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\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

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@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

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\n \n\n \n \n \n \n \n \n Genetic and structural basis of the human anti-α-galactosyl antibody response.\n \n \n \n \n\n\n \n Langley, D.; Schofield, P.; Nevoltris, D.; Jackson, J.; Jackson, K.; Peters, T.; Burk, M.; Matthews, J.; Basten, A.; Goodnow, C.; van Nunen, S.; Reed, J.; and Christ, D.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 119(28). 2022.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Genetic$ 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

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@ARTICLE{Langley2022,\nauthor={Langley, D.B. and Schofield, P. and Nevoltris, D. and Jackson, J. and Jackson, K.J.L. and Peters, T.J. and Burk, M. and Matthews, J.M. and Basten, A. and Goodnow, C.C. and van Nunen, S. and Reed, J.H. and Christ, D.},\ntitle={Genetic and structural basis of the human anti-α-galactosyl antibody response},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2022},\nvolume={119},\nnumber={28},\ndoi={10.1073/pnas.2123212119},\nart_number={e2123212119},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85133878764&doi=10.1073%2fpnas.2123212119&partnerID=40&md5=6a6b2ec125eea5018f2a29d473743c43},\naffiliation={Garvan Institute of Medical Research, Darlinghurst, NSW  2010, Australia; Tick-induced Allergies Research and Awareness Centre, Sydