay, J.P. and Crossley, M.},\ntitle={Pentaprobe: a comprehensive sequence for the one-step detection of DNA-binding activities.},\njournal={Nucleic acids research},\nyear={2003},\nvolume={31},\nnumber={20},\npages={e124},\ndoi={10.1093/nar/gng124},\nnote={cited By 24},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-1542499131&doi=10.1093%2fnar%2fgng124&partnerID=40&md5=f9bc0fa8e99b18106e195b60bb983200},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, G08NSW  2006, Australia},\nabstract={The rapid increase in the number of novel proteins identified in genome projects necessitates simple and rapid methods for assigning function. We describe a strategy for determining whether novel proteins possess typical sequence-specific DNA-binding activity. Many proteins bind recognition sequences of 5 bp or less. Given that there are 4(5) possible 5 bp sites, one might expect the length of sequence required to cover all possibilities would be 4(5) x 5 or 5120 nt. But by allowing overlaps, utilising both strands and using a computer algorithm to generate the minimum sequence, we find the length required is only 516 base pairs. We generated this sequence as six overlapping double-stranded oligonucleotides, termed pentaprobe, and used it in gel retardation experiments to assess DNA binding by both known and putative DNA-binding proteins from several protein families. We have confirmed binding by the zinc finger proteins BKLF, Eos and Pegasus, the Ets domain protein PU.1 and the treble clef N- and C-terminal fingers of GATA-1. We also showed that the N-terminal zinc finger domain of FOG-1 does not behave as a typical DNA-binding domain. Our results suggest that pentaprobe, and related sequences such as hexaprobe, represent useful tools for probing protein function.},\nkeywords={DNA;  DNA binding protein, algorithm;  article;  binding competition;  binding site;  gel mobility shift assay;  genetics;  metabolism;  molecular genetics;  nucleotide sequence;  oligonucleotide probe;  protein binding, Algorithms;  Base Sequence;  Binding Sites;  Binding, Competitive;  DNA;  DNA-Binding Proteins;  Electrophoretic Mobility Shift Assay;  Molecular Sequence Data;  Oligonucleotide Probes;  Protein Binding, MLCS;  MLOWN},\ncorrespondence_address1={Kwan, A.H.},\nissn={13624962},\npubmed_id={14530457},\nlanguage={English},\nabbrev_source_title={Nucleic Acids Res.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2002\n \n \n (11)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Biophysical characterization of the α-globin binding protein α-hemoglobin stabilizing protein.\n \n \n \n \n\n\n \n Dvid, G.; Yi, K.; Eaton A, S.; Weiss C, M.; and Mackay E, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 277(43): 40602-40609. 2002.\n cited By 100\n\n\n\n
\n\n\n\n \n \n $\"Biophysical$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Dvid200240602,\nauthor={Dvid, G. and Yi, K. and Eaton A, S.A. and Weiss C, M.J. and Mackay E, J.P.},\ntitle={Biophysical characterization of the α-globin binding protein α-hemoglobin stabilizing protein},\njournal={Journal of Biological Chemistry},\nyear={2002},\nvolume={277},\nnumber={43},\npages={40602-40609},\ndoi={10.1074/jbc.M206084200},\nnote={cited By 100},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037175053&doi=10.1074%2fjbc.M206084200&partnerID=40&md5=dfc7fc39939de1069490a5423e9d4903},\naffiliation={A School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia; Children's Hospital of Philadelphia, Division of Hematology, Philadelphia, PA 19104, United States},\nabstract={α-Hemoglobin stabilizing protein (AHSP) is a small (12 kDa) and abundant erythroid-specific protein that binds specifically to free α-(hemo)globin and prevents its precipitation. When present in excess over β-globin, its normal binding partner, α-globin can have severe cytotoxic effects that contribute to important human diseases such as β-thalassemia. Because AHSP might act as a chaperone to prevent the harmful aggregation of α-globin during normal erythroid cell development and in diseases of globin chain imbalance, it is important to characterize the biochemical properties of the AHSP·α-globin complex. Here we provide the first structural information about AHSP and its interaction with α-globin. We find that AHSP is a predominantly α-helical globular protein with a somewhat asymmetric shape. AHSP and α-globin are both monomeric in solution as determined by analytical ultracentrifugation and bind each other to form a complex with 1:1 subunit stoichiometry, as judged by gel filtration and amino acid analysis. We have used isothermal titration calorimetry to show that the interaction is of moderate affinity with an association constant of 1 × 107 M-1 and is thus likely to be biologically significant given the concentration of AHSP (∼0.1 mM) and hemoglobin (∼4 mm) in the late pro-erythroblast.},\nkeywords={Amino acids;  Calorimetry;  Centrifugation;  Diseases;  Filtration;  Hemoglobin;  Monomers;  Precipitation (chemical);  Proteins;  Stoichiometry, Cytotoxic effects, Biochemistry, alpha globin;  alpha hemoglobin stabilizing protein;  beta globin;  binding protein;  unclassified drug, amino acid analysis;  article;  beta thalassemia;  calorimetry;  cell maturation;  cytotoxicity;  erythroblast;  erythroid cell;  gel filtration;  nucleotide sequence;  priority journal;  protein aggregation;  protein analysis;  protein binding;  stoichiometry;  ultracentrifugation, Amino Acid Sequence;  Biophysics;  Blood Proteins;  Calorimetry;  Globins;  Humans;  Molecular Chaperones;  Molecular Sequence Data;  Protein Binding;  Sequence Homology, Amino Acid;  Solutions;  Ultracentrifugation},\ncorrespondence_address1={Mackay, J.P.; School of Molecular/Microbial Sci., , Sydney, NSW 2006, Australia; email: j.mackay@mmb.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={12192002},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Hop is an unusual homeobox gene that modulates cardiac development.\n \n \n \n \n\n\n \n Chen, F.; Kook, H.; Milewski, R.; Gitler, A.; Lu, M.; Li, J.; Nazarian, R.; Schnepp, R.; Jen, K.; Biben, C.; Runke, G.; Mackay, J.; Novotny, J.; Schwartz, R.; Harvey, R.; Mullins, M.; and Epstein, J.\n\n\n \n\n\n\n Cell, 110(6): 713-723. 2002.\n cited By 227\n\n\n\n
\n\n\n\n \n \n $\"Hop$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Chen2002713,\nauthor={Chen, F. and Kook, H. and Milewski, R. and Gitler, A.D. and Lu, M.M. and Li, J. and Nazarian, R. and Schnepp, R. and Jen, K. and Biben, C. and Runke, G. and Mackay, J.P. and Novotny, J. and Schwartz, R.J. and Harvey, R.P. and Mullins, M.C. and Epstein, J.A.},\ntitle={Hop is an unusual homeobox gene that modulates cardiac development},\njournal={Cell},\nyear={2002},\nvolume={110},\nnumber={6},\npages={713-723},\ndoi={10.1016/S0092-8674(02)00932-7},\nnote={cited By 227},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-18644374460&doi=10.1016%2fS0092-8674%2802%2900932-7&partnerID=40&md5=85de7404f0cccf96209fa6b0b4c2def6},\naffiliation={Department of Medicine, University of Pennsylvania Health System, Philadelphia, PA 19104, United States; Department of Cell and Developmental Biology, University of Pennsylvania Health System, Philadelphia, PA 19104, United States; Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculties of Medicine and Life Sciences, University of New South Wales, Kensington, NSW 2051, Australia; School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Sydney, Australia; Department of Cell Biology, Baylor College of Medicine, Houston, TX 77030, United States},\nabstract={Hop is a small, divergent homeodomain protein that lacks certain conserved residues required for DNA binding. Hop gene expression initiates early in cardiogenesis and continues in cardiomyocytes throughout embryonic and postnatal development. Genetic and biochemical data indicate that Hop functions directly downstream of Nkx2-5. Inactivation of Hop in mice by homologous recombination results in a partially penetrant embryonic lethal phenotype with severe developmental cardiac defects involving the myocardium. Inhibition of Hop activity in zebrafish embryos likewise disrupts cardiac development and results in severely impaired cardiac function. Hop physically interacts with serum response factor (SRF) and inhibits activation of SRF-dependent transcription by inhibiting SRF binding to DNA. Hop encodes an unusual homeodomain protein that modulates SRF-dependent cardiac-specific gene expression and cardiac development.},\nkeywords={homeodomain protein;  protein hop;  serum response factor;  transcription factor Nkx2.5;  unclassified drug, amino acid sequence;  animal cell;  animal tissue;  article;  controlled study;  DNA binding;  embryo;  embryo development;  gene expression;  heart development;  heart failure;  heart function;  heart muscle cell;  mouse;  nonhuman;  phenotype;  postnatal development;  priority journal;  promoter region;  protein DNA binding;  protein function;  protein protein interaction;  zebra fish, Animalia;  Danio rerio;  Humulus},\ncorrespondence_address1={Epstein, J.A.; Department of Cell Biology, , Philadelphia, PA 19104, United States; email: epsteinj@mail.med.upenn.edu},\npublisher={Elsevier B.V.},\nissn={00928674},\ncoden={CELLB},\npubmed_id={12297045},\nlanguage={English},\nabbrev_source_title={Cell},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Characterization of the conserved interaction between GATA and FOG family proteins.\n \n \n \n \n\n\n \n Kowalski, K.; Liew, C.; Matthews, J.; Gell, D.; Crossley, M.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 277(38): 35720-35729. 2002.\n cited By 20\n\n\n\n
\n\n\n\n \n \n $\"Characterization$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Kowalski200235720,\nauthor={Kowalski, K. and Liew, C.K. and Matthews, J.M. and Gell, D.A. and Crossley, M. and Mackay, J.P.},\ntitle={Characterization of the conserved interaction between GATA and FOG family proteins},\njournal={Journal of Biological Chemistry},\nyear={2002},\nvolume={277},\nnumber={38},\npages={35720-35729},\ndoi={10.1074/jbc.M204663200},\nnote={cited By 20},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037144459&doi=10.1074%2fjbc.M204663200&partnerID=40&md5=e7221d9b4d750075e421c779b7c1bd73},\naffiliation={Sch. of Molec./Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={The N-terminal zinc finger (ZnF) from GATA transcription factors mediates interactions with FOG family proteins. In FOG proteins, the interacting domains are also ZnFs; these domains are related to classical CCHH fingers but have an His → Cys substitution at the final zinc-ligating position. Here we demonstrate that different CCHC fingers in the FOG family protein U-shaped contact the N-terminal ZnF of GATA-1 in the same fashion although with different affinities. We also show that these interactions are of moderate affinity, which is interesting given the presumed low concentrations of these proteins in the nucleus. Furthermore, we demonstrate that the variant CCHC topology enhances binding affinity, although the His → Cys change is not essential for the formation of a stably folded domain. To ascertain the structural basis for the contribution of the CCHC arrangement, we have determined the structure of a CCHH mutant of finger nine from U-shaped. The structure is very similar overall to the wild-type domain, with subtle differences at the C terminus that result in loss of the interaction in vivo. Taken together, these results suggest that the CCHC zinc binding topology is required for the integrity of GATA-FOG interactions and that weak interactions can play important roles in vivo.},\nkeywords={Molecular structure;  Topology;  Zinc, Zinc finger (ZnF), Proteins, cytosine;  FOG protein;  histidine;  protein;  transcription factor GATA 1;  unclassified drug;  zinc finger protein, amino acid substitution;  amino terminal sequence;  article;  binding affinity;  priority journal;  protein analysis;  protein family;  protein folding;  protein interaction;  protein stability, Amino Acid Sequence;  Conserved Sequence;  Molecular Sequence Data;  Nuclear Magnetic Resonance, Biomolecular;  Protein Conformation;  Sequence Homology, Amino Acid;  Transcription Factors;  Zinc Fingers},\ncorrespondence_address1={Kowalski, K.; Sch. of Molec./Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.mackay@biochem.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={12110675},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Ikaros: A key regulator of haematopoiesis.\n \n \n \n \n\n\n \n Westman, B.; Mackay, J.; and Gell, D.\n\n\n \n\n\n\n International Journal of Biochemistry and Cell Biology, 34(10): 1304-1307. 2002.\n cited By 26\n\n\n\n
\n\n\n\n \n \n $\"Ikaros:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Westman20021304,\nauthor={Westman, B.J. and Mackay, J.P. and Gell, D.},\ntitle={Ikaros: A key regulator of haematopoiesis},\njournal={International Journal of Biochemistry and Cell Biology},\nyear={2002},\nvolume={34},\nnumber={10},\npages={1304-1307},\ndoi={10.1016/S1357-2725(02)00070-5},\nnote={cited By 26},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035986647&doi=10.1016%2fS1357-2725%2802%2900070-5&partnerID=40&md5=7c2cab8d7bce954851531f84e1cca5ff},\naffiliation={Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Ikaros is an essential transcription factor for normal lymphocyte development. Because of its interaction with a number of closely related factors, Ikaros is required for correct regulation of differentiation and cell proliferation in T- and B-cell lineages. Interestingly, Ikaros appears to function both as a transcriptional repressor and as an activator through its ability to bind a large number of nuclear factors, including components of both histone deacetylase and ATP-dependent chromatin remodelling complexes. In addition, nuclear localisation is important for Ikaros function - unlike most transcription factors, Ikaros is localised to discrete nuclear foci in lymphoid cells, suggesting it employs novel mechanisms to regulate transcription. © 2002 Elsevier Science Ltd. All rights reserved.},\nauthor_keywords={Haematopoiesis;  Ikaros;  Pericentromeric-heterochromatin;  Transcription},\nkeywords={adenosine triphosphate;  histone acetyltransferase;  Ikaros transcription factor;  nuclear factor;  transcription factor;  unclassified drug;  DNA binding protein;  Ikaros transcription factor, accuracy;  article;  B lymphocyte;  cell differentiation;  cell maturation;  cell nucleus;  cell proliferation;  cellular distribution;  chromatin;  hematopoiesis;  lymphocyte;  lymphoid cell;  protein binding;  protein function;  protein interaction;  protein localization;  regulatory mechanism;  T lymphocyte;  transcription initiation;  transcription regulation;  animal;  chemistry;  genetics;  physiology;  protein conformation;  review, Animal;  Hematopoiesis;  Protein Conformation;  Support, Non-U.S. Gov't;  Transcription Factors;  Animals;  DNA-Binding Proteins;  Ikaros Transcription Factor;  Protein Conformation},\ncorrespondence_address1={Westman, B.J.; Sch. of Molec. and Microbial Biosci., , Sydney, NSW 2006, Australia; email: b.westman@mmb.usyd.edu.au},\nissn={13572725},\ncoden={IJBBF},\npubmed_id={12127581},\nlanguage={English},\nabbrev_source_title={Int. J. Biochem. Cell Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n 1H, 15N and 13C assignments of FLIN4, an intramolecular LMO4:ldb1 complex [8].\n \n \n \n \n\n\n \n Deane, J.; Visvader, J.; Mackay, J.; and Matthews, J.\n\n\n \n\n\n\n Journal of Biomolecular NMR, 23(2): 165-166. 2002.\n cited By 4\n\n\n\n
\n\n\n\n \n \n $\"1H,$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Deane2002165,\nauthor={Deane, J.E. and Visvader, J.E. and Mackay, J.P. and Matthews, J.M.},\ntitle={1H, 15N and 13C assignments of FLIN4, an intramolecular LMO4:ldb1 complex [8]},\njournal={Journal of Biomolecular NMR},\nyear={2002},\nvolume={23},\nnumber={2},\npages={165-166},\ndoi={10.1023/A:1016363414644},\nnote={cited By 4},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035996732&doi=10.1023%2fA%3a1016363414644&partnerID=40&md5=8a6d80a838e83bbdacb3d78a60359041},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia; Walter and Eliza Hall Institute for Medical Research, Parkville, Vic. 3050, Australia},\nkeywords={amino acid;  autoantigen;  carbon 13;  homeodomain protein;  hybrid protein;  nitrogen 15;  nuclear protein;  oncoprotein;  protein FLIN4;  proton;  unclassified drug;  DNA binding protein;  FLIN4 protein, human;  homeodomain protein;  LDB1 protein, human;  LMO4 protein, human;  Lmo4 protein, mouse;  oncoprotein;  transcription factor, amino terminal sequence;  animal cell;  animal tissue;  binding affinity;  breast carcinogenesis;  breast epithelium;  breast tumor;  carbon nuclear magnetic resonance;  carboxy terminal sequence;  cell proliferation;  complex formation;  controlled study;  epithelium cell;  gene control;  gene overexpression;  genetic transcription;  human;  human cell;  human tissue;  letter;  leukemogenesis;  mouse;  nonhuman;  nuclear magnetic resonance spectroscopy;  oncogene;  priority journal;  protein binding;  protein domain;  protein family;  protein function;  protein structure;  proton nuclear magnetic resonance;  structure analysis;  T lymphocyte;  transgenic mouse;  chemistry;  macromolecule;  metabolism;  nuclear magnetic resonance;  protein conformation, Animalia;  Mus musculus, DNA-Binding Proteins;  Homeodomain Proteins;  Humans;  Macromolecular Substances;  Nuclear Magnetic Resonance, Biomolecular;  Oncogene Proteins, Fusion;  Protein Conformation;  Transcription Factors},\ncorrespondence_address1={Matthews, J.M.; School of Mol./Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.matthews@mmb.usyd.edu.au},\nissn={09252738},\ncoden={JBNME},\npubmed_id={12153047},\nlanguage={English},\nabbrev_source_title={J. Biomol. NMR},\ndocument_type={Letter},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Type I shorthorn sculpin antifreeze protein: Recombinant synthesis, solution conformation, and ice growth inhibition studies.\n \n \n \n \n\n\n \n Fairley, K.; Westman, B.; Pham, L.; Haymet, A.; Harding, M.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 277(27): 24073-24080. 2002.\n cited By 27\n\n\n\n
\n\n\n\n \n \n $\"Type$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Fairley200224073,\nauthor={Fairley, K. and Westman, B.J. and Pham, L.H. and Haymet, A.D.J. and Harding, M.M. and Mackay, J.P.},\ntitle={Type I shorthorn sculpin antifreeze protein: Recombinant synthesis, solution conformation, and ice growth inhibition studies},\njournal={Journal of Biological Chemistry},\nyear={2002},\nvolume={277},\nnumber={27},\npages={24073-24080},\ndoi={10.1074/jbc.M200307200},\nnote={cited By 27},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037025376&doi=10.1074%2fjbc.M200307200&partnerID=40&md5=0a1840ef82caa15de68ea65e2c6cc7e7},\naffiliation={School of Chemistry, Houston, TX 77204-5003, United States; Department of Biochemistry, University of Sydney, NSW 2006, Australia; Department of Chemistry, University of Houston, Houston, TX 77204-5003, United States; School of Chemistry, University of Sydney, NSW, Australia},\nabstract={A number of structurally diverse classes of "antifreeze" proteins that allow fish to survive in sub-zero ice-laden waters have been isolated from the blood plasma of cold water teleosts. However, despite receiving a great deal of attention, the one or more mechanisms through which these proteins act are not fully understood. In this report we have synthesized a type I antifreeze polypeptide (AFP) from the shorthorn sculpin Myoxocephalus scorpius using recombinant methods. Construction of a synthetic gene with optimized codon usage and expression as a glutathione S-transferase fusion protein followed by purification yielded milligram amounts of polypeptide with two extra residues appended to the N terminus. Circular dichroism and NMR experiments, including residual dipolar coupling measurements on a 15N-labeled recombinant polypeptide, show that the polypeptides are α-helical with the first four residues being more flexible than the remainder of the sequence. Both the recombinant and synthetic polypeptides modify ice growth, forming facetted crystals just below the freezing point, but display negligible thermal hysteresis. Acetylation of Lys-10, Lys-20, and Lys-21 as well as the N terminus of the recombinant polypeptide gave a derivative that displays both thermal hysteresis (0.4°C at 15 mg/ml) and ice crystal faceting. These results confirm that the N terminus of wild-type polypeptide is functionally important and support our previously proposed mechanism for all type I proteins, in which the hydrophobic face is oriented toward the ice at the ice/water interface.},\nkeywords={Aquaculture;  Blood;  Conformations;  Genes;  Hysteresis;  Nuclear magnetic resonance;  Polypeptides;  Synthesis (chemical), Dipolar coupling, Proteins, antifreeze protein;  hybrid protein;  sculpin;  unclassified drug, amino terminal sequence;  article;  cell survival;  codon usage;  crystal structure;  growth inhibition;  high performance liquid chromatography;  hydrogen bond;  hydrophobicity;  hysteresis;  nonhuman;  priority journal;  protein conformation;  teleost, Amino Acid Sequence;  Animals;  Antifreeze Proteins;  Base Sequence;  Circular Dichroism;  DNA Primers;  Fish Proteins;  Genes, Synthetic;  Ice;  Magnetic Resonance Spectroscopy;  Microscopy, Video;  Molecular Sequence Data;  Protein Conformation;  Recombinant Proteins;  Scorpions;  Solutions, Myoxocephalus;  Myoxocephalus scorpius;  Teleostei},\ncorrespondence_address1={Harding, M.M.; School of Chemistry, , Sydney NSW 2006, Australia; email: harding@chem.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={11940576},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The Bacillus subtilis cell division proteins FtsL and DivIC are intrinsically unstable and do not interact with one another in the absence of other septasomal components.\n \n \n \n \n\n\n \n Robson, S.; Michie, K.; Mackay, J.; Harry, E.; and King, G.\n\n\n \n\n\n\n Molecular Microbiology, 44(3): 663-674. 2002.\n cited By 34\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Robson2002663,\nauthor={Robson, S.A. and Michie, K.A. and Mackay, J.P. and Harry, E. and King, G.F.},\ntitle={The Bacillus subtilis cell division proteins FtsL and DivIC are intrinsically unstable and do not interact with one another in the absence of other septasomal components},\njournal={Molecular Microbiology},\nyear={2002},\nvolume={44},\nnumber={3},\npages={663-674},\ndoi={10.1046/j.1365-2958.2002.02920.x},\nnote={cited By 34},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036096858&doi=10.1046%2fj.1365-2958.2002.02920.x&partnerID=40&md5=0fe6fb3e47a8fa5fe0d70b848c28fc28},\naffiliation={Department of Biochemistry, University of Connecticut Health Center, Farmington, CT 06032, United States; Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia; Department of Microbiology, University of Connecticut Health Center, Farmington, CT 06032, United States},\nabstract={The bacterial septum appears to comprise a macromolecular assembly of essential cell division proteins (the 'septasome') that are responsible for physically dividing the cell during cytokinesis. FtsL and DivIC are essential components of this division machinery in Bacillus subtilis. We used yeast two-hybrid analysis as well as a variety of biochemical and biophysical methods to examine the proposed interaction between Bacillus subtilis FtsL and DivIC. We show that FtsL and DivIC are thermodynamically unstable proteins that are likely to be unfolded and therefore targeted for degradation unless stabilized by interactions with other components of the septasome. However, we show that this stabilization does not result from a direct interaction between FtsL and DivIC. We propose that the observed interdependence of DivIC and FtsL stability is a result of indirect interactions that are mediated by other septasomal proteins.},\nkeywords={bacterial protein;  protein DivlC;  protein FtsL;  unclassified drug, article;  Bacillus subtilis;  bacterial cell;  cell division;  controlled study;  magnetic resonance angiography;  nonhuman;  priority journal;  protein degradation;  protein domain;  protein folding;  protein protein interaction;  protein stability;  thermostability;  two hybrid system, Amino Acid Sequence;  Bacillus subtilis;  Bacterial Proteins;  Cell Cycle Proteins;  Cell Division;  Circular Dichroism;  Escherichia coli Proteins;  Isoelectric Point;  Macromolecular Substances;  Membrane Proteins;  Molecular Sequence Data;  Nephelometry and Turbidimetry;  Nuclear Magnetic Resonance, Biomolecular;  Protein Denaturation;  Protein Folding;  Protein Interaction Mapping;  Protein Structure, Tertiary;  Recombinant Fusion Proteins;  Saccharomyces cerevisiae;  Sequence Alignment;  Sequence Homology, Amino Acid;  Structure-Activity Relationship;  Thermodynamics;  Two-Hybrid System Techniques;  Ultracentrifugation, Bacillus subtilis;  Bacteria (microorganisms);  Posibacteria},\ncorrespondence_address1={King, G.F.; Department of Biochemistry, , Farmington, CT 06032, United States; email: glenn@psel.uchc.edu},\nissn={0950382X},\ncoden={MOMIE},\npubmed_id={11994149},\nlanguage={English},\nabbrev_source_title={Mol. Microbiol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n A new zinc binding fold underlines the versatility of zinc binding modules in protein evolution.\n \n \n \n \n\n\n \n Sharpe, B.; Matthews, J.; Kwan, A.; Newton, A.; Gell, D.; Crossley, M.; and Mackay, J.\n\n\n \n\n\n\n Structure, 10(5): 639-648. 2002.\n cited By 22\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Sharpe2002639,\nauthor={Sharpe, B.K. and Matthews, J.M. and Kwan, A.H.Y. and Newton, A. and Gell, D.A. and Crossley, M. and Mackay, J.P.},\ntitle={A new zinc binding fold underlines the versatility of zinc binding modules in protein evolution},\njournal={Structure},\nyear={2002},\nvolume={10},\nnumber={5},\npages={639-648},\ndoi={10.1016/S0969-2126(02)00757-8},\nnote={cited By 22},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036098873&doi=10.1016%2fS0969-2126%2802%2900757-8&partnerID=40&md5=82f1cfe561bb838cefc6836f27f6f1a8},\naffiliation={Department of Biochemistry, University of Sydney, NSW 2006, Australia},\nabstract={Many different zinc binding modules have been identified. Their abundance and variety suggests that the formation of zinc binding folds might be relatively common. We have determined the structure of CH11, a 27-residue peptide derived from the first cysteine/histidine-rich region (CH1) of CREB binding protein (CBP). This peptide forms a highly ordered zinc-dependent fold that is distinct from known folds. The structure differs from a subsequently determined structure of a larger region from the CH3 region of CBP, and the CH11 fold probably represents a nonphysiologically active form. Despite this, the fold is thermostable and tolerant to both multiple alanine mutations and changes in the zinc-ligand spacing. Our data support the idea that zinc binding domains may arise frequently. Additionally, such structures may prove useful as scaffolds for protein design, given their stability and robustness.},\nauthor_keywords={CBP;  Protein design;  Protein evolution;  Structure;  Zinc fingers},\nkeywords={alanine;  cyclic AMP responsive element binding protein binding protein;  cysteine;  histidine;  ligand;  peptide;  protein CH1;  unclassified drug;  zinc;  Crebbp protein, mouse;  nuclear protein;  transactivator protein, article;  binding affinity;  binding site;  chelation;  molecular evolution;  mutation;  physiology;  priority journal;  protein analysis;  protein conformation;  protein folding;  protein quality;  protein structure;  structure analysis;  thermostability;  amino acid sequence;  animal;  chemical structure;  chemistry;  circular dichroism;  genetics;  metabolism;  molecular evolution;  molecular genetics;  mouse;  nuclear magnetic resonance;  protein tertiary structure;  sequence alignment;  temperature, Amino Acid Sequence;  Animal;  Binding Sites;  Circular Dichroism;  Cysteine;  Evolution, Molecular;  Histidine;  Mice;  Models, Molecular;  Molecular Sequence Data;  Molecular Structure;  Nuclear Magnetic Resonance, Biomolecular;  Nuclear Proteins;  Peptides;  Protein Folding;  Protein Structure, Tertiary;  Sequence Alignment;  Support, Non-U.S. Gov't;  Temperature;  Trans-Activators;  Zinc;  Amino Acid Sequence;  Animals;  Binding Sites;  Circular Dichroism;  CREB-Binding Protein;  Cysteine;  Histidine;  Mice;  Models, Molecular;  Molecular Sequence Data;  Molecular Structure;  Nuclear Magnetic Resonance, Biomolecular;  Protein Folding;  Sequence Alignment;  Temperature},\ncorrespondence_address1={Mackay, J.P.; Department of Biochemistry, , Sydney, NSW 2006, Australia; email: j.mackay@biochem.usyd.edu.au},\nissn={09692126},\ncoden={STRUE},\npubmed_id={12015147},\nlanguage={English},\nabbrev_source_title={Structure},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Solution structure of a hydrophobic analogue of the winter flounder antifreeze protein.\n \n \n \n \n\n\n \n Liepinsh, E.; Otting, G.; Harding, M.; Ward, L.; Mackay, J.; and Haymet, A.\n\n\n \n\n\n\n European Journal of Biochemistry, 269(4): 1259-1266. 2002.\n cited By 26\n\n\n\n
\n\n\n\n \n \n $\"Solution$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Liepinsh20021259,\nauthor={Liepinsh, E. and Otting, G. and Harding, M.M. and Ward, L.G. and Mackay, J.P. and Haymet, A.D.J.},\ntitle={Solution structure of a hydrophobic analogue of the winter flounder antifreeze protein},\njournal={European Journal of Biochemistry},\nyear={2002},\nvolume={269},\nnumber={4},\npages={1259-1266},\ndoi={10.1046/j.1432-1033.2002.02766.x},\nnote={cited By 26},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036177164&doi=10.1046%2fj.1432-1033.2002.02766.x&partnerID=40&md5=baeaea2d1a367201a71ec2e80a2b4a90},\naffiliation={Karolinska Institute, Tomtebodavägen, Stockholm, Sweden; School of Chemistry, University of Sydney, NSW, Australia; Department of Biochemistry, University of Sydney, NSW, Australia; Department of Chemistry, Institute for Molecular Design, University of Houston, TX, United States; School of Chemistry, F11, University of Sydney, NSW 2006, Australia},\nabstract={The solution structure of a synthetic mutant type I antifreeze protein (AFP I) was determined in aqueous solution at pH 7.0 using nuclear magnetic resonance (NMR) spectroscopy. The mutations comprised the replacement of the four Thr residues by Val and the introduction of two additional Lys-Glu salt bridges. The antifreeze activity of this mutant peptide, VVVV2KE, has been previously shown to be similar to that of the wild type protein, HPLC6 (defined here as TTTT). The solution structure reveals an ahelix bent in the same direction as the more bent conformer of the published crystalstructure of TTTT, while the side chain χ1 rotamers of VVVV2KE are similar to those of the straighter conformer in the crystal of TTTT. The Val side chains of VVVV2KE assume the same orientations as the Thr side chains of TTTT, confirming the conservative nature of this mutation. The combined data suggest that AFP I undergoes an equilibrium between straight and bent helices in solution, combined with independent equilibria between different side chain rotamers for some of the amino acid residues. The present study presents the first complete sequence-specific resonance assignments and the first complete solution structure determination by NMR of any AFP I protein.},\nauthor_keywords={α helices;  Antifreeze;  NMR spectroscopy;  Proteins;  Winter flounder},\nkeywords={antifreeze protein;  glucose;  lysine;  threonine;  valine, alpha helix;  aqueous solution;  article;  crystal structure;  flounder;  mutant;  mutation;  nuclear magnetic resonance spectroscopy;  pH;  priority journal;  protein structure;  structure activity relation, Animals;  Antifreeze Proteins, Type I;  Flounder;  Hydrophobicity;  Models, Molecular;  Nuclear Magnetic Resonance, Biomolecular;  Protein Structure, Secondary;  Recombinant Proteins;  Solutions, Pleuronectoidei;  Pseudopleuronectes americanus},\ncorrespondence_address1={Harding, M.M.; School of Chemistry, , Sydney, NSW 2006, Australia; email: harding@chem.usyd.edu.au},\nissn={00142956},\ncoden={EJBCA},\npubmed_id={11856360},\nlanguage={English},\nabbrev_source_title={Eur. J. Biochem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The solution structure and intramolecular associations of the Tec kinase Src homology 3 domain.\n \n \n \n \n\n\n \n Pursglove, S.; Mulhern, T.; Mackay, J.; Hinds, M.; and Booker, G.\n\n\n \n\n\n\n Journal of Biological Chemistry, 277(1): 755-762. 2002.\n cited By 30\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Pursglove2002755,\nauthor={Pursglove, S.E. and Mulhern, T.D. and Mackay, J.P. and Hinds, M.G. and Booker, G.W.},\ntitle={The solution structure and intramolecular associations of the Tec kinase Src homology 3 domain},\njournal={Journal of Biological Chemistry},\nyear={2002},\nvolume={277},\nnumber={1},\npages={755-762},\ndoi={10.1074/jbc.M108318200},\nnote={cited By 30},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037016721&doi=10.1074%2fjbc.M108318200&partnerID=40&md5=2b366de8a6aceb464ff89178b1bff1c2},\naffiliation={Department of Molecular Biosciences, University of Adelaide, Adelaide, 5005, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, 3010, Australia; Department of Biochemistry, University of Sydney, Sydney, 2000, Australia; Biomolecular Research Institute, 343 Royal Parade, Parkville, 305, Australia; Walter and Eliza Hall Institute of Medical Research, PO, Royal Melbourne Hospital, 3050, Australia; Dept. of Molecular Biosciences, University of Adelaide, Adelaide, SA 5005, Australia},\nabstract={Tec is the prototypic member of a family of intracellular tyrosine kinases that includes Txk, Bmx, Itk, and Btk. Tec family kinases share similarities in domain structure with Src family kinases, but one of the features that differentiates them is a proline-rich region (PRR) preceding their Src homology (SH) 3 domain. Evidence that the PRR of Itk can bind in an intramolecular fashion to its SH3 domain and the lack of a regulatory tyrosine in the C terminus indicates that Tec kinases must be regulated by a different set of intramolecular interactions to the Src kinases. We have determined the solution structure of the Tec SH3 domain and have investigated interactions with its PRR, which contains two SH3-binding sites. We demonstrate that in vitro, the Tec PRR can bind in an intramolecular fashion to the SH3. However, the affinity is lower than that for dimerization via reciprocal PRR-SH3 association. Using site-directed mutagenesis we show that both sites can bind the Tec SH3 domain; site 1 (155KTLPPAP161) binds intramolecularly, while site 2 (165KRRPPPPIPP174) cannot and binds in an intermolecular fashion. These distinct roles for the SH3 binding sites in Tec family kinases could be important for protein targeting and enzyme activation.},\nkeywords={Dimerization;  Enzymes;  Mutagenesis;  Proteins;  Solutions, Kinases, Association reactions, proline;  protein tyrosine kinase;  Tec kinase;  tyrosine;  unclassified drug, article;  binding site;  carboxy terminal sequence;  enzyme activation;  enzyme binding;  enzyme regulation;  enzyme structure;  molecular interaction;  priority journal;  protein domain;  site directed mutagenesis, Amino Acid Sequence;  Binding Sites;  Molecular Sequence Data;  Protein-Tyrosine Kinases;  Solutions;  src Homology Domains;  Surface Plasmon Resonance;  Ultracentrifugation},\ncorrespondence_address1={Booker, G.W.; Dept. of Molecular Biosciences, , Adelaide, SA 5005, Australia; email: grant.booker@adelaide.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={11684687},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Siah ubiquitin ligase is structurally related to traf and modulates tnf-α signaling.\n \n \n \n \n\n\n \n Polekhina, G.; House, C.; Traficante, N.; Mackay, J.; Relaix, F.; Sassoon, D.; Parker, M.; and Bowtell, D.\n\n\n \n\n\n\n Nature Structural Biology, 9(1): 68-75. 2002.\n cited By 115\n\n\n\n
\n\n\n\n \n \n $\"Siah$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Polekhina200268,\nauthor={Polekhina, G. and House, C.M. and Traficante, N. and Mackay, J.P. and Relaix, F. and Sassoon, D.A. and Parker, M.W. and Bowtell, D.D.L.},\ntitle={Siah ubiquitin ligase is structurally related to traf and modulates tnf-α signaling},\njournal={Nature Structural Biology},\nyear={2002},\nvolume={9},\nnumber={1},\npages={68-75},\ndoi={10.1038/nsb743},\nnote={cited By 115},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036143826&doi=10.1038%2fnsb743&partnerID=40&md5=c995dabe69e21dac39e8e73b565c346b},\naffiliation={Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy VIC 3065, Australia; Trescowthick Research Laboratories, Peter MacCallum Cancer Institute, Locked Bag 1 A'Beckett St., Melbourne VIC 8006, Australia; Department of Biochemistry, University of Sydney, Sydney NSW 2006, Australia; Department of Biochemistry and Molecular Biology, Mount Sinai School of Medicine, 1 G. Levy Place, New York NY 10029, United States; Department of Molecular Biology, Pasteur Institute, 25 rue du Dr Roux, Paris Cedex 15, France},\nabstract={Members of the Siah (seven in absentia homolog) family of RING domain proteins are components of E3 ubiquitin ligase complexes that catalyze ubiquitination of proteins. We have determined the crystal structure of the substrate-binding domain (SBD) of murine Siah1a to 2.6 Å resolution. The structure reveals that Siah is a dimeric protein and that the SBD adopts an eight-stranded β-sandwich fold that is highly similar to the TRAF-C region of TRAF (TNF-receptor associated factor) proteins. The TRAF-C region interacts with TNF-α receptors and TNF-receptor associated death-domain (TRADD) proteins; however, our findings indicate that these interactions are unlikely to be mimicked by Siah. The Siah structure also reveals two novel zinc fingers in a region with sequence similarity to TRAF. We find that the Siah1a SBD potentiates TNF-α-mediated NF-κB activation. Therefore, Siah proteins share important similarities with the TRAF family of proteins, including their overall domain architecture, three-dimensional structure and functional activity. © 2002 Nature Publishing Group.},\nkeywords={immunoglobulin enhancer binding protein;  protein ring;  protein siah;  tumor necrosis factor alpha;  tumor necrosis factor receptor associated death domain;  tumor necrosis factor receptor associated factor;  ubiquitin protein ligase;  unclassified drug;  zinc finger protein, amino acid sequence;  article;  binding site;  crystal structure;  enzyme structure;  molecular model;  molecular recognition;  priority journal;  protein domain;  protein folding;  protein protein interaction;  protein structure;  signal transduction;  structure activity relation, Amino Acid Sequence;  Animals;  Binding Sites;  Crystallography, X-Ray;  Dimerization;  Humans;  Mice;  Models, Molecular;  Molecular Sequence Data;  NF-kappa B;  Nuclear Proteins;  Peptide Fragments;  Protein Binding;  Protein Structure, Quaternary;  Protein Structure, Tertiary;  Proteins;  Receptors, Tumor Necrosis Factor;  Sequence Alignment;  Sequence Homology, Amino Acid;  Signal Transduction;  Trans-Activation (Genetics);  Tumor Necrosis Factor-alpha;  Ubiquitin-Protein Ligases;  Zinc;  Zinc Fingers, Murinae},\nissn={10728368},\npubmed_id={11742346},\nlanguage={English},\nabbrev_source_title={Nat. Struct. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2001\n \n \n (6)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n 1H, 15N and 13C assignments of FLIN2, an intramolecular LMO2:ldb1 complex [2].\n \n \n \n \n\n\n \n Matthews, J.; Visvader, J.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biomolecular NMR, 21(4): 385-386. 2001.\n cited By 4\n\n\n\n
\n\n\n\n \n \n $\"1H,$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Matthews2001385,\nauthor={Matthews, J.M. and Visvader, J.E. and Mackay, J.P.},\ntitle={1H, 15N and 13C assignments of FLIN2, an intramolecular LMO2:ldb1 complex [2]},\njournal={Journal of Biomolecular NMR},\nyear={2001},\nvolume={21},\nnumber={4},\npages={385-386},\ndoi={10.1023/A:1013373203772},\nnote={cited By 4},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035544158&doi=10.1023%2fA%3a1013373203772&partnerID=40&md5=4afdf2a3da3707133154abd60f3116c1},\naffiliation={Department of Biochemistry, University of Sydney, NSW 2006, Australia; Walter and Eliza Hall Institute for Medical Research, Parkville, Vic. 3050, Australia},\nauthor_keywords={FLIN2;  IdB1;  LMO2;  NMR assignments},\nkeywords={amino acid;  carbon 13;  hybrid protein;  nitrogen 15;  protein;  proton;  carbon;  DNA binding protein;  FLIN2 protein, recombinant;  hydrogen;  metalloprotein;  nitrogen;  oncoprotein;  zinc finger protein, carbon nuclear magnetic resonance;  controlled study;  letter;  priority journal;  protein conformation;  protein domain;  protein interaction;  protein structure;  proton nuclear magnetic resonance;  sequence homology;  amino acid sequence;  chemistry;  genetics;  macromolecule;  molecular weight;  nuclear magnetic resonance, Amino Acid Sequence;  Carbon Isotopes;  DNA-Binding Proteins;  Hydrogen;  Macromolecular Substances;  Metalloproteins;  Molecular Weight;  Nitrogen Isotopes;  Nuclear Magnetic Resonance, Biomolecular;  Protein Conformation;  Proto-Oncogene Proteins;  Recombinant Fusion Proteins;  Zinc Fingers},\ncorrespondence_address1={Matthews, J.M.; Department of Biochemistry, , Sydney, NSW 2006, Australia; email: j.matthews@biochem.usyd.edu.au},\nissn={09252738},\ncoden={JBNME},\npubmed_id={11824760},\nlanguage={English},\nabbrev_source_title={J. Biomol. NMR},\ndocument_type={Letter},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Discovery and Structure of a Potent and Highly Specific Blocker of Insect Calcium Channels.\n \n \n \n \n\n\n \n Wang, X.; Connor, M.; Wilson, D.; Wilson, H.; Nicholson, G.; Smith, R.; Shaw, D.; Mackay, J.; Alewood, P.; Christie, M.; and King, G.\n\n\n \n\n\n\n Journal of Biological Chemistry, 276(43): 40306-40312. 2001.\n cited By 69\n\n\n\n
\n\n\n\n \n \n $\"Discovery$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Wang200140306,\nauthor={Wang, X.-H. and Connor, M. and Wilson, D. and Wilson, H.I. and Nicholson, G.M. and Smith, R. and Shaw, D. and Mackay, J.P. and Alewood, P.F. and Christie, M.J. and King, G.F.},\ntitle={Discovery and Structure of a Potent and Highly Specific Blocker of Insect Calcium Channels},\njournal={Journal of Biological Chemistry},\nyear={2001},\nvolume={276},\nnumber={43},\npages={40306-40312},\ndoi={10.1074/jbc.M105206200},\nnote={cited By 69},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035955737&doi=10.1074%2fjbc.M105206200&partnerID=40&md5=8be0c58cb75dcb0d4278c44842032c2f},\naffiliation={Department of Biochemistry, Univ. of Connecticut Health Center, Farmington, CT 06032, United States; Department of Pharmacology, University of Sydney, Sydney, NSW 2006, Australia; Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia; Department of Biochemistry, University of Queensland, Brisbane, QLD 4072, Australia; Department of Health Sciences, University of Technology, Sydney, NSW 2007, Australia; John Curtin Sch. of Medical Research, Australian National University, Canberra, ACT 0200, Australia; Dept. of Biochemistry, MC3305, Univ. of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06032, United States},\nabstract={We have isolated a novel family of insect-selective neurotoxins that appear to be the most potent blockers of insect voltage-gated calcium channels reported to date. These toxins display exceptional phylogenetic specificity, with at least a 10,000-fold preference for insect versus vertebrate calcium channels. The structure of one of the toxins reveals a highly structured, disulfide-rich core and a structurally disordered C-terminal extension that is essential for channel blocking activity. Weak structural/functional homology with ω-agatoxin-IVA/B, the prototypic inhibitor of vertebrate P-type calcium channels, suggests that these two toxin families might share a similar mechanism of action despite their vastly different phylogenetic specificities.},\nkeywords={Calcium;  Toxic materials, Neurotoxins, Biochemistry, calcium channel;  calcium channel P type;  neurotoxin;  omega agatoxin IVA;  calcium channel blocking agent;  insecticide;  neurotoxin;  omega agatoxin IVA;  omega atracotoxin Hv2a;  omega-atracotoxin Hv2a;  protein precursor;  recombinant protein;  spider venom, article;  carboxy terminal sequence;  channel gating;  controlled study;  insect;  nonhuman;  nucleotide sequence;  phylogeny;  priority journal;  protein family;  protein function;  protein isolation;  protein structure;  sequence homology;  vertebrate;  amino acid sequence;  animal;  bee;  chemical structure;  chemistry;  cytology;  drug effect;  genetics;  insect control;  methodology;  molecular genetics;  nerve cell;  nuclear magnetic resonance;  patch clamp;  spider, Insecta;  Iva;  Vertebrata, Amino Acid Sequence;  Animals;  Bees;  Calcium Channel Blockers;  Insect Control;  Insecticides;  Models, Molecular;  Molecular Sequence Data;  Neurons;  Neurotoxins;  Nuclear Magnetic Resonance, Biomolecular;  omega-Agatoxin IVA;  Patch-Clamp Techniques;  Protein Precursors;  Recombinant Proteins;  Spider Venoms;  Spiders},\ncorrespondence_address1={King, G.F.; Dept. of Biochemistry, 263 Farmington Ave., Farmington, CT 06032, United States; email: glenn@psel.uchc.edu},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={11522785},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The N-terminal Zinc Finger of the Erythroid Transcription Factor GATA-1 Binds GATC Motifs in DNA.\n \n \n \n \n\n\n \n Newton, A.; Mackay, J.; and Crossley, M.\n\n\n \n\n\n\n Journal of Biological Chemistry, 276(38): 35794-35801. 2001.\n cited By 70\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Newton200135794,\nauthor={Newton, A. and Mackay, J. and Crossley, M.},\ntitle={The N-terminal Zinc Finger of the Erythroid Transcription Factor GATA-1 Binds GATC Motifs in DNA},\njournal={Journal of Biological Chemistry},\nyear={2001},\nvolume={276},\nnumber={38},\npages={35794-35801},\ndoi={10.1074/jbc.M106256200},\nnote={cited By 70},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035929608&doi=10.1074%2fjbc.M106256200&partnerID=40&md5=d067b4296b213a08b05daea2a919c1ca},\nabstract={The mammalian transcription factor GATA-1 is required for normal erythroid and megakaryocytic development. GATA-1 contains two zinc fingers, the C-terminal finger, which is known to bind (A/T)GATA(A/G) motifs in DNA and the N-finger, which is important for interacting with co-regulatory proteins such as Friend of GATA (FOG). We now show that, like the C-finger, the N-finger of GATA-1 is also capable of binding DNA but recognizes distinct sequences with the core GATC. We demonstrate that the GATA-1 N-finger can bind these sequences in vitro and that in cellular assays, GATA-1 can activate promoters containing GATC motifs. Experiments with mutant GATA-1 proteins confirm the importance of the N-finger, as the C-finger is not required for transactivation from GATC sites. Recently four naturally occurring mutations in GATA-1 have been shown to be associated with familial blood disorders. These mutations all map to the N-finger domain. We have investigated the effect of these mutations on the recognition of GATC sites by the N-finger and show that one mutation R216Q abolishes DNA binding, whereas the others have only minor effects.},\nkeywords={Assays;  Blood;  Cells;  Chemical activation;  Mutagenesis;  Proteins;  Zinc, Mutations, DNA, 5 aminolevulinate synthase;  DNA;  Friend of GATA protein;  glutathione transferase;  recombinant protein;  regulator protein;  thrombocyte factor 4;  transcription factor GATA 1;  unclassified drug;  zinc finger protein;  DNA;  DNA binding protein;  erythroid specific DNA binding factor;  Gata1 protein, mouse;  primer DNA;  transcription factor;  transcription factor GATA 1;  zinc finger protein, amino terminal sequence;  animal cell;  article;  carboxy terminal sequence;  cell strain 3T3;  controlled study;  erythroid cell;  gel mobility shift assay;  in vitro study;  mouse;  nonhuman;  priority journal;  promoter region;  protein DNA binding;  protein domain;  protein motif;  transactivation;  transcription regulation;  amino acid sequence;  animal;  binding site;  chemistry;  metabolism;  molecular genetics;  nucleotide sequence;  sequence homology;  site directed mutagenesis, Animalia;  Mammalia, Amino Acid Sequence;  Animals;  Base Sequence;  Binding Sites;  DNA;  DNA Primers;  DNA-Binding Proteins;  Erythroid-Specific DNA-Binding Factors;  GATA1 Transcription Factor;  Mice;  Molecular Sequence Data;  Mutagenesis, Site-Directed;  Sequence Homology, Amino Acid;  Transcription Factors;  Zinc Fingers},\ncorrespondence_address1={email: M.Crossley@biochem.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={11445591},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Probing site specificity of DNA binding metallointercalators by NMR spectroscopy and molecular modeling.\n \n \n \n \n\n\n \n Proudfoot, E.; Mackay, J.; and Karuso, P.\n\n\n \n\n\n\n Biochemistry, 40(15): 4867-4878. 2001.\n cited By 54\n\n\n\n
\n\n\n\n \n \n $\"Probing$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Proudfoot20014867,\nauthor={Proudfoot, E.M. and Mackay, J.P. and Karuso, P.},\ntitle={Probing site specificity of DNA binding metallointercalators by NMR spectroscopy and molecular modeling},\njournal={Biochemistry},\nyear={2001},\nvolume={40},\nnumber={15},\npages={4867-4878},\ndoi={10.1021/bi001655f},\nnote={cited By 54},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035901518&doi=10.1021%2fbi001655f&partnerID=40&md5=26ff4820384e3ffc437b43f4f5bc3dd9},\naffiliation={Department of Chemistry, Macquarie University, Sydney, NSW 2109, Australia; Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={The molecular recognition of oligonucleotides by chiral ruthenium complexes has been probed by NMR spectroscopy using the template Δ-cis-α- and Δ-cis-β-[Ru(RR-picchxnMe2) (bidentate)]2+, where the bidentate ligand is one of phen (1,10-phenanthroline), dpq (dipyrido[3,2-f:2′,3′-h]quinoxaline), or phi (9,10-phenanthrenequinone diimine) and picchxnMe2 is N,N′-dimethyl-N,N′-di(2-picolyl)-1,2-diaminocyclohexane. By varying only the bidentate ligand in a series of complexes, it was shown that the bidentate alone can alter binding modes. DNA binding studies of the Δ-cis-α,-[Ru(RR-picchxnMe2)(phen)]2+ complex indicate fast exchange kinetics on the chemical shift time scale and a "partial intercalation" mode of binding. This complex binds to [d(CGCGATCGCG)]2 and [d(ATATCGATAT)]2 at AT, TA, and GA sites from the minor groove, as well as to the ends of the oligonucleotide at low temperature. Studies of the Δ-cis-β-[Ru(RR-picchxnMe2)(phen)]2+ complex with [d(CGCGATCGCG)]2 showed that the complex binds only weakly to the ends of the oligonucleotide. The interaction of Δ-cis-α-[Ru(RR-picchxnMe2)-(dpq)]2+ with [d(CGCGATCGCG)]2 showed intermediate exchange kinetics and evidence of minor groove intercalation at the GA base step. In contrast to the phen and dpq complexes, Δ-cis-α- and Δ-cis-β-[Ru-(RR-picchxnMe2)(phi)]2+ showed evidence of major groove binding independent of the metal ion configuration. DNA stabilization induced by complex binding to [d(CGCGATCGCG)]2 (measured as ΔTm) increases in the order phen &lt; dpq and DNA affinity in the order phen &lt; dpq &lt; phi. The groove binding preferences exhibited by the different bidentate ligands is explained with the aid of molecular modeling experiments.},\nkeywords={Molecular modeling, Complexation;  Ion exchange;  Nuclear magnetic resonance spectroscopy;  Ruthenium compounds, DNA, 1,10 phenanthroline;  cyclohexane derivative;  ligand;  quinoxaline derivative;  ruthenium complex, article;  binding affinity;  DNA binding;  intercalation complex;  kinetics;  molecular model;  molecular recognition;  molecular stability;  nuclear magnetic resonance;  priority journal;  stereochemistry, Binding Sites;  Cobalt;  DNA;  DNA Adducts;  Heat;  Intercalating Agents;  Models, Molecular;  Nuclear Magnetic Resonance, Biomolecular;  Nucleic Acid Denaturation;  Oligodeoxyribonucleotides;  Organometallic Compounds;  Phenanthrolines;  Picolines;  Pyridines;  Quinoxalines;  Ruthenium;  Stereoisomerism;  Thermodynamics},\ncorrespondence_address1={Karuso, P.; Department of Chemistry, , Sydney, NSW 2109, Australia; email: Peter.Karuso@mq.edu.au},\nissn={00062960},\ncoden={BICHA},\npubmed_id={11294655},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The hydrophobin EAS is largely unstructured in solution and functions by forming amyloid-like structures.\n \n \n \n \n\n\n \n Mackay, J.; Matthews, J.; Winefield, R.; Mackay, L.; Haverkamp, R.; and Templeton, M.\n\n\n \n\n\n\n Structure, 9(2): 83-91. 2001.\n cited By 138\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mackay200183,\nauthor={Mackay, J.P. and Matthews, J.M. and Winefield, R.D. and Mackay, L.G. and Haverkamp, R.G. and Templeton, M.D.},\ntitle={The hydrophobin EAS is largely unstructured in solution and functions by forming amyloid-like structures},\njournal={Structure},\nyear={2001},\nvolume={9},\nnumber={2},\npages={83-91},\ndoi={10.1016/S0969-2126(00)00559-1},\nnote={cited By 138},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035089501&doi=10.1016%2fS0969-2126%2800%2900559-1&partnerID=40&md5=8822f97c143ff961147ecce95fbe866e},\naffiliation={Department of Biochemistry, University of Sydney, NSW 2006, Sydney, Australia; Institute of Technology, Engineering Massey University, Palmerston North, New Zealand; Horticulture and Food Research Institute of New Zealand, Mt Albert Research Centre, Auckland, New Zealand; Australian Government Analytical Laboratories, Pymble, NSW, Australia},\nabstract={Background: Fungal hydrophobin proteins have the remarkable ability to self-assemble into polymeric, amphipathic monolayers on the surface of aerial structures such as spores and fruiting bodies. These monolayers are extremely resistant to degradation and as such offer the possibility of a range of biotechnological applications involving the reversal of surface polarity. The molecular details underlying the formation of these monolayers, however, have been elusive. We have studied EAS, the hydrophobin from the ascomycete Neurospora crassa, in an effort to understand the structural aspects of hydrophobin polymerization. Results: We have purified both wild-type and uniformly 15N-labeled EAS from N. crassa conidia, and used a range of physical methods including multidimensional NMR spectroscopy to provide the first high resolution structural information on a member of the hydrophobin family. We have found that EAS is monomeric but mostly unstructured in solution, except for a small region of antiparallel β sheet that is probably stabilized by four intramolecular disulfide bonds. Polymerised EAS appears to contain substantially higher amounts of β sheet structure, and shares many properties with amyloid fibers, including a characteristic gold-green birefringence under polarized light in the presence of the dye Congo Red. Conclusions: EAS joins an increasing number of proteins that undergo a disorder→order transition in carrying out their normal function. This report is one of the few examples where an amyloid-like state represents the wild-type functional form. Thus the mechanism of amyloid formation, now thought to be a general property of polypeptide chains, has actually been applied in nature to form these remarkable structures.},\nauthor_keywords={Amphipathic monolayer;  EAS, hydrophobin;  Neurospora crassa;  Self-assembly},\nkeywords={amyloid;  congo red;  hydrophobin, aqueous solution;  article;  beta sheet;  birefringence;  controlled study;  disulfide bond;  Neurospora crassa;  nonhuman;  nuclear magnetic resonance spectroscopy;  polymerization;  priority journal;  protein assembly;  protein structure;  structure activity relation;  structure analysis, Amino Acid Sequence;  Amyloid;  Circular Dichroism;  Coloring Agents;  Congo Red;  Fungal Proteins;  Molecular Sequence Data;  Neurospora crassa;  Nuclear Magnetic Resonance, Biomolecular;  Protein Isoforms;  Protein Structure, Secondary;  Solutions, Neurospora crassa},\ncorrespondence_address1={Mackay, J.P.; Department of Biochemistry, , Sydney, NSW 2006, Australia; email: j.mackay@biochem.usyd.edu.au},\nissn={09692126},\ncoden={STRUE},\npubmed_id={11250193},\nlanguage={English},\nabbrev_source_title={Structure},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Design, production and characterization of FLIN2 and FLIN4: The engineering of intramolecular ldb1:LMO complexes.\n \n \n \n \n\n\n \n Deane, J.; Sum, E.; Mackay, J.; Lindeman, G.; Visvader, J.; and Matthews, J.\n\n\n \n\n\n\n Protein Engineering, 14(7): 493-499. 2001.\n cited By 31\n\n\n\n
\n\n\n\n \n \n $\"Design,$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Deane2001493,\nauthor={Deane, J.E. and Sum, E. and Mackay, J.P. and Lindeman, G.J. and Visvader, J.E. and Matthews, J.M.},\ntitle={Design, production and characterization of FLIN2 and FLIN4: The engineering of intramolecular ldb1:LMO complexes},\njournal={Protein Engineering},\nyear={2001},\nvolume={14},\nnumber={7},\npages={493-499},\ndoi={10.1093/protein/14.7.493},\nnote={cited By 31},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034855611&doi=10.1093%2fprotein%2f14.7.493&partnerID=40&md5=e8559971ad66ce57791c690f8e471023},\naffiliation={Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia; Walter and Eliza Hall Institute of Medical Research, Royal Melbourne Hospital, Melbourne, Vic. 3050, Australia},\nabstract={The nuclear LIM-only (LMO) transcription factors LMO2 and LMO4 play important roles in both normal and leukemic T-cell development. LIM domains are cysteine/histidine-rich domains that contain two structural zinc ions and that function as protein-protein adaptors; members of the LMO family each contain two closely spaced LIM domains. These LMO proteins all bind with high affinity to the nuclear protein LIM domain binding protein 1 (ldb1). The LMO-ldb1 interaction is mediated through the N-terminal LIM domain (LIM1) of LMO proteins and a 38-residue region towards the C-terminus of ldb1 [ldb1(LID)]. Unfortunately, recombinant forms of LMO2 and LMO4 have limited solubility and stability, effectively preventing structural analysis. Therefore, we have designed and constructed a fusion protein in which ldb1(LID) and LIM1 of LMO2 can form an intramolecular complex. The engineered protein, FLIN2 (fusion of the LIM interacting domain of ldb1 and the N-terminal LIM domain of LMO2) has been expressed and purified in milligram quantities. FLIN2 is monomeric, contains significant levels of secondary structure and yields a sharp and well-dispersed one-dimensional 1H NMR spectrum. The analogous LMO4 protein, FLIN4, has almost identical properties. These data suggest that we will be able to obtain high-resolution structural information about the LMO-ldb1 interactions.},\nauthor_keywords={Fusion protein;  ldb1;  LMO transcription factors},\nkeywords={adaptor protein;  cysteine;  histidine;  hybrid protein;  LIM protein;  nuclear protein;  protein FLIN2;  protein FLIN4;  protein ldb1;  protein LMO;  recombinant protein;  transcription factor;  transcription factor LMO2;  transcription factor LMO4;  unclassified drug;  zinc, amino terminal sequence;  article;  binding affinity;  carboxy terminal sequence;  complex formation;  genetic engineering;  priority journal;  protein analysis;  protein domain;  protein family;  protein protein interaction;  protein secondary structure;  protein stability;  protein structure;  proton nuclear magnetic resonance;  solubility},\ncorrespondence_address1={Matthews, J.M.; Department of Biochemistry, , Sydney, NSW 2006, Australia},\npublisher={Oxford University Press},\nissn={02692139},\ncoden={PRENE},\npubmed_id={11522923},\nlanguage={English},\nabbrev_source_title={Protein Eng.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2000\n \n \n (5)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Interfacial asparagine residues within an amide tetrad contribute to Max helix-loop-helix leucine zipper homodimer stability.\n \n \n \n \n\n\n \n Tchan, M.; Choy, K.; Mackay, J.; Lyons, A.; Bains, N.; and Weiss, A.\n\n\n \n\n\n\n Journal of Biological Chemistry, 275(48): 37454-37461. 2000.\n cited By 8\n\n\n\n
\n\n\n\n \n \n $\"Interfacial$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Tchan200037454,\nauthor={Tchan, M.C. and Choy, K.J. and Mackay, J.P. and Lyons, A.T.L. and Bains, N.P.S. and Weiss, A.S.},\ntitle={Interfacial asparagine residues within an amide tetrad contribute to Max helix-loop-helix leucine zipper homodimer stability},\njournal={Journal of Biological Chemistry},\nyear={2000},\nvolume={275},\nnumber={48},\npages={37454-37461},\ndoi={10.1074/jbc.M004264200},\nnote={cited By 8},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034529186&doi=10.1074%2fjbc.M004264200&partnerID=40&md5=b99b819df6b33db19c35b96f65101b14},\naffiliation={Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia; Department of Biochemistry, University of Connecticut Health Center, Farmington, CT 06030, United States},\nabstract={The transcription factor Max is the obligate dimerization partner of the Myc oncoprotein. The pivotal role of Max within the Myc regulatory network is dependent upon its ability to dimerize via the helix-loop-helix leucine zipper domain. The Max homodimer contains a tetrad of polar residues at the interface of the leucine zipper domain. A conserved interfacial Asn residue at an equivalent position in two other leucine zipper proteins has been shown to decrease homodimer stability. The unusual arrangement of this Gln-Asn/Gln'-Asn' tetrad prompted us to investigate whether Asn92 plays a similar role in destabilizing the Max homodimer. This residue was sequentially replaced with aliphatic and charged residues. Thermal denaturation, redox time course and analytical ultracentrifugation studies show that the N92V mutation does not increase homodimer stability. Replacing this residue with negatively charged side chains in N92D and N92E destabilizes the mutant homodimer. Further replacement of Gln91 indicated that H bonding between Gln91 and Asn92 residues is not significant to the stability of the native protein. These data collectively demonstrate the central role of Asn92 in homodimer interactions. Molecular modelling studies illustrate the favorable packing of the native Asn residue at the dimer interface compared with that of the mutant Max peptides.},\nkeywords={asparagine;  helix loop helix protein;  leucine zipper protein;  transcription factor, article;  denaturation;  dimerization;  hydrogen bond;  molecular interaction;  oxidation reduction reaction;  priority journal;  protein stability;  ultracentrifugation, Amides;  Asparagine;  Base Sequence;  Circular Dichroism;  Dimerization;  DNA Primers;  Helix-Loop-Helix Motifs;  Leucine Zippers;  Models, Molecular;  Mutagenesis;  Oxidation-Reduction;  Protein Denaturation},\ncorrespondence_address1={Weiss, A.S.; Department of Biochemistry, , Sydney, NSW 2006, Australia; email: aweiss@mail.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={10978321},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Solution structures of two CCHC zinc fingers from the FOG family protein U-shaped that mediate protein-protein interactions.\n \n \n \n \n\n\n \n Liew, C. K.; Kowalski, K.; Fox, A.; Newton, A.; Sharpe, B.; Crossley, M.; and Mackay, J.\n\n\n \n\n\n\n Structure, 8(11): 1157-1166. 2000.\n cited By 38\n\n\n\n
\n\n\n\n \n \n $\"Solution$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{ChuKongLiew20001157,\nauthor={Chu Kong Liew and Kowalski, K. and Fox, A.H. and Newton, A. and Sharpe, B.K. and Crossley, M. and Mackay, J.P.},\ntitle={Solution structures of two CCHC zinc fingers from the FOG family protein U-shaped that mediate protein-protein interactions},\njournal={Structure},\nyear={2000},\nvolume={8},\nnumber={11},\npages={1157-1166},\ndoi={10.1016/S0969-2126(00)00527-X},\nnote={cited By 38},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034435420&doi=10.1016%2fS0969-2126%2800%2900527-X&partnerID=40&md5=424bae130d10926c80483f90d4ecac76},\naffiliation={Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Background: Zinc finger domains have traditionally been regarded as sequence-specific DNA binding motifs. However, recent evidence indicates that many zinc fingers mediate specific protein-protein interactions. For instance, several zinc fingers from FOG family proteins have been shown to interact with the N-terminal zinc finger of GATA-1. Results: We have used NMR spectroscopy to determine the first structures of two FOG family zinc fingers that are involved in protein-protein interactions: fingers 1 and 9 from U-shaped. These fingers resemble classical TFIIIA-like zinc fingers, with the exception of an unusual extended portion of the polypeptide backbone prior to the fourth zinc ligand. [15N,1H]-HSQC titrations have been used to define the GATA binding surface of USH-F1, and comparison with other FOG family proteins indicates that the recognition mechanism is conserved across species. The surface of FOG-type fingers that interacts with GATA-1 overlaps substantially with the surface through which classical fingers typically recognize DNA. This suggests that these fingers could not contact both GATA and DNA simultaneously. In addition, results from NMR, gel filtration, and sedimentation equilibrium experiments suggest that the interactions are of moderate affinity. Conclusions: Our results demonstrate unequivocally that zinc fingers comprising the classical ββα fold are capable of mediating specific contacts between proteins. The existence of this alternative function has implications for the prediction of protein function from sequence data and for the evolution of protein function.},\nauthor_keywords={GATA-1;  Structure;  Transcription;  U-shaped;  Zinc fingers},\nkeywords={DNA;  protein subunit;  transcription factor GATA 1;  zinc finger protein, amino acid sequence;  analytic method;  article;  binding site;  genetic procedures;  nuclear magnetic resonance spectroscopy;  priority journal;  protein analysis;  protein binding;  protein family;  protein protein interaction;  protein structure, Amino Acid Sequence;  Animals;  Carrier Proteins;  DNA-Binding Proteins;  Drosophila melanogaster;  Drosophila Proteins;  Erythroid-Specific DNA-Binding Factors;  GATA1 Transcription Factor;  Insect Proteins;  Magnetic Resonance Spectroscopy;  Mice;  Models, Molecular;  Molecular Sequence Data;  Multigene Family;  Nuclear Proteins;  Protein Binding;  Protein Conformation;  Recombinant Fusion Proteins;  Sequence Alignment;  Sequence Homology, Amino Acid;  Transcription Factors;  Zinc Fingers},\ncorrespondence_address1={Mackay, J.P.; Department of Biochemistry, , Sydney, NSW 2006, Australia; email: j.mackay@biochem.usyd.edu.au},\nissn={09692126},\ncoden={STRUE},\npubmed_id={11080638},\nlanguage={English},\nabbrev_source_title={Structure},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The core of the respiratory syncytial virus fusion protein is a trimeric coiled coil.\n \n \n \n \n\n\n \n Matthews, J.; Young, T.; Tucker, S.; and Mackay, J.\n\n\n \n\n\n\n Journal of Virology, 74(13): 5911-5920. 2000.\n cited By 67\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Matthews20005911,\nauthor={Matthews, J.M. and Young, T.F. and Tucker, S.P. and Mackay, J.P.},\ntitle={The core of the respiratory syncytial virus fusion protein is a trimeric coiled coil},\njournal={Journal of Virology},\nyear={2000},\nvolume={74},\nnumber={13},\npages={5911-5920},\ndoi={10.1128/JVI.74.13.5911-5920.2000},\nnote={cited By 67},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034086980&doi=10.1128%2fJVI.74.13.5911-5920.2000&partnerID=40&md5=897c11d2c0d174b1683c68fa1686cb46},\naffiliation={Biota Holdings Ltd., Melbourne, Vic. 3004, Australia; Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Entry into the host cell by enveloped viruses is mediated by fusion (F) or transmembrane glycoproteins. Many of these proteins share a fold comprising a trimer of antiparallel coiled-coil heterodimers, where the heterodimers are formed by two discontinuous heptad repeat motifs within the proteolytically processed chain. The F protein of human respiratory syncytial virus (RSV; the major cause of lower respiratory tract infections in infants) contains two corresponding regions that are predicted to form coiled coils (HR1 and HR2), together with a third predicted heptad repeat (HR3) located in a nonhomologous position. In order to probe the structures of these three domains and ascertain the nature of the interactions between them, we have studied the isolated HR1, HR2, and HR3 domains of RSV F by using a range of biophysical techniques, including circular dichroism, nuclear magnetic resonance spectroscopy, and sedimentation equilibrium. HR1 forms a symmetrical, trimeric coiled coil in solution (K3 ≃ 2.2 x 1011 M-2) which interacts with HR2 to form a 3:3 hexamer. The HR1-HR2 interaction domains have been mapped using limited proteolysis, reversed-phase high- performance liquid chromatography, and electrospray-mass spectrometry. HR2 in isolation exists as a largely unstructured monomer, although it exhibits a tendency to form aggregates with β-sheet-like characteristics. Only a small increase in α-helical content was observed upon the formation of the hexamer. This suggests that the RSV F glycoprotein contains a domain that closely resembles the core structure of the simian parainfluenza virus 5 fusion protein (K. A. Baker, R. E. Dutch, R. A. Lamb, and T. S. Jardetzky, Mol. Cell 3:309-319, 1999). Finally, HR3 forms weak α-helical homodimers that do not appear to interact with HR1, HR2, or the HR1-HR2 complex. The results of these studies support the idea that viral fusion proteins have a common core architecture.},\nkeywords={hybrid protein;  membrane protein, amino acid sequence;  article;  circular dichroism;  host cell;  lower respiratory tract infection;  mass spectrometry;  nonhuman;  nuclear magnetic resonance spectroscopy;  priority journal;  protein degradation;  protein domain;  protein interaction;  protein structure;  Respiratory syncytial pneumovirus;  reversed phase high performance liquid chromatography;  virus envelope, Amino Acid Sequence;  Circular Dichroism;  HN Protein;  Humans;  Molecular Sequence Data;  Nuclear Magnetic Resonance, Biomolecular;  Oligopeptides;  Peptide Biosynthesis;  Protein Structure, Secondary;  Protein Structure, Tertiary;  Respiratory Syncytial Virus, Human;  Viral Envelope Proteins;  Viral Proteins},\ncorrespondence_address1={Matthews, J.M.; Department of Biochemistry, , Sydney, NSW 2006, Australia; email: j.matthews@biochem.usyd.edu.au},\nissn={0022538X},\ncoden={JOVIA},\npubmed_id={10846072},\nlanguage={English},\nabbrev_source_title={J. Virol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The transactivation domain within cysteine/histidine-rich region 1 of CBP comprises two novel zinc-binding modules.\n \n \n \n \n\n\n \n Newton, A.; Sharped, B.; Kwan, A.; Mackay, J.; and Crossley, M.\n\n\n \n\n\n\n Journal of Biological Chemistry, 275(20): 15128-15134. 2000.\n cited By 40\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Newton200015128,\nauthor={Newton, A.L. and Sharped, B.K. and Kwan, A. and Mackay, J.P. and Crossley, M.},\ntitle={The transactivation domain within cysteine/histidine-rich region 1 of CBP comprises two novel zinc-binding modules},\njournal={Journal of Biological Chemistry},\nyear={2000},\nvolume={275},\nnumber={20},\npages={15128-15134},\ndoi={10.1074/jbc.M910396199},\nnote={cited By 40},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034686027&doi=10.1074%2fjbc.M910396199&partnerID=40&md5=96b1c6fed7e29f11534b665e4d7fdace},\naffiliation={Department of Biochemistry, G08, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={cAMP-response element-binding protein-binding protein (CBP) is a transcriptional coactivator that interacts with a number of DNA-binding proteins and cofactor proteins involved in the regulation of transcription. Relatively little is known about the structure of CBP, but it has been noted that it contains three domains that are rich in cysteine and histidine (CH1, CH2, and CH3). The sequence of CH2 conforms to that of a leukemia-associated protein domain (PHD finger), and it has been postulated that this and both CH1 and CH3 may be zinc finger domains. This has not, however, been demonstrated experimentally. We have studied CH1 and show that it is composed of two novel zinc-binding modules, which we term 'zinc bundles.' Each bundle contains the sequence Cys-X4-Cys-X8-His-X3-Cys, and we show that a synthetic peptide comprising one zinc bundle from CH1 can fold in a zinc- dependent manner. CH3 also appears to contain two zinc bundles, one with the variant sequence Cys-X2-Cys-X9-His-X3-Cys, and we demonstrate that this variant motif also undergoes Zn(II)-induced folding. CH1 acts as a transcriptional activation domain in cellular assays. We show that mutations in any of the four zinc-chelating residues in either zinc bundle of CH1 significantly impair this activity and that these mutations also interfere with certain protein-protein interactions mediated by CH1. Our results indicate that CBP is a genuine zinc-binding protein and introduce zinc bundles as novel protein interaction domains.},\nkeywords={binding protein;  cyclic AMP responsive element binding protein binding protein;  unclassified drug, amino acid sequence;  article;  metal binding;  nucleotide sequence;  priority journal;  protein binding;  protein protein interaction;  protein structure;  structure analysis;  transactivation;  transcription regulation, Amino Acid Sequence;  Animals;  Arabidopsis;  Binding Sites;  Caenorhabditis elegans;  Circular Dichroism;  CREB-Binding Protein;  Cysteine;  Drosophila melanogaster;  Histidine;  Humans;  Mice;  Molecular Sequence Data;  Nuclear Proteins;  Plants, Toxic;  Protein Folding;  Sequence Alignment;  Sequence Homology, Amino Acid;  Tobacco;  Trans-Activation (Genetics);  Trans-Activators;  Zinc;  Zinc Fingers},\ncorrespondence_address1={Crossley, M.; Department of Biochemistry, , Sydney, NSW 2006, Australia; email: m.crossley@biochem.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={10748221},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n A class of zinc fingers involved in protein-protein interactions.\n \n \n \n \n\n\n \n Matthews, J.; Kowalski, K.; Liew, C.; Sharpe, B.; Fox, A.; Crossley, M.; and Mackay, J.\n\n\n \n\n\n\n European Journal of Biochemistry, 267(4): 1030-1038. 2000.\n cited By 53\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Matthews20001030,\nauthor={Matthews, J.M. and Kowalski, K. and Liew, C.K. and Sharpe, B.K. and Fox, A.H. and Crossley, M. and Mackay, J.P.},\ntitle={A class of zinc fingers involved in protein-protein interactions},\njournal={European Journal of Biochemistry},\nyear={2000},\nvolume={267},\nnumber={4},\npages={1030-1038},\ndoi={10.1046/j.1432-1327.2000.01095.x},\nnote={cited By 53},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033965643&doi=10.1046%2fj.1432-1327.2000.01095.x&partnerID=40&md5=48c9aa43e7b455a4fc76f01e96642314},\naffiliation={Department of Biochemistry, University of Sydney, NSW 2006, Australia},\nabstract={Zinc fingers (ZnFs) are extremely common protein domains. Several classes of ZnFs are distinguished by the nature and spacing of their zinc- coordinating residues. While the structure and function of some ZnFs are well characterized, many others have been identified only through their amino acid sequence. A number of proteins contain a conserved C-X2-C-X12-H-X1-5-C sequence, which is similar to the spacing observed for the 'classic' CCHH ZnFs. Although these domains have been implicated in protein-protein (and not protein-nucleic acid) interactions, nothing is known about their structure or function at a molecular level. Here, we address this problem through the expression and biophysical characterization of several CCHC-type zinc fingers from the erythroid transcription factor FOG and the related Drosophila protein U-shaped. Each of these domains does indeed fold in a zinc-dependent fashion, coordinating the metal in a tetrahedral manner through the sidechains of one histidine and three cysteine residues, and forming extremely thermostable structures. Analysis of CD spectra suggests an overall fold similar to that of the CCHH fingers, and indeed a point mutant of FOG-F1 in which the final cysteine residue is replaced by histidine remains capable of folding. However, the CCHC (as opposed to CCHH) motif is a prerequisite for GATA-1 binding activity, demonstrating that CCHC and CCHH topologies are not interchangeable. This demonstration that members of a structurally distinct subclass of genuine zinc finger domains are involved in the mediation of protein-protein interactions has implications for the prediction of protein function from nucleotide sequences.},\nauthor_keywords={Protein-protein interactions;  Transcription;  Zinc finger},\nkeywords={transcription factor GATA 1;  zinc finger protein, article;  conformational transition;  Drosophila;  molecular dynamics;  nonhuman;  priority journal;  protein domain;  protein folding;  protein protein interaction, Amino Acid Sequence;  Animals;  Carrier Proteins;  Cysteine;  DNA-Binding Proteins;  Drosophila melanogaster;  Drosophila Proteins;  Erythroid-Specific DNA-Binding Factors;  Histidine;  Hydrogen-Ion Concentration;  Insect Proteins;  Molecular Sequence Data;  Mutation;  Nuclear Proteins;  Protein Binding;  Protein Folding;  Protein Structure, Secondary;  Recombinant Fusion Proteins;  Spectrum Analysis;  Temperature;  Thermodynamics;  Transcription Factors;  Two-Hybrid System Techniques;  Zinc;  Zinc Fingers},\nissn={00142956},\npubmed_id={10672011},\nlanguage={English},\nabbrev_source_title={Eur. J. Biochem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 1999\n \n \n (5)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Transcriptional cofactors of the FOG family interact with GATA proteins by means of multiple zinc fingers.\n \n \n \n \n\n\n \n Fox, A.; Liew, C.; Holmes, M.; Kowalski, K.; Mackay, J.; and Crossley, M.\n\n\n \n\n\n\n EMBO Journal, 18(10): 2812-2822. 1999.\n cited By 224\n\n\n\n
\n\n\n\n \n \n $\"Transcriptional$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Fox19992812,\nauthor={Fox, A.H. and Liew, C. and Holmes, M. and Kowalski, K. and Mackay, J. and Crossley, M.},\ntitle={Transcriptional cofactors of the FOG family interact with GATA proteins by means of multiple zinc fingers},\njournal={EMBO Journal},\nyear={1999},\nvolume={18},\nnumber={10},\npages={2812-2822},\ndoi={10.1093/emboj/18.10.2812},\nnote={cited By 224},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033577703&doi=10.1093%2femboj%2f18.10.2812&partnerID=40&md5=d6c651a1a9f67226ce224ae3b0cc36dd},\nabstract={Friend of GATA-1 (FOG-1) is a zinc finger protein that has been shown to interact physically with the erythroid DNA-binding protein GATA-1 and modulate its transcriptional activity. Recently, two new members of the FOG family have been identified: a mammalian protein, FOG-2, that also associates with GATA-1 and other mammalian GATA factors; and U-shaped, a Drosophila protein that interacts with the Drosophila GATA protein Pannier. FOG proteins contain multiple zinc fingers and it has been shown previously that the sixth finger of FOG-1 interacts specifically with the N-finger but not the C-finger of GATA-1. Here we show that fingers 1, 5 and 9 of FOG-1 also interact with the N-finger of GATA-1 and that FOG-2 and U-shaped also contain multiple GATA-interacting fingers. We define the key contact residues and show that these residues are highly conserved in GATA-interacting fingers. We examine the effect of selectively mutating the four interacting fingers of FOG-1 and show that each contributes to FOG-1's ability to modulate GATA-1 activity. Finally, we show that FOG-1 can repress GATA-1-mediated activation and present evidence that this ability involves the recently described CtBP co-repressor proteins that recognize all known FOG proteins.},\nauthor_keywords={FOG;  GATA-1;  Gene expression;  Transcription;  Zinc finger},\nkeywords={DNA binding protein;  mutant protein;  transcription factor;  zinc finger protein, amino acid sequence;  animal cell;  article;  controlled study;  mouse;  nonhuman;  priority journal;  protein DNA binding;  protein protein interaction;  structure activity relation, Amino Acid Sequence;  Animals;  Carrier Proteins;  Conserved Sequence;  DNA-Binding Proteins;  Erythroid-Specific DNA-Binding Factors;  GATA1 Transcription Factor;  Genes, Reporter;  Humans;  Mice;  Models, Molecular;  Molecular Sequence Data;  Mutagenesis;  Nuclear Proteins;  Phosphoproteins;  Promoter Regions (Genetics);  Protein Binding;  Repressor Proteins;  Sequence Alignment;  Transcription Factors;  Yeasts;  Zinc Fingers, Animalia;  Mammalia},\ncorrespondence_address1={Crossley, M.email: M.Crossley@biochem.usyd.edu.au},\nissn={02614189},\ncoden={EMJOD},\npubmed_id={10329627},\nlanguage={English},\nabbrev_source_title={EMBO J.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The solution structure of the N-terminal zinc finger of GATA-1 reveals a specific binding face for the transcriptional co-factor FOG.\n \n \n \n \n\n\n \n Kowalski, K.; Czolij, R.; King, G.; Crossley, M.; and Mackay, J.\n\n\n \n\n\n\n Journal of Biomolecular NMR, 13(3): 249-262. 1999.\n cited By 50\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Kowalski1999249,\nauthor={Kowalski, K. and Czolij, R. and King, G.F. and Crossley, M. and Mackay, J.P.},\ntitle={The solution structure of the N-terminal zinc finger of GATA-1 reveals a specific binding face for the transcriptional co-factor FOG},\njournal={Journal of Biomolecular NMR},\nyear={1999},\nvolume={13},\nnumber={3},\npages={249-262},\ndoi={10.1023/A:1008309602929},\nnote={cited By 50},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033003563&doi=10.1023%2fA%3a1008309602929&partnerID=40&md5=9ce94f56a705a1693b58269b9d72d1f3},\naffiliation={Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Zinc fingers (ZnFs) are generally regarded as DNA-binding motifs. However, a number of recent reports have implicated particular ZnFs in the mediation of protein-protein interactions. The N-terminal ZnF of GATA-1 (NF) is one such finger, having been shown to interact with a number of other proteins, including the recently discovered transcriptional co-factor FOG. Here we solve the three-dimensional structure of the NF in solution using multidimensional 1H/15N NMR spectroscopy, and we use 1H/15N spin relaxation measurements to investigate its backbone dynamics. The structure consists of two distorted β-hairpins and a single α-helix, and is similar to that of the C-terminal ZnF of chicken GATA-1. Comparisons of the NF structure with those of other C4-type zinc binding motifs, including hormone receptor and LIM domains, also reveal substantial structural homology. Finally, we use the structure to map the spatial locations of NF residues shown by mutagenesis to be essential for FOG binding, and demonstrate that these residues all lie on a single face of the NF. Notably, this face is well removed from the putative DNA-binding face of the NF, an observation which is suggestive of simultaneous roles for the NF; that is, stabilisation of GATA- 1 DNA complexes and recruitment of FOG to GATA-1-controlled promoter regions.},\nauthor_keywords={GATA-1;  Protein-protein interactions;  Solution structure;  Zinc finger},\nkeywords={nitrogen 15;  transcription factor gata 1;  zinc finger protein, article;  binding affinity;  DNA binding;  escherichia coli;  genetic transcription;  geometry;  nonhuman;  nuclear magnetic resonance;  priority journal;  protein protein interaction;  proton nuclear magnetic resonance, Amino Acid Sequence;  Animals;  Binding Sites;  Carrier Proteins;  Computer Simulation;  DNA-Binding Proteins;  Erythroid-Specific DNA-Binding Factors;  GATA1 Transcription Factor;  Mice;  Models, Molecular;  Molecular Sequence Data;  Nuclear Magnetic Resonance, Biomolecular;  Nuclear Proteins;  Protein Structure, Secondary;  Recombinant Proteins;  Sequence Alignment;  Sequence Homology, Amino Acid;  Software;  Transcription Factors;  Zinc Fingers},\ncorrespondence_address1={Mackay, J.P.; Department of Biochemistry, , Sydney, NSW 2006, Australia; email: j.mackay@biochem.usyd.edu.au},\nissn={09252738},\ncoden={JBNME},\npubmed_id={10212985},\nlanguage={English},\nabbrev_source_title={J. Biomol. NMR},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The dimerization and topological specificity functions of MinE reside in a structurally autonomous C-terminal domain.\n \n \n \n \n\n\n \n King, G.; Rowland, S.; Pan, B.; Mackay, J.; Mullen, G.; and Rothfield, L.\n\n\n \n\n\n\n Molecular Microbiology, 31(4): 1161-1169. 1999.\n cited By 31\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{King19991161,\nauthor={King, G.F. and Rowland, S.L. and Pan, B. and Mackay, J.P. and Mullen, G.P. and Rothfield, L.I.},\ntitle={The dimerization and topological specificity functions of MinE reside in a structurally autonomous C-terminal domain},\njournal={Molecular Microbiology},\nyear={1999},\nvolume={31},\nnumber={4},\npages={1161-1169},\ndoi={10.1046/j.1365-2958.1999.01256.x},\nnote={cited By 31},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033038056&doi=10.1046%2fj.1365-2958.1999.01256.x&partnerID=40&md5=78b44d8c3a0631c9794dd054199e9a5a},\naffiliation={Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia; Department of Microbiology, Univ. of Connecticut Health Center, Farmington, CT 06030, United States; Department of Biochemistry, Univ. of Connecticut Health Center, Farmington, CT 06030, United States},\nabstract={Correct placement of the division septum in Escherichia coli requires the co-ordinated action of three proteins, MinC, MinD and MinE. MinC and MinD interact to form a non-specific division inhibitor that blocks septation at all potential division sites. MinE is able to antagonize MinCD in a topologically sensitive manner, as it restricts MinCD activity to the unwanted division sites at the cell poles. Here, we show that the topological specificity function of MinE residues in a structurally autonomous, trypsin-resistant domain comprising residues 31-88. Nuclear magnetic resonance (NMR) and circular dichroic spectroscopy indicate that this domain includes both α and β secondary structure, while analytical ultracentrifugation reveals that it also contains a region responsible for MinE homodimerization. While trypsin digestion indicates that the anti-MinCD domain of MinE (residues 1-22) does not form a tightly folded structural domain, NMR analysis of a peptide corresponding to MinE1-22 indicates that this region forms a nascent helix in which the peptide rapidly interconverts between disordered (random coil) and α-helical conformations. This suggests that the N-terminal region of MinE may be poised to adopt an α-helical conformation when it interacts with the target of its anti-MinCD activity, presumably MinD.},\nkeywords={bacterial protein;  trypsin, alpha helix;  article;  carboxy terminal sequence;  cell division;  circular dichroism;  controlled study;  dimerization;  nonhuman;  nuclear magnetic resonance spectroscopy;  priority journal;  protein domain;  protein localization;  protein secondary structure;  structure activity relation;  ultracentrifugation, Amino Acid Sequence;  Bacterial Proteins;  Cell Cycle Proteins;  Circular Dichroism;  Dimerization;  Escherichia coli;  Escherichia coli Proteins;  Magnetic Resonance Spectroscopy;  Mass Spectrometry;  Molecular Sequence Data;  Protein Structure, Secondary;  Structure-Activity Relationship;  Substrate Specificity;  Ultracentrifugation, Bacteria (microorganisms);  Escherichia coli},\ncorrespondence_address1={King, G.F.; Department of Biochemistry, , Sydney, NSW 2006, Australia; email: glenn@biochem.usyd.edu.au},\nissn={0950382X},\ncoden={MOMIE},\npubmed_id={10096083},\nlanguage={English},\nabbrev_source_title={Mol. Microbiol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Use of altered specificity mutants to probe a specific protein-protein interaction in differentiation: The GATA-1:FOG complex.\n \n \n \n \n\n\n \n Crispino, J.; Lodish, M.; MacKay, J.; and Orkin, S.\n\n\n \n\n\n\n Molecular Cell, 3(2): 219-228. 1999.\n cited By 208\n\n\n\n
\n\n\n\n \n \n $\"Use$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Crispino1999219,\nauthor={Crispino, J.D. and Lodish, M.B. and MacKay, J.P. and Orkin, S.H.},\ntitle={Use of altered specificity mutants to probe a specific protein-protein interaction in differentiation: The GATA-1:FOG complex},\njournal={Molecular Cell},\nyear={1999},\nvolume={3},\nnumber={2},\npages={219-228},\ndoi={10.1016/S1097-2765(00)80312-3},\nnote={cited By 208},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033083804&doi=10.1016%2fS1097-2765%2800%2980312-3&partnerID=40&md5=1883d264ea26ecc8ccd7ca1b8dd79089},\naffiliation={Division of Hematology-Oncology, Children's Hospital, Dana Farber Cancer Institute, Boston, MA 02115, United States; Department of Pediatrics, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA 02115, United States; Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={GATA-1 and FOG (Friend of GATA-1) are each essential for erythroid and megakaryocyte development. FOG, a zinc finger protein, interacts with the amino (N) finger of GATA-1 and cooperates with GATA-1 to promote differentiation. To determine whether this interaction is critical for GATA- 1 action, we selected GATA-1 mutants in yeast that fail to interact with FOG but retain normal DNA binding, as well a compensatory FOG mutant that restores interaction. These novel GATA-1 mutants do not promote erythroid differentiation of GATA-1- erythroid cells. Differentiation is rescued by the second-site FOG mutant. Thus, interaction of FOG with GATA-1 is essential for the function of GATA-1 in erythroid differentiation. These findings provide a paradigm for dissecting protein-protein associations involved in mammalian development.},\nkeywords={cell protein;  protein fog;  transcription factor GATA 1;  unclassified drug, amino terminal sequence;  article;  binding affinity;  cell culture;  cell differentiation;  complex formation;  dissociation constant;  DNA binding;  erythropoiesis;  gene control;  mammal;  megakaryopoiesis;  mutant;  protein protein interaction, Mammalia},\ncorrespondence_address1={Orkin, S.H.; Division of Hematology-Oncology, , Boston, MA 02115, United States; email: orkin@rascal.med.harvard.edu},\npublisher={Cell Press},\nissn={10972765},\ncoden={MOCEF},\npubmed_id={10078204},\nlanguage={English},\nabbrev_source_title={Mol. Cell},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Autonomous folding of a peptide corresponding to the N-terminal β- hairpin from ubiquitin.\n \n \n \n \n\n\n \n Zerella, R.; Evans, P.; Ionides, J.; Packman, L.; Trotter, B.; Mackay, J.; and Williams, D.\n\n\n \n\n\n\n Protein Science, 8(6): 1320-1331. 1999.\n cited By 58\n\n\n\n
\n\n\n\n \n \n $\"Autonomous$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Zerella19991320,\nauthor={Zerella, R. and Evans, P.A. and Ionides, J.M.C. and Packman, L.C. and Trotter, B.W. and Mackay, J.P. and Williams, D.H.},\ntitle={Autonomous folding of a peptide corresponding to the N-terminal β- hairpin from ubiquitin},\njournal={Protein Science},\nyear={1999},\nvolume={8},\nnumber={6},\npages={1320-1331},\ndoi={10.1110/ps.8.6.1320},\nnote={cited By 58},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033028620&doi=10.1110%2fps.8.6.1320&partnerID=40&md5=b9058534636a2e274b40676038a595a8},\naffiliation={Cambridge Ctr. for Molec. Recog., University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom; Cambridge Ctr. for Molec. Recog., Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QW, United Kingdom; Cambridge Ctr. for Molec. Recog., MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom; Department of Biochemistry, University of Cambridge, Old Addenbrooke's Site, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom; Dept. of Chem. and Chemical Biology, Harvard University, Cambridge, MA 02138, United States; University of Sydney, Department of Biochemistry, Sydney, NSW 2006, Australia},\nabstract={The N-terminal 17 residues of ubiquitin have been shown by 1H NMR to fold autonomously into a β-hairpin structure in aqueous solution. This structure has a specific, native-like register, though side-chain contacts differ in detail from those observed in the intact protein. An autonomously folding hairpin has previously been identified in the case of streptococcal protein G, which is structurally homologous with ubiquitin, but remarkably, the two are not in topologically equivalent positions in the fold. This suggests that the organization of folding may be quite different for proteins sharing similar tertiary structures. Two smaller peptides have also been studied, corresponding to the isolated arms of the N-terminal hairpin of ubiquitin, and significant differences from simple random coil predictions observed in the spectra of these subfragments, suggestive of significant limitation of the backbone conformational space sampled, presumably as a consequence of the strongly β-structure favoring composition of the sequences. This illustrates the ability of local sequence elements to express a propensity for β-structure even in the absence of actual sheet formation. Attempts were made to estimate the population of the folded state of the hairpin, in terms of a simple two-state folding model. Using published 'random coil' values to model the unfolded state, and values derived from native ubiquitin for the putative unique, folded state, it was found that the apparent population varied widely for different residues and with different NMR parameters. Use of the spectra of the subfragment peptides to provide a more realistic model of the unfolded state led to better agreement in the estimates that could be obtained from chemical shift and coupling constant measurements, while making it clear that some other approaches to population estimation could not give meaningful results, because of the tendency to populate the β-region of conformational space even in the absence of the hairpin structure.},\nauthor_keywords={Chemical shifts;  Coupling constants;  Peptide conformations;  Ubiquitin;  β-hairpin;  β-sheet},\nkeywords={ubiquitin, amino terminal sequence;  article;  conformational transition;  nuclear Overhauser effect;  priority journal;  protein folding;  protein secondary structure;  proton nuclear magnetic resonance},\ncorrespondence_address1={Evans, P.A.; Department of Biochemistry, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom; email: pe@mole.bio.cam.ac.uk},\npublisher={Cambridge University Press},\nissn={09618368},\ncoden={PRCIE},\npubmed_id={10386882},\nlanguage={English},\nabbrev_source_title={Protein Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n

\n The N-terminal 17 residues of ubiquitin have been shown by 1H NMR to fold autonomously into a β-hairpin structure in aqueous solution. This structure has a specific, native-like register, though side-chain contacts differ in detail from those observed in the intact protein. An autonomously folding hairpin has previously been identified in the case of streptococcal protein G, which is structurally homologous with ubiquitin, but remarkably, the two are not in topologically equivalent positions in the fold. This suggests that the organization of folding may be quite different for proteins sharing similar tertiary structures. Two smaller peptides have also been studied, corresponding to the isolated arms of the N-terminal hairpin of ubiquitin, and significant differences from simple random coil predictions observed in the spectra of these subfragments, suggestive of significant limitation of the backbone conformational space sampled, presumably as a consequence of the strongly β-structure favoring composition of the sequences. This illustrates the ability of local sequence elements to express a propensity for β-structure even in the absence of actual sheet formation. Attempts were made to estimate the population of the folded state of the hairpin, in terms of a simple two-state folding model. Using published 'random coil' values to model the unfolded state, and values derived from native ubiquitin for the putative unique, folded state, it was found that the apparent population varied widely for different residues and with different NMR parameters. Use of the spectra of the subfragment peptides to provide a more realistic model of the unfolded state led to better agreement in the estimates that could be obtained from chemical shift and coupling constant measurements, while making it clear that some other approaches to population estimation could not give meaningful results, because of the tendency to populate the β-region of conformational space even in the absence of the hairpin structure.\n

\n\n\n

\n\n\n\n\n\n

\n

\n \n 1998\n \n \n (5)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Key residues characteristic of GATA N-fingers are recognized by FOG.\n \n \n \n \n\n\n \n Fox, A.; Kowalski, K.; King, G.; Mackay, J.; and Crossley, M.\n\n\n \n\n\n\n Journal of Biological Chemistry, 273(50): 33595-33603. 1998.\n cited By 75\n\n\n\n
\n\n\n\n \n \n $\"Key$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Fox199833595,\nauthor={Fox, A.H. and Kowalski, K. and King, G.F. and Mackay, J.P. and Crossley, M.},\ntitle={Key residues characteristic of GATA N-fingers are recognized by FOG},\njournal={Journal of Biological Chemistry},\nyear={1998},\nvolume={273},\nnumber={50},\npages={33595-33603},\ndoi={10.1074/jbc.273.50.33595},\nnote={cited By 75},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032509511&doi=10.1074%2fjbc.273.50.33595&partnerID=40&md5=e901c35e0b8ec9c59c45e1f631127f59},\naffiliation={Department of Biochemistry, University of Sydney, New South Wales, 2006, Australia; Dept. of Biochemistry, G08, University of Sydney, NSW, 2006, Australia},\nabstract={Protein-protein interactions play significant roles in the control of gene expression. These interactions often occur between small, discrete domains within different transcription factors. In particular, zinc fingers, usually regarded as DNA-binding domains, are now also known to be involved in mediating contacts between proteins. We have investigated the interaction between the erythroid transcription factor GATA-1 and its partner, the 9 zinc finger protein, FOG (Friend Of GATA). We demonstrate that this interaction represents a genuine finger-finger contact, which is dependent on zinc- coordinating residues within each protein. We map the contact domains to the core of the N-terminal zinc finger of GATA-1 and the 6th zinc finger of FOG. Using a scanning substitution strategy we identify key residues within the GATA-1 N-finger which are required for FOG binding. These residues are conserved in the N-fingers of all GATA proteins known to bind FOG, but are not found in the respective C-fingers. This observation may, therefore, account for the particular specificity of FOG for N-fingers. Interestingly, the key N-finger residues are seen to form a contiguous surface, when mapped onto the structure of the N-finger of GATA-1.},\nkeywords={protein fog;  transcription factor gata 1;  unclassified drug;  zinc finger protein, amino terminal sequence;  article;  carboxy terminal sequence;  circular dichroism;  DNA binding;  gene expression regulation;  gene mutation;  immunoblotting;  priority journal;  protein domain;  protein protein interaction;  site directed mutagenesis;  stoichiometry;  transactivation, 3T3 Cells;  Amino Acid Sequence;  Animals;  Base Sequence;  Carrier Proteins;  Conserved Sequence;  DNA Primers;  DNA-Binding Proteins;  Erythroid-Specific DNA-Binding Factors;  GATA1 Transcription Factor;  Mice;  Models, Molecular;  Molecular Sequence Data;  Mutagenesis, Site-Directed;  Nuclear Proteins;  Promoter Regions (Genetics);  Protein Binding;  Protein Conformation;  Sequence Homology, Amino Acid;  Transcription Factors;  Zinc Fingers},\ncorrespondence_address1={Crossley, M.; Dept. of Biochemistry, , Sydney, NSW 2006, Australia; email: M.Crossley@biochem.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={9837943},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The C-terminal region of the stalk domain of ubiquitous human kinesin heavy chain contains the binding site for kinesin light chain.\n \n \n \n \n\n\n \n Diefenbach, R.; Mackay, J.; Armati, P.; and Cunningham, A.\n\n\n \n\n\n\n Biochemistry, 37(47): 16663-16670. 1998.\n cited By 107\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Diefenbach199816663,\nauthor={Diefenbach, R.J. and Mackay, J.P. and Armati, P.J. and Cunningham, A.L.},\ntitle={The C-terminal region of the stalk domain of ubiquitous human kinesin heavy chain contains the binding site for kinesin light chain},\njournal={Biochemistry},\nyear={1998},\nvolume={37},\nnumber={47},\npages={16663-16670},\ndoi={10.1021/bi981163r},\nnote={cited By 107},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032564307&doi=10.1021%2fbi981163r&partnerID=40&md5=b7be3a1db0546f5c431dd4fa75f2977e},\naffiliation={Centre for Virus Research, Westmead Institutes of Hlth. Res., Westmead Hospital, Westmead, NSW 2145, Australia},\nabstract={The motor protein kinesin is a heterotetramer composed of two heavy chains of ~120 kDa and two light chains of ~6 kDa protein. Kinesin motor activity is dependent on the presence of ATP and microtubules. The kinesin light chain-binding site in human kinesin heavy chain was determined by reconstituting in vitro a complex of recombinant heavy and light chains. The proteins expressed in bacteria included oligohistidine-tagged fragments of human ubiquitous kinesin heavy chain, spanning most of the stalk and all of the tail domain (amino acids 555-963); and untagged, essentially full-length human kinesin light chain (4-569) along with N-terminal (4-363)and C-terminal (364-569) light chain fragments. Heavy chain fragments were attached to Ni2+-charged beads and incubated with untagged light chain fragments. Analysis of eluted complexes by SDS-PAGE and immunoblotting mapped the light chain-binding site in heavy chain to amino acids 771-813, a region close to the C-terminal end of the heavy chain stalk domain. In addition, only the full-length and N-terminal kinesin light chain fragments bound to this heavy chain region. Within this heavy chain region are four highly conserved contiguous heptad repeats (775-802) which are predicted to form a tight α- helical coiled-coil interaction with the heptad repeat-containing N-terminus of the light chain, in particular region 106-152 of human light chain. This predicted hydrophobic, α-helical coiled-coil interaction is supported by both circular dichroism spectroscopy of the recombinant kinesin heavy chain fragment 771-963, which displays an α-helical content of 70%, and the resistance of the heavy/light chain interdiction to high salt (0.5 M).},\nkeywords={adenosine triphosphate;  amino acid;  histidine;  kinesin;  nickel, amino terminal sequence;  article;  binding site;  carboxy terminal sequence;  circular dichroism;  immunoblotting;  polyacrylamide gel electrophoresis;  priority journal, Amino Acid Sequence;  Animals;  Binding Sites;  Cattle;  Decapodiformes;  Drosophila;  Humans;  Kinesin;  Mice;  Microtubule-Associated Proteins;  Molecular Sequence Data;  Neurons;  Peptide Fragments;  Protein Structure, Secondary;  Protein Structure, Tertiary;  Recombinant Fusion Proteins;  Sea Urchins},\ncorrespondence_address1={Diefenbach, R.J.; Centre for Virus Research, , Westmead, NSW 2145, Australia; email: russelld@westgate.wh.usyd.edu.au},\nissn={00062960},\ncoden={BICHA},\npubmed_id={9843434},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Involvement of the N-finger in the self-association of GATA-1.\n \n \n \n \n\n\n \n Mackay, J.; Kowalski, K.; Fox, A.; Czolij, R.; King, G.; and Crossley, M.\n\n\n \n\n\n\n Journal of Biological Chemistry, 273(46): 30560-30567. 1998.\n cited By 54\n\n\n\n
\n\n\n\n \n \n $\"Involvement$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mackay199830560,\nauthor={Mackay, J.P. and Kowalski, K. and Fox, A.H. and Czolij, R. and King, G.F. and Crossley, M.},\ntitle={Involvement of the N-finger in the self-association of GATA-1},\njournal={Journal of Biological Chemistry},\nyear={1998},\nvolume={273},\nnumber={46},\npages={30560-30567},\ndoi={10.1074/jbc.273.46.30560},\nnote={cited By 54},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032515037&doi=10.1074%2fjbc.273.46.30560&partnerID=40&md5=30c3a43baeb46a5d963a6f06e90177fd},\naffiliation={Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Zinc fingers are recognized as small protein domains that bind to specific DNA sequences. Recently however, zinc fingers from a number of proteins, in particular the GATA family of transcription factors, have also been implicated in specific protein-protein interactions. The erythroid protein GATA-1 contains two zinc fingers: the C-finger, which is sufficient for sequence-specific DNA-binding, and the N-finger, which appears both to modulate DNA-binding and to interact with other transcription factors. We have expressed and purified the N-finger domain and investigated its involvement in the self-association of GATA-1. We demonstrate that this domain does not homodimerize but instead makes intermolecular contacts with the C-finger, suggesting that GATA dimers are maintained by reciprocal N- finger-C-finger contacts. Deletion analysis identifies a 25-residue region, C-terminal to the core N-finger domain, that is sufficient for interaction with intact GATA-1. A similar subdomain exists C-terminal to the C-finger, and we show that self-association is substantially reduced when both subdomains are disrupted by mutation. Moreover, mutations that impair GATA-1 self-association also interfere with its ability to activate transcription in transfection studies.},\nkeywords={transcription factor gata 1;  zinc finger protein, amino acid sequence;  article;  carboxy terminal sequence;  dimerization;  DNA sequence;  gene deletion;  genetic transcription;  molecular interaction;  nucleotide sequence;  priority journal;  protein DNA binding;  protein domain;  protein folding;  protein protein interaction, Amino Acid Sequence;  Animals;  Circular Dichroism;  Cobalt;  DNA-Binding Proteins;  Erythroid-Specific DNA-Binding Factors;  GATA1 Transcription Factor;  Mice;  Molecular Sequence Data;  Nuclear Proteins;  Protein Conformation;  Protein Folding;  Spectrophotometry, Ultraviolet;  Transcription Factors;  Zinc Fingers},\ncorrespondence_address1={Crossley, M.; Department of Biochemistry, , Sydney, NSW 2006, Australia; email: M.Crossley@biochem.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={9804826},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Interactions of the Antitumor Agent Molybdocene Dichloride with Oligonucleotides.\n \n \n \n \n\n\n \n Harding, M.; Mokdsi, G.; Mackay, J.; Prodigalidad, M.; and Lucas, S.\n\n\n \n\n\n\n Inorganic Chemistry, 37(10): 2432-2437. 1998.\n cited By 54\n\n\n\n
\n\n\n\n \n \n $\"Interactions$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Harding19982432,\nauthor={Harding, M.M. and Mokdsi, G. and Mackay, J.P. and Prodigalidad, M. and Lucas, S.W.},\ntitle={Interactions of the Antitumor Agent Molybdocene Dichloride with Oligonucleotides},\njournal={Inorganic Chemistry},\nyear={1998},\nvolume={37},\nnumber={10},\npages={2432-2437},\ndoi={10.1021/ic971205k},\nnote={cited By 54},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0001340544&doi=10.1021%2fic971205k&partnerID=40&md5=87e8f798ff43a71f6db12d00dea965a4},\naffiliation={School of Chemistry, University of Sydney, NSW 2006, Australia; Department of Biochemistry, University of Sydney, NSW 2006, Australia},\nabstract={The interactions between the antitumor-active metallocene molybdocene dichloride (Cp2MoCl2) and four oligonucleotides have been studied by 1H and 31P NMR spectroscopy. In 50 mM salt solutions of molybdocene dichloride, hydrolysis of the halide ligands occurs to give a solution with pD 2, containing a species in which both Cp rings remain metal bound for 24 h. At pD 7, however, partial hydrolysis of the Cp rings (∼30%) occurs after 24 h. Addition of an aqueous solution of molybdocene dichloride in 50 mM salt to the self-complementary sequence d(CGCATATGCG)2, maintaining the pD at 6.0-7.0, showed no evidence for the formation of a metallocene-oligonucleotide complex, and only peaks arising from hydrolysis of molybdocene dichloride were detected. A similar result was obtained in titration experiments with the single-stranded sequence d(ATGGTA) at pD 6.5-7.0. However, at pD 3.0, new signals assigned to a molybdocene-oligonuleotide complex or complexes were detected in the 1H NMR spectrum. No change was observed in the 31P NMR spectrum. The complex or complexes formed between molybdocene dichloride and d(ATGGTA) are stable for hours at pD 3.0; at higher pD, the complex is destabilized and only peaks arising from hydrolysis of molybdocene dichloride are detected. Titration experiments at low pD with the dinucleotide dCpG showed a new set of signals in the 1H NMR spectrum, tentatively assigned to formation of a complex arising due to coordination of molybdenum to guanine N7 and/or cytosine N3. At pD 7.0, these signals disappeared. The results obtained show that stable oligonucleotide adducts are not formed in 50 mM salt at pD 7.0, and hence it is highly unlikely that formation of molybdocene - DNA adducts in vivo is the primary action that is responsible for the antitumor properties of molybdocene dichloride.},\ncorrespondence_address1={Harding, M.M.; School of Chemistry, , NSW 2006, Australia},\npublisher={American Chemical Society},\nissn={00201669},\ncoden={INOCA},\nlanguage={English},\nabbrev_source_title={Inorg. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Zinc fingers are sticking together.\n \n \n \n \n\n\n \n Mackay, J.; and Crossley, M.\n\n\n \n\n\n\n Trends in Biochemical Sciences, 23(1): 1-4. 1998.\n cited By 381\n\n\n\n
\n\n\n\n \n \n $\"Zinc$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mackay19981,\nauthor={Mackay, J.P. and Crossley, M.},\ntitle={Zinc fingers are sticking together},\njournal={Trends in Biochemical Sciences},\nyear={1998},\nvolume={23},\nnumber={1},\npages={1-4},\ndoi={10.1016/S0968-0004(97)01168-7},\nnote={cited By 381},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0031892446&doi=10.1016%2fS0968-0004%2897%2901168-7&partnerID=40&md5=9d8aed28b3af0b013f58d699fd482692},\nkeywords={DNA;  zinc finger protein, genetic transcription;  nonhuman;  priority journal;  protein analysis;  protein DNA binding;  protein protein interaction;  review;  signal transduction},\ncorrespondence_address1={Crossley, M.; Department of Biochemistry, , Sydney, NSW 2006, Australia; email: m.crossley@biochem.usyd.edu.au},\npublisher={Elsevier Ltd},\nissn={09680004},\ncoden={TBSCD},\npubmed_id={9478126},\nlanguage={English},\nabbrev_source_title={Trends Biochem. Sci.},\ndocument_type={Note},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n

\n\n\n\n\n\n

\n

\n \n 1997\n \n \n (6)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Zipping up transcription factors: Rational design of anti-Jun and anti-Fos peptides.\n \n \n \n \n\n\n \n Bains, N.; Wilce, J.; Heuer, K.; Tunstall, M.; Mackay, J.; Bennett, M.; Weiss, A.; and King, G.\n\n\n \n\n\n\n International Journal of Peptide Research and Therapeutics, 4(2): 67-77. 1997.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Zipping$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Bains199767,\nauthor={Bains, N.P.S. and Wilce, J.A. and Heuer, K.H. and Tunstall, M. and Mackay, J.P. and Bennett, M.R. and Weiss, A.S. and King, G.F.},\ntitle={Zipping up transcription factors: Rational design of anti-Jun and anti-Fos peptides},\njournal={International Journal of Peptide Research and Therapeutics},\nyear={1997},\nvolume={4},\nnumber={2},\npages={67-77},\ndoi={10.1007/BF02443517},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-53249117776&doi=10.1007%2fBF02443517&partnerID=40&md5=82a8308b9070743d577c2b9ad4d2b5c4},\naffiliation={Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia; Institute for Biomedical Research, Department of Physiology, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Various members of the bZip and bHLH-Zip families of eukaryotic transcription factors, including Jun, Fos, and Myc, have been identified as oncoproteins; mutation or deregulated expression of these proteins leads to certain types of cancer. These proteins can only bind to their cognate DNA enhancer sites following homodimerization, or heterodimerization with another family member, via their leucine zipper domain. Thus, a novel anticancer strategy would be to inhibit dimerization of these proteins, thereby blocking their DNA binding and transactivation functions. In this paper we show that it is possible to rationally design leucine zipper peptides that bind with high affinity to the leucine zipper dimerization domains of c-Jun and c-Fos, thus preventing the formation of functional c-Jun homodimers and c-Jun:c-Fos heterodimers; we refer to such peptides as superzippers (SZs). In vivo, c-Jun:SZ and c-Fos:SZ heterodimers should be nonfunctional as they lack one of the two basic domains that are essential for DNA binding. While the transport of a peptidic agent into cells often poses a severe obstacle to its therapeutic use, we show that a 46-residue leucine zipper peptide can be transported into HeLa cells by coupling it to a 17-residue carrier peptide from the Antennapedia homeodomain, thus paving the way for detailed studies of the therapeutic potential of superzipper peptides. © 1997 ESCOM Science Publishers B.V.},\nauthor_keywords={Anticancer drugs;  Fos;  Jun;  Leucine zipper;  Peptide delivery;  Peptide drug;  Transcription factors},\ncorrespondence_address1={King, G.F.; Department of Biochemistry, , Sydney, NSW 2006, Australia},\npublisher={Springer New York},\nissn={15733149},\ncoden={IJPRF},\nlanguage={English},\nabbrev_source_title={Int. J. Pept. Res. Ther.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n DMA-binding studies of XSPTSPSZ, derivatives of the intercalating heptad repeat of RNA polymerase II.\n \n \n \n \n\n\n \n Harding, M.; Krippner, G.; Shelton, C.; Rodger, A.; Sanders, K.; Mackay, J.; and Prakash, A.\n\n\n \n\n\n\n Biopolymers - Nucleic Acid Sciences Section, 42(4): 387-398. 1997.\n cited By 5\n\n\n\n
\n\n\n\n \n \n $\"DMA-binding$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Harding1997387,\nauthor={Harding, M.M. and Krippner, G.Y. and Shelton, C.J. and Rodger, A. and Sanders, K.J. and Mackay, J.P. and Prakash, A.S.},\ntitle={DMA-binding studies of XSPTSPSZ, derivatives of the intercalating heptad repeat of RNA polymerase II},\njournal={Biopolymers - Nucleic Acid Sciences Section},\nyear={1997},\nvolume={42},\nnumber={4},\npages={387-398},\ndoi={10.1002/(SICI)1097-0282(19971005)42:4<387::AID-BIP2>3.0.CO;2-M},\nnote={cited By 5},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0031555008&doi=10.1002%2f%28SICI%291097-0282%2819971005%2942%3a4%3c387%3a%3aAID-BIP2%3e3.0.CO%3b2-M&partnerID=40&md5=d8dc2482ff0d3b70283b099b98a6b89a},\naffiliation={School of Chemistry, University of Sydney, NSW, 2006, Australia; Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom; Department of Biochemistry, University of Sydney, NSW, 2006, Australia; National Research Centre for Environmental Toxicology, Coopers Plains 4108, Australia; School of Chemistry Fl, University of Sydney, NSW, 2006, Australia},\nabstract={The synthesis, solution conformation, and interaction with DNA of three 8-residiie peptides structurally related to the heptad repeat unit found at the C-termimis ofRNA polymerase II are reported. Peptides QQ, XQ, and PQ are derived from the parent sequence YSPTSPSY (peptide YY), which was reported to bind to DNA by bisintercalation [M. Suzuki (1990) Nature, Vol. 344, pp. 562-565], and contain either a 2-qiiinolyl (Q), 2-quinoxolyl (X), or 5phenanthrolyl (P) group in place of the aromatic side chains of the N- and C-tenninal tyrosine residues present in the parent sequence. The combined results of linear dichroism and induced CD measurements of peptides QQ, XQ, and PQ with calf thymus DNA are consistent with weak binding of the peptides to DNA in a preferred orientation in which the chromophores are intercalated. Small increases in the melting temperatures ofpoly[d(A-T)2] are also consistent with the peptides interacting with DNA. While enzymatic footprinting with DNase I showed no protection from cleavage by the enzyme, chemical footprinting with fotemustine showed that the peptides modify the reactivity of the major groove, presumably via minor groove binding. Peptide QQ inhibited fotemustine alkylation significantly more than either XQ or PQ, and slightly more than YY. In aqueous solution, nmr experiments on QQ, XQ, and PQ show a significant population of a conformation in which Ser2-Pro3-Thr4-Ser5 form both type I and type II β-tum conformations in equilibrium with open chain conformations. Nuclear magnetic resonance titration experiments ofPQ with (GCGTACGC)2 showed small changes in chemical shifts, consistent with the formation of a weak nonspecific complex. Analogous experiments, using peptides QQ and XQ with (GCGTACGC)2, and peplide YY with (CGTACG)2, showed no evidence for the interaction of the peptides with these oligonucleotides. These results show that peptides of general structure XSPTSPSZ are weak nonspecific DNA binders that differ significantly from previously characterized S(T)PXX DNA-binding motifs that are generally AT-selective minor groove binders. ©1997 John Wiley &amp; Sons, Inc.},\nauthor_keywords={CD;  DNA chemical footprinting;  Fotemiistine;  Intercalation;  Linear dichroism;  RNA polymerase II;  SPXX peptides;  YSPTSPSY;  β-tum},\nkeywords={Alkylation;  Chemical bonds;  Conformations;  DNA;  Enzymes;  RNA;  Temperature, Chemical footprinting;  Chromopores;  Fotemustine;  Linear dichroism;  Peptide;  Polymerase, Polypeptides, intercalating agent;  rna polymerase ii, article;  dna alkylation;  dna footprinting;  intercalation complex;  nonhuman;  peptide synthesis;  protein dna binding;  protein dna interaction, Amino Acid Sequence;  Base Sequence;  DNA;  Intercalating Agents;  Oligopeptides;  Repetitive Sequences, Nucleic Acid;  RNA Polymerase II, Lateolabrax japonicus},\npublisher={John Wiley and Sons Inc.},\nissn={00063525},\ncoden={BNSSF},\npubmed_id={9283289},\nlanguage={English},\nabbrev_source_title={Biopolym. Nucleic Acid Sci. Sect.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n

\n The synthesis, solution conformation, and interaction with DNA of three 8-residiie peptides structurally related to the heptad repeat unit found at the C-termimis ofRNA polymerase II are reported. Peptides QQ, XQ, and PQ are derived from the parent sequence YSPTSPSY (peptide YY), which was reported to bind to DNA by bisintercalation [M. Suzuki (1990) Nature, Vol. 344, pp. 562-565], and contain either a 2-qiiinolyl (Q), 2-quinoxolyl (X), or 5phenanthrolyl (P) group in place of the aromatic side chains of the N- and C-tenninal tyrosine residues present in the parent sequence. The combined results of linear dichroism and induced CD measurements of peptides QQ, XQ, and PQ with calf thymus DNA are consistent with weak binding of the peptides to DNA in a preferred orientation in which the chromophores are intercalated. Small increases in the melting temperatures ofpoly[d(A-T)2] are also consistent with the peptides interacting with DNA. While enzymatic footprinting with DNase I showed no protection from cleavage by the enzyme, chemical footprinting with fotemustine showed that the peptides modify the reactivity of the major groove, presumably via minor groove binding. Peptide QQ inhibited fotemustine alkylation significantly more than either XQ or PQ, and slightly more than YY. In aqueous solution, nmr experiments on QQ, XQ, and PQ show a significant population of a conformation in which Ser2-Pro3-Thr4-Ser5 form both type I and type II β-tum conformations in equilibrium with open chain conformations. Nuclear magnetic resonance titration experiments ofPQ with (GCGTACGC)2 showed small changes in chemical shifts, consistent with the formation of a weak nonspecific complex. Analogous experiments, using peptides QQ and XQ with (GCGTACGC)2, and peplide YY with (CGTACG)2, showed no evidence for the interaction of the peptides with these oligonucleotides. These results show that peptides of general structure XSPTSPSZ are weak nonspecific DNA binders that differ significantly from previously characterized S(T)PXX DNA-binding motifs that are generally AT-selective minor groove binders. ©1997 John Wiley & Sons, Inc.\n

\n\n\n

\n \n\n \n \n \n \n \n \n The structure of versutoxin (δ-atracotoxin-Hv1) provides insights into the binding of site 3 neurotoxins to the voltage-gated sodium channel.\n \n \n \n \n\n\n \n Fletcher, J.; Chapman, B.; Mackay, J.; Howden, M.; and King, G.\n\n\n \n\n\n\n Structure, 5(11): 1525-1535. 1997.\n cited By 107\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Fletcher19971525,\nauthor={Fletcher, J.I. and Chapman, B.E. and Mackay, J.P. and Howden, M.E.H. and King, G.F.},\ntitle={The structure of versutoxin (δ-atracotoxin-Hv1) provides insights into the binding of site 3 neurotoxins to the voltage-gated sodium channel},\njournal={Structure},\nyear={1997},\nvolume={5},\nnumber={11},\npages={1525-1535},\ndoi={10.1016/S0969-2126(97)00301-8},\nnote={cited By 107},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030727613&doi=10.1016%2fS0969-2126%2897%2900301-8&partnerID=40&md5=d532b9c49f89c80a563f66653a02c062},\naffiliation={Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia; Department of Pharmacology, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Background: Versutoxin (δ-ACTX-Hv1) is the major component of the venom of the Australian Blue Mountains funnel web spider, Hadronyche versuta. δ-ACTX-Hv1 produces potentially fatal neurotoxic symptoms in primates by slowing the inactivation of voltage-gated sodium channels; δ-ACTX-Hv1 is therefore a useful tool for studying sodium channel function. We have determined the three-dimensional structure of δ-ACTX-Hv1 as the first step towards understanding the molecular basis of its interaction with these channels. Results: The solution structure of δ-ACTX-Hv1, determined using NMR spectroscopy, comprises a core β region containing a triple-stranded antiparallel β sheet, a thumb-like extension protruding from the β region and a C-terminal 310 helix that is appended to the β domain by virtue of a disulphide bond. The β region contains a cystine knot motif similar to that seen in other neurotoxic polypeptides. The structure shows homology with μ-agatoxin-I, a spider toxin that also modifies the inactivation kinetics of vertebrate voltage-gated sodium channels. More surprisingly, δ-ACTX-Hv1 shows both sequence and structural homology with gurmarin, a plant polypeptide. This similarity leads us to suggest that the sweet-taste suppression elicited by gurmarin may result from an interaction with one of the downstream ion channels involved in sweet-taste transduction. Conclusions: δ-ACTX-Hv1 shows no structural homology with either sea anemone or α-scorpion toxins, both of which also modify the inactivation kinetics of voltage-gated sodium channels by interacting with channel recognition site 3. However, we have shown that δ-ACTX-Hv1 contains charged residues that are topologically related to those implicated in the binding of sea anemone and α-scorpion toxins to mammalian voltage-gated sodium channels, suggesting similarities in their mode of interaction with these channels.},\nauthor_keywords={Anthopleurin;  Gurmarin;  Sodium channel inactivation;  Versutoxin;  α-scorpion toxin},\ncorrespondence_address1={King, G.F.; Department of Biochemistry, , Sydney, NSW 2006, Australia; email: glenn@biochem.usyd.edu.au},\npublisher={Cell Press},\nissn={09692126},\ncoden={STRUE},\npubmed_id={9384567},\nlanguage={English},\nabbrev_source_title={STRUCTURE},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Zipping up transcription factors: Rational design of anti-Jun and anti-Fos peptides.\n \n \n \n \n\n\n \n Bains, N.; Wilce, J.; Heuer, K.; Tunstall, M.; Mackay, J.; Bennett, M.; Weiss, A.; and King, G.\n\n\n \n\n\n\n Letters in Peptide Science, 4(2): 67-77. 1997.\n cited By 10\n\n\n\n
\n\n\n\n \n \n $\"Zipping$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Bains199767,\nauthor={Bains, N.P.S. and Wilce, J.A. and Heuer, K.H. and Tunstall, M. and Mackay, J.P. and Bennett, M.R. and Weiss, A.S. and King, G.F.},\ntitle={Zipping up transcription factors: Rational design of anti-Jun and anti-Fos peptides},\njournal={Letters in Peptide Science},\nyear={1997},\nvolume={4},\nnumber={2},\npages={67-77},\ndoi={10.1007/BF02443517},\nnote={cited By 10},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0010214023&doi=10.1007%2fBF02443517&partnerID=40&md5=1ddb2573da8c2ef75ec767929c37a36b},\naffiliation={Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia; Institute for Biomedical Research, Department of Physiology, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Various members of the bZip and bHLH-Zip families of eukaryotic transcription factors, including Jun, Fos, and Myc, have been identified as oncoproteins; mutation or deregulated expression of these proteins leads to certain types of cancer. These proteins can only bind to their cognate DNA enhancer sites following homodimerization, or heterodimerization with another family member, via their leucine zipper domain. Thus, a novel anticancer strategy would be to inhibit dimerization of these proteins, thereby blocking their DNA binding and transactivation functions. In this paper we show that it is possible to rationally design leucine zipper peptides that bind with high affinity to the leucine zipper dimerization domains of c-Jun and c-Fos, thus preventing the formation of functional c-Jun homodimers and c-Jun:c-Fos heterodimers; we refer to such peptides as superzippers (SZs). In vivo, c-Jun:SZ and c-Fos:SZ heterodimers should be nonfunctional as they lack one of the two basic domains that are essential for DNA binding. While the transport of a peptidic agent into cells often poses a severe obstacle to its therapeutic use, we show that a 46-residue leucine zipper peptide can be transported into HeLa cells by coupling it to a 17-residue carrier peptide from the Antennapedia homeodomain, thus paving the way for detailed studies of the therapeutic potential of superzipper peptides.},\nauthor_keywords={Anticancer drugs;  Fos;  Jun;  Leucine zipper;  Peptide delivery;  Peptide drug;  Transcription factors},\ncorrespondence_address1={King, G.F.; Department of Biochemistry, , Sydney, NSW 2006, Australia},\npublisher={Springer Netherlands},\nissn={09295666},\ncoden={LPSCE},\nlanguage={English},\nabbrev_source_title={Lett. Pept. Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Measuring macromolecular diffusion using heteronuclear multiple-quantum pulsed-field-gradient NMR.\n \n \n \n \n\n\n \n Dingley, A.; Mackay, J.; Shaw, G.; Hambly, B.; and King, G.\n\n\n \n\n\n\n Journal of Biomolecular NMR, 10(1): 1-8. 1997.\n cited By 26\n\n\n\n
\n\n\n\n \n \n $\"Measuring$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Dingley19971,\nauthor={Dingley, A.J. and Mackay, J.P. and Shaw, G.L. and Hambly, B.D. and King, G.F.},\ntitle={Measuring macromolecular diffusion using heteronuclear multiple-quantum pulsed-field-gradient NMR},\njournal={Journal of Biomolecular NMR},\nyear={1997},\nvolume={10},\nnumber={1},\npages={1-8},\ndoi={10.1023/A:1018339526108},\nnote={cited By 26},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0005088423&doi=10.1023%2fA%3a1018339526108&partnerID=40&md5=a1431cbf67286cef120ee816000751d1},\naffiliation={Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia; Department of Pathology, University of Sydney, Sydney, NSW 2006, Australia; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom},\nabstract={We have previously shown that 1H pulsed-field-gradient (PFG) NMR spectroscopy provides a facile method for monitoring protein self-association and can be used, albeit with some caveats, to measure the apparent molecular mass of the diffusant [Dingley et al. (1995) J. Biomol. NMR, 6, 321-328]. In this paper we show that, for 15N-labelled proteins, selection of 1H-15N multiple-quantum (MQ) coherences in PFG diffusion experiments provides several advantages over monitoring 1H single-quantum (SQ) magnetization. First, the use of a gradient-selected MQ filter provides a convenient means of suppressing resonances from both the solvent and unlabelled solutes. Second, 1H-15N zero-quantum coherence dephases more rapidly than 1H SQ coherence under the influence of a PFG This allows the diffusion coefficients of larger proteins to be measured more readily. Alternatively, the gradient length and/or the diffusion delay may be decreased, thereby reducing signal losses from relaxation. In order to extend the size of macromolecules to which these experiments can be applied, we have developed a new MQ PFG diffusion experiment in which the magnetization is stored as longitudinal two-spin order for most of the diffusion period, thus minimizing sensitivity losses due to transverse relaxation and J-coupling evolution.},\nauthor_keywords={Macromolecules;  Pulsed-field-gradient NMR;  Self-association;  Solvent suppression;  Translational diffusion coefficient},\ncorrespondence_address1={King, G.F.; Department of Biochemistry, , Sydney, NSW 2006, Australia},\npublisher={Springer Netherlands},\nissn={09252738},\ncoden={JBNME},\nlanguage={English},\nabbrev_source_title={J. Biomol. NMR},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Δ-cis-α-[Ru(RR-picchxnMe2)(phen)]2+ shows minor groove AT selectivity with oligonucleotides.\n \n \n \n \n\n\n \n Proudfoot, E.; Mackay, J.; Vagg, R.; Vickery, K.; Williams, P.; and Karuso, P.\n\n\n \n\n\n\n Chemical Communications, (17): 1623-1624. 1997.\n cited By 19\n\n\n\n
\n\n\n\n \n \n $\"Δ-cis-α-[Ru(RR-picchxnMe2)(phen)]2+$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Proudfoot19971623,\nauthor={Proudfoot, E.M. and Mackay, J.P. and Vagg, R.S. and Vickery, K.A. and Williams, P.A. and Karuso, P.},\ntitle={Δ-cis-α-[Ru(RR-picchxnMe2)(phen)]2+ shows minor groove AT selectivity with oligonucleotides},\njournal={Chemical Communications},\nyear={1997},\nnumber={17},\npages={1623-1624},\ndoi={10.1039/a704001f},\nnote={cited By 19},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0002537121&doi=10.1039%2fa704001f&partnerID=40&md5=4894ac67a468d94d9466a2e4f7d68a13},\naffiliation={School of Chemistry, Macquarie University, NSW, 2109, Australia; School of Biochemistry, University of Sydney, NSW, 2006, Australia; Department of Chemistry, University of Western Sydney, Nepean, NSW 2747, Australia},\nabstract={NMR studies show that the ternary octahedral Δ-cis-α-[Ru(RR-picchxnMe2)(phen)]2+ cation binds with AT selectivity in the minor groove of [d(CGCGATCGCG)2] and [d(ATATCGATAT)2] duplexes through a non-intercalative interaction.},\npublisher={Royal Society of Chemistry},\nissn={13597345},\ncoden={CHCOF},\nlanguage={English},\nabbrev_source_title={Chem. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 1996\n \n \n (3)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Development of a sensitive peptide-based immunoassay: Application to detection of the Jun and Fos oncoproteins.\n \n \n \n \n\n\n \n Heuer, K.; Mackay, J.; Podzebenko, P.; Bains, N.; Weiss, A.; King, G.; and Easterbrook-Smith, S.\n\n\n \n\n\n\n Biochemistry, 35(28): 9069-9075. 1996.\n cited By 33\n\n\n\n
\n\n\n\n \n \n $\"Development$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Heuer19969069,\nauthor={Heuer, K.H. and Mackay, J.P. and Podzebenko, P. and Bains, N.P.S. and Weiss, A.S. and King, G.F. and Easterbrook-Smith, S.B.},\ntitle={Development of a sensitive peptide-based immunoassay: Application to detection of the Jun and Fos oncoproteins},\njournal={Biochemistry},\nyear={1996},\nvolume={35},\nnumber={28},\npages={9069-9075},\ndoi={10.1021/bi952817o},\nnote={cited By 33},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030006796&doi=10.1021%2fbi952817o&partnerID=40&md5=4cf4063090b74534625e27e6076425ba},\naffiliation={Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={c-Jun and c-Fos belong to the bZIP class of transcriptional activator proteins, many of which have been implicated in the neoplastic transformation of cells. We are interested in engineering dominant-negative leucine zipper (LZ) peptides as a means of sequestering these proteins in vivo in order to suppress their transcriptional regulatory activity. Toward this end, we have developed a novel immunoassay for measuring the dimerization affinities of dimeric Jun and Fos complexes. This peptide-based ELISA relies on the fact that Jun and Fos preferentially form heterodimers via their leucine zipper domains. Recombinant Jun leucine zipper peptides (either native JunLZ or a V36→E point mutant) were labeled with biotin and specifically bound through a leucine zipper interaction to a FosLZ-glutathione S-transferase fusion protein adsorbed onto the wells of an ELISA tray. Jun:Fos complexes were subsequently detected using a recently developed streptavidin-based amplification system known as enzyme complex amplification [Wilson, M. R., and Easterbrook-Smith, S. B. (1993) Anal. Biochem. 209, 183-187]. This ELISA system can detect subnanomolar concentrations of Jun and Fos, thus allowing determination of the dissociation constants for complex formation. The dissociation constant for formation of the native JunLZ:FosLZ heterodimer at 37 °C was determined to be 0.99 ± 0.30 nM, while that for JunLZ(V36E):FosLZ heterodimer was 0.90 ± 0.13 μM. These results demonstrate that the novel peptide-based ELISA described herein is simple and sensitive and can be used to rapidly screen for potential dominant-negative leucine zipper peptides.},\nkeywords={leucine zipper protein;  oncoprotein, article;  cancer;  carcinogenesis;  immunoassay;  nonhuman;  oncogene c fos;  oncogene c jun;  priority journal;  protein dna interaction;  transcription initiation;  transcription regulation, Amino Acid Sequence;  Biotin;  Electrophoresis, Polyacrylamide Gel;  Enzyme-Linked Immunosorbent Assay;  Escherichia coli;  Glutathione Transferase;  Leucine Zippers;  Molecular Sequence Data;  Oncogene Protein p65(gag-jun);  Oncogene Proteins v-fos;  Peptides;  Protein Conformation;  Recombinant Fusion Proteins;  Sensitivity and Specificity},\ncorrespondence_address1={King, G.F.; Department of Biochemistry, , Sydney, NSW 2006, Australia},\nissn={00062960},\ncoden={BICHA},\npubmed_id={8703910},\nlanguage={English},\nabbrev_source_title={BIOCHEMISTRY},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Backbone dynamics of the c-Jun leucine zipper: 15N NMR relaxation studies.\n \n \n \n \n\n\n \n Mackay, J.; Shaw, G.; and King, G.\n\n\n \n\n\n\n Biochemistry, 35(15): 4867-4877. 1996.\n cited By 49\n\n\n\n
\n\n\n\n \n \n $\"Backbone$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mackay19964867,\nauthor={Mackay, J.P. and Shaw, G.L. and King, G.F.},\ntitle={Backbone dynamics of the c-Jun leucine zipper: 15N NMR relaxation studies},\njournal={Biochemistry},\nyear={1996},\nvolume={35},\nnumber={15},\npages={4867-4877},\ndoi={10.1021/bi952761y},\nnote={cited By 49},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029868591&doi=10.1021%2fbi952761y&partnerID=40&md5=8894f7738e20b0732e06e268d18507b9},\naffiliation={Department of Biochemistry, University of Sydney, Sydney, NSW 2006, Australia; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom},\nabstract={The backbone dynamics of the coiled-coil leucine zipper domain of c-Jun have been studied using proton-detected two-dimensional 1H-15N NMR spectroscopy. Longitudinal (T1) and transverse (T2) 15N relaxation times, together with {1H}15N NOEs, were measured and analyzed by considering the protein to approximate a prolate ellipsoid. An analysis of the T1/T2 ratios for residues in the well-structured section of the protein showed that a model for the spectral density function in which the protein is considered to reorient anisotropically fitted the data significantly better than an isotropic model. Order parameters (S2) in the range 0.7-0.9 were observed for most residues, with lower values near the C-terminus, consistent with fraying of the two helices comprising the coiled-coil. Because nearly all of the N-H vectors have small angles to the long axis of the molecule, there was some uncertainty in the value of the rotational diffusion coefficient Dpar, which describes rotation about the long axis. Thus, an alternative method was examined for its ability to provide independent estimates of Dpar and Dperp (the diffusion coefficient describing rotation about axes perpendicular to the long axis); the translational diffusion coefficient (Dt) of the protein was measured, and hydrodynamic calculations were used to predict Dpar and Dperp. However, the derived rotational diffusion coefficients proved to be very dependent on the hydrodynamic model used to relate Dt to Dpar and Dperp, and consequently the values obtained from the T1/T2 analysis were used in the order-parameter analysis. Although it has previously been reported that the side chain of a polar residue at the dimer interface, Asn22, undergoes a conformational exchange process and destabilizes the dimer, no evidence of increased backbone mobility in this region was detected, suggesting that this process is confined to the Asn side chain.},\nkeywords={leucine zipper protein;  oncoprotein, anisotropy;  article;  conformational transition;  diffusion coefficient;  human;  human cell;  hydrodynamics;  mathematical model;  nuclear magnetic resonance spectroscopy;  priority journal;  protein domain;  protein structure;  structure analysis, Amino Acid Sequence;  Leucine Zippers;  Magnetic Resonance Spectroscopy;  Models, Chemical;  Molecular Sequence Data;  Proto-Oncogene Proteins c-jun;  Recombinant Proteins},\ncorrespondence_address1={Mackay, J.P.; Department of Biochemistry, , Sydney, NSW 2006, Australia},\npublisher={American Chemical Society},\nissn={00062960},\ncoden={BICHA},\npubmed_id={8664278},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Assignment of the 1H NMR spectrum and solution conformation of the antitumour antibiotic ditrisarubicin B.\n \n \n \n \n\n\n \n Mackay, J.; Shelton, C.; and Harding, M.\n\n\n \n\n\n\n Tetrahedron, 52(15): 5617-5624. 1996.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Assignment$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mackay19965617,\nauthor={Mackay, J.P. and Shelton, C.J. and Harding, M.M.},\ntitle={Assignment of the 1H NMR spectrum and solution conformation of the antitumour antibiotic ditrisarubicin B},\njournal={Tetrahedron},\nyear={1996},\nvolume={52},\nnumber={15},\npages={5617-5624},\ndoi={10.1016/0040-4020(96)00198-6},\nnote={cited By 1},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029935539&doi=10.1016%2f0040-4020%2896%2900198-6&partnerID=40&md5=e8b280584ff988d4227b448c4ba45079},\naffiliation={School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Complete assignment of the 1H NMR spectrum of ditrisarubicin B, a member of the anthracycline antitumour antibiotics, in acetonitrile is reported. The two trisaccharide chains are highly structured and their conformation supports their role as preorganised DNA minor groove binders which bind to DNA on intercalation of the tetracyclic chromophore.},\nkeywords={antineoplastic antibiotic;  ditrisarubicin B, article;  drug structure;  nuclear magnetic resonance;  priority journal},\ncorrespondence_address1={Harding, M.M.; School of Chemistry, , Sydney, NSW 2006, Australia},\npublisher={Elsevier Ltd},\nissn={00404020},\ncoden={TETRA},\nlanguage={English},\nabbrev_source_title={TETRAHEDRON},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 1995\n \n \n (1)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Measuring protein self-association using pulsed-field-gradient NMR spectroscopy: Application to myosin light chain 2.\n \n \n \n \n\n\n \n Dingley, A.; Mackay, J.; Chapman, B.; Morris, M.; Kuchel, P.; Hambly, B.; and King, G.\n\n\n \n\n\n\n Journal of Biomolecular NMR, 6(3): 321-328. 1995.\n cited By 121\n\n\n\n
\n\n\n\n \n \n $\"Measuring$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Dingley1995321,\nauthor={Dingley, A.J. and Mackay, J.P. and Chapman, B.E. and Morris, M.B. and Kuchel, P.W. and Hambly, B.D. and King, G.F.},\ntitle={Measuring protein self-association using pulsed-field-gradient NMR spectroscopy: Application to myosin light chain 2},\njournal={Journal of Biomolecular NMR},\nyear={1995},\nvolume={6},\nnumber={3},\npages={321-328},\ndoi={10.1007/BF00197813},\nnote={cited By 121},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029400890&doi=10.1007%2fBF00197813&partnerID=40&md5=729a76e73c3ea495bbfb0f114379dda4},\naffiliation={Department of Biochemistry, University of Sydney, Sydney, 2006, New South Wales, Australia; Department of Pathology, University of Sydney, Sydney, 2006, New South Wales, Australia},\nabstract={At the millimolar concentrations required for structural studies, NMR spectra of the calcium-binding protein myosin light chain 2 (MLC2) showed resonance line widths indicative of extensive self-association. Pulsed-field-gradient (PFG) NMR spectroscopy was used to examine whether MLC2 aggregation could be prevented by the zwitterionic bile salt derivative 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS). PFG NMR measurements indicated that CHAPS was capable of preventing MLC2 self-association, but only at concentrations well above the critical micelle concentration of ∼7.5 mM. CHAPS was most effective at a concentration of 22.5 mM, where the apparent molecular mass of MLC2 correponded to a protein monomer plus seven molecules of bound detergent. The resolution and sensitivity of 2D 15N-1H HSQC spectra of MLC2 were markedly improved by the addition of 25 mM CHAPS, consistent with a reduction in aggregation following addition of the detergent. The average amide nitrogen T2 value for MLC2 increased from ∼30 ms in the absence of CHAPS to ∼56 ms in the presence of 25 mM CHAPS. The results of this study lead us to propose that PFG NMR spectroscopy can be used as a facile alternative to conventional techniques such as analytical ultracentrifugation for examining the self-association of biological macromolecules. © 1995 ESCOM Science Publishers B.V.},\nauthor_keywords={CHAPS;  Myosin light chain;  Pulsed-field-gradient NMR;  Self-association;  Translational diffusion coefficient},\nkeywords={3 ((3 cholamidopropyl)dimethylammonium) 1 propanesulfonate;  3-((3-cholamidopropyl)dimethylammonium)-1-propanesulfonate;  cholic acid derivative;  myosin light chain, animal;  article;  chemistry;  chicken;  nuclear magnetic resonance spectroscopy;  protein binding;  protein conformation;  theoretical model, Animals;  Chickens;  Cholic Acids;  Magnetic Resonance Spectroscopy;  Models, Theoretical;  Myosin Light Chains;  Protein Binding;  Protein Conformation},\ncorrespondence_address1={King, G.F.; Department of Biochemistry, , Sydney, 2006, New South Wales, Australia},\npublisher={ESCOM Science Publishers B.V., Leiden/Kluwer Academic Publishers},\nissn={09252738},\ncoden={JBNME},\npubmed_id={8520223},\nlanguage={English},\nabbrev_source_title={J Biomol NMR},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 1994\n \n \n (4)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Dissection of the Contributions toward Dimerization of Glycopeptide Antibiotics.\n \n \n \n \n\n\n \n Mackay, J.; Gerhard, U.; Beauregard, D.; Maplestone, R.; and Williams, D.\n\n\n \n\n\n\n Journal of the American Chemical Society, 116(11): 4573-4580. 1994.\n cited By 137\n\n\n\n
\n\n\n\n \n \n $\"Dissection$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mackay19944573,\nauthor={Mackay, J.P. and Gerhard, U. and Beauregard, D.A. and Maplestone, R.A. and Williams, D.H.},\ntitle={Dissection of the Contributions toward Dimerization of Glycopeptide Antibiotics},\njournal={Journal of the American Chemical Society},\nyear={1994},\nvolume={116},\nnumber={11},\npages={4573-4580},\ndoi={10.1021/ja00090a005},\nnote={cited By 137},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0028023298&doi=10.1021%2fja00090a005&partnerID=40&md5=21c62410fdf721b13cc0704b8c2d4061},\naffiliation={Cambridge Centre for Molecular Recognition, University Chemical Laboratory, Lensfield Road, Cambridge CB2 IEW, United Kingdom},\nabstract={A procedure for the determination of association constants in aqueous solution using hydrogen-deuterium exchange has been developed and used to measure the dimerization constant, Kam, for a number of strongly dimerizing glycopeptide antibiotics. These values provide further insight into the thermodynamic contributions of various structural epitopes to the dimerization of these antibiotics. Consideration of ligand binding affinities together with dimerization potentials provides evidence that dimerization is implicated in the physiological mode of action of these antibiotics. © 1994, American Chemical Society. All rights reserved.},\nkeywords={aglycovancomycin;  antibiotic agent;  chloroorienticin a;  eremomycin;  glycopeptide;  unclassified drug;  vancomycin, article;  chemical structure;  dimerization;  nuclear magnetic resonance;  thermodynamics;  ultraviolet spectrophotometry},\nissn={00027863},\nlanguage={English},\nabbrev_source_title={J. Am. Chem. Soc.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Glycopeptide Antibiotic Activity and the Possible Role of Dimerization: A Model for Biological Signaling.\n \n \n \n \n\n\n \n Mackay, J.; Gerhard, U.; Beauregard, D.; Westwell, M.; Searle, M.; and Williams, D.\n\n\n \n\n\n\n Journal of the American Chemical Society, 116(11): 4581-4590. 1994.\n cited By 202\n\n\n\n
\n\n\n\n \n \n $\"Glycopeptide$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Mackay19944581,\nauthor={Mackay, J.P. and Gerhard, U. and Beauregard, D.A. and Westwell, M.S. and Searle, M.S. and Williams, D.H.},\ntitle={Glycopeptide Antibiotic Activity and the Possible Role of Dimerization: A Model for Biological Signaling},\njournal={Journal of the American Chemical Society},\nyear={1994},\nvolume={116},\nnumber={11},\npages={4581-4590},\ndoi={10.1021/ja00090a006},\nnote={cited By 202},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0027936628&doi=10.1021%2fja00090a006&partnerID=40&md5=caad2ce913a84b32cf50aa7e3a16e2a0},\naffiliation={Cambridge Centre for Molecular Recognition, University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom},\nabstract={It is demonstrated that the presence of bacterial cell wall analogues may either enhance or, in the case of ristocetin A, oppose dimerization of glycopeptide antibiotics. These observations may imply that dimerization plays a role in the mode of action of these antibiotics, and a mechanism is proposed to take account of this possibility. The glycopeptide dimers are also found to be formed more exothermically in the presence of cell wall analogues, and the nature of biological signaling events is discussed in this context. It is pointed out that binding enthalpy (rather than simply binding free energy, ΔG) may be an important quantity in signaling events. If this is so, then oligomers may be abundant in signaling processes partly because the extended aggregates they form are able to cooperatively amplify the conformational changes which are incurred on ligand binding, which occur through relatively small changes in free energy but larger opposing changes in enthalpy and entropy. © 1994, American Chemical Society. All rights reserved.},\nkeywords={aglycovancomycin;  antibiotic agent;  chloroorienticin a;  eremomycin;  glycopeptide;  ristocetin a;  teicoplanin;  unclassified drug;  vancomycin, antimicrobial activity;  article;  bacterial membrane;  chemical structure;  dimerization;  ligand binding;  nuclear magnetic resonance;  ultraviolet spectrophotometry},\ncorrespondence_address1={Williams, D.H.; Cambridge Centre for Molecular Recognition, Lensfield Road, Cambridge CB2 1EW, United Kingdom},\nissn={00027863},\nlanguage={English},\nabbrev_source_title={J. Am. Chem. Soc.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Functional roles of natural products: The involvement of extended arrays of weak interactions in cooperative binding phenomena.\n \n \n \n \n\n\n \n Williams, D.; Searle, M.; Groves, P.; Mackay, J.; Westwell, M.; Beauregard, D.; and Cristofaro, M.\n\n\n \n\n\n\n Pure and Applied Chemistry, 66(10-11): 1975-1982. 1994.\n cited By 5\n\n\n\n
\n\n\n\n \n \n $\"Functional$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Williams19941975,\nauthor={Williams, D.H. and Searle, M.S. and Groves, P. and Mackay, J.P. and Westwell, M.S. and Beauregard, D.A. and Cristofaro, M.F.},\ntitle={Functional roles of natural products: The involvement of extended arrays of weak interactions in cooperative binding phenomena},\njournal={Pure and Applied Chemistry},\nyear={1994},\nvolume={66},\nnumber={10-11},\npages={1975-1982},\ndoi={10.1351/pac199466101975},\nnote={cited By 5},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-2142814913&doi=10.1351%2fpac199466101975&partnerID=40&md5=35ac3eff8517f2d2208deef8611b8cdf},\naffiliation={Cambridge Centre for Molecular Recognition, University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom},\nabstract={A factorisation of the free energy of binding into various “costs” and “benefits” has provided the basis for a semi-quantitation of some weak interactions in solution. It has become clear that the entropie cost of motional restriction on binding (A + B → A.B) increases with increasing exothermicity of the association; this exothermicity must of course reflect not only interactions at the interface between A and B, but also the change in bonding throughout B (if B represents the receptor). We illustrate cooperativity and anti-cooperativity by reference to effects of ligand binding (as models of classical agonists and antagonists) on the dimerisation of vancomycin-group antibiotics. Since dimerization of receptors (promoted by ligand binding) is a common theme in biological signalling, it must presumably have an advantage in natural selection. We suggest that concurrent demands of ligand binding and receptor dimerization may permit a more specific control of those ligand structures which can cause signal transmission. In this way, specificity in biological signalling might be aided. © 1994 IUPAC},\nissn={00334545},\nlanguage={English},\nabbrev_source_title={Pure Appl. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The structure of an asymmetric dimer relevant to the mode of action of the glycopeptide antibiotics.\n \n \n \n \n\n\n \n Groves, P.; Searle, M.; Mackay, J.; and Williams, D.\n\n\n \n\n\n\n Structure, 2(8): 747-754. 1994.\n cited By 74\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Groves1994747,\nauthor={Groves, P. and Searle, M.S. and Mackay, J.P. and Williams, D.H.},\ntitle={The structure of an asymmetric dimer relevant to the mode of action of the glycopeptide antibiotics},\njournal={Structure},\nyear={1994},\nvolume={2},\nnumber={8},\npages={747-754},\ndoi={10.1016/S0969-2126(94)00075-1},\nnote={cited By 74},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0028774039&doi=10.1016%2fS0969-2126%2894%2900075-1&partnerID=40&md5=513f5b7ccd62da122f132e212ddf0487},\naffiliation={Cambridge for Molecular Recognition, University Chemical Laboratories, Lensfield Road, Cambridge, CB2 1EW, United Kingdom},\nabstract={Background Glycopeptide antibiotics of the vancomycin group are of crucial clinical importance in the treatment of methicillin resistant Staphylococcus aureus (MRSA) - the often lethal 'super-bug ' - characterized by its resistance to a wide range of antibiotics in common use. The antibiotics exert their physiological action by blocking cell wall synthesis through recognition of nascent cell wall mucopeptides terminating in the sequence -D-Ala-D -Ala. Evidence suggests that the antibiotics are able to enhance their biological activity by the formation of homodimers, and this is supported by the observation that dimerization and peptide binding in vitro are cooperative phenomena. The basis of this enhancement is not understood at the molecular level. Results The first detailed structure of a dimeric glycopeptide antibiotic, that of eremomycin, is presented based upon solution NMR data. The overall structure of the dimer complex is asymmetric. The source of this asymmetry - a parallel alignment and mutual interaction of the disaccharides - appears to promote dimerization through specific sugar- sugar recognition. Conclusions A molecular basis for the observed cooperativity of cell wall peptide binding by eremomycin is evident from these studies of the dimer. The carboxylate anion of the cell wall component, which is crucial to binding, forms an amide-mediated ion-pair interaction to the alkylammonium ion of the ring 6 sugar in the other half of the dimer making the structure and positioning of this sugar important in mediating cooperativity. © 1994 Elsevier Science Ltd. All rights reserved.},\nauthor_keywords={asymetric dimer;  cooperatively;  glycopeptide antibiotics;  NMR structure},\nkeywords={disaccharide;  eremomycin;  N(2) acetyllysyl alanyl alanine;  N(2)-acetyllysyl-alanyl-alanine;  oligopeptide;  polypeptide antibiotic agent;  vancomycin, amino acid sequence;  article;  binding site;  cell wall;  chemical structure;  chemistry;  computer simulation;  hydrogen bond;  metabolism;  molecular genetics;  nuclear magnetic resonance spectroscopy;  protein binding;  protein conformation, Amino Acid Sequence;  Antibiotics, Glycopeptide;  Binding Sites;  Cell Wall;  Computer Simulation;  Disaccharides;  Hydrogen Bonding;  Magnetic Resonance Spectroscopy;  Models, Molecular;  Molecular Sequence Data;  Oligopeptides;  Protein Binding;  Protein Conformation;  Support, Non-U.S. Gov't;  Vancomycin},\ncorrespondence_address1={Groves, P.; Cambridge for Molecular Recognition, University Chemical Laboratories, Lensfield Road, Cambridge, CB2 1EW, United Kingdom},\nissn={09692126},\ncoden={STRUE},\npubmed_id={7994574},\nlanguage={English},\nabbrev_source_title={Structure},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 1993\n \n \n (2)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Toward an estimation of binding constants in aqueous solution: Studies of associations of vancomycin group antibiotics.\n \n \n \n \n\n\n \n Williams, D.; Searle, M.; Mackay, J.; Gerhard, U.; and Maplestone, R.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 90(4): 1172-1178. 1993.\n cited By 167\n\n\n\n
\n\n\n\n \n \n $\"Toward$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Williams19931172,\nauthor={Williams, D.H. and Searle, M.S. and Mackay, J.P. and Gerhard, U. and Maplestone, R.A.},\ntitle={Toward an estimation of binding constants in aqueous solution: Studies of associations of vancomycin group antibiotics},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={1993},\nvolume={90},\nnumber={4},\npages={1172-1178},\ndoi={10.1073/pnas.90.4.1172},\nnote={cited By 167},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0027475726&doi=10.1073%2fpnas.90.4.1172&partnerID=40&md5=82f4bb681a9d1574d7980337e66c6485},\naffiliation={University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom},\nabstract={An approach toward the estimation of binding constants for organic molecules in aqueous solution is presented, based upon a partitioning of the free energy of binding. Consideration is given to polar and hydrophobic contributions and to the entropic cost of rotor restrictions and bimolecular associations. Several parameters (derived from an analysis of entropy changes upon the melting of crystals and from the binding of cell wall peptide analogues to the antibiotic ristocetin A) which may be useful guides to a crude understanding of binding phenomena are presented: (i) amide-amide hydrogen bond strengths of -(1 to 7) ± 2 kJ·mol-1, (ii) a hydrophobic effect of -0.2 ± 0.05 kJ·mol-1·Å-2 of hydrocarbon removed from exposure to water in the binding process, and (iii) free energy costs for rotor restrictions of 3.5-5.0 kJ·mol-1. The validity of the parameters for hydrogen bond strengths is dependent on the validity of the other two parameters. The phenomenon of entropy/enthalpy compensation is considered, with the conclusion that enthalpic barriers to dissociations will result in larger losses in translational and rotational entropy in the association step. The dimerization of some vancomycin group antibiotics is strongly exothermic (-36 to -51 kJ·mol-1) and is promoted by a factor of 50-100 by a disaccharide attached to ring 4 (in vancomycin and eremomycin) and by a factor of ca. 1000 by an amino-sugar attached to the benzylic position of ring 6 in eremomycin. The dimerization process (which, as required for an exothermic association, appears to be costly in entropy) may be relevant to the mode of action of the antibiotics.},\nauthor_keywords={Amide-amide hydrogen bond strengths;  Enthalpic barriers;  Enthalpy;  Entropy compensation;  Hydrophobic effect;  Rotor restrictions},\nkeywords={ristocetin;  vancomycin derivative, aqueous solution;  binding affinity;  conference paper;  dimerization;  enthalpy;  entropy;  hydrogen bond;  hydrophobicity;  molecular interaction;  priority journal;  protein binding, Antibiotics, Glycopeptide;  Calorimetry;  Comparative Study;  Dipeptides;  Hydrogen Bonding;  Protein Binding;  Protein Conformation;  Ristocetin;  Solutions;  Support, Non-U.S. Gov't;  Thermodynamics;  Vancomycin},\ncorrespondence_address1={Williams, D.H.; University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom},\npublisher={National Academy of Sciences},\nissn={00278424},\ncoden={PNASA},\npubmed_id={8433979},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The Role of the Sugar and Chlorine Substituents in the Dimerization of Vancomycin Antibiotics.\n \n \n \n \n\n\n \n Gerhard, U.; Mackay, J.; Maplestone, R.; and Williams, D.\n\n\n \n\n\n\n Journal of the American Chemical Society, 115(1): 232-237. 1993.\n cited By 177\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 3 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n

\n

@ARTICLE{Gerhard1993232,\nauthor={Gerhard, U. and Mackay, J.P. and Maplestone, R.A. and Williams, D.H.},\ntitle={The Role of the Sugar and Chlorine Substituents in the Dimerization of Vancomycin Antibiotics},\njournal={Journal of the American Chemical Society},\nyear={1993},\nvolume={115},\nnumber={1},\npages={232-237},\ndoi={10.1021/ja00054a033},\nnote={cited By 177},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0027401261&doi=10.1021%2fja00054a033&partnerID=40&md5=32aec92bf4343774de576e56b0c011b0},\naffiliation={Cambridge Centre for Molecular Recognition, University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom},\nabstract={Evidence is presented for the formation of dimers in aqueous solutions of the glycopeptide antibiotics eremomycin, A82846B, vancomycin, and eremomycin-ψ. The dimerization constant Kdim is determined by 1H NMR spectroscopy for the last two compounds and also for the related compound ristocetin-ψ, for which dimerization has previously been reported in mixed solvents. Values of Kdim are obtained for these compounds over a range of temperatures, and thus ΔHdim and ΔSdim are calculated. In addition, a lower limit for Kdim in the case of eremomycin is calculated (105 M−1). This is a remarkably large value, and it may be that dimerization is implicated in antibiotic action. The possibility that natural selection has led to adaptations which promote dimerization (such as the nature and sites of attachment of the sugars and a ring 2 chlorine atom) is discussed. © 1993, American Chemical Society. All rights reserved.},\nkeywords={antibiotic a82846b;  eremomycin;  ristocetin;  unclassified drug;  vancomycin;  vancomycin derivative, article;  dimerization;  drug structure;  nuclear magnetic resonance},\ncorrespondence_address1={Williams, D.H.; Cambridge Centre for Molecular Recognition, Lensfield Road, Cambridge CB2 1EW, United Kingdom},\nissn={00027863},\nlanguage={English},\nabbrev_source_title={J. Am. Chem. Soc.},\ndocument_type={Article},\nsource={Scopus},\n}\n

\n

\n\n\n\n\n\n

\n

\n \n undefined\n \n \n (3)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n .\n \n \n \n\n\n \n \n\n\n \n\n\n\n . .\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 9 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n .\n \n \n \n\n\n \n \n\n\n \n\n\n\n . .\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 9 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n .\n \n \n \n\n\n \n \n\n\n \n\n\n\n . .\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 9 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

\n\n\n\n

\n\n\n\n\n\n

\n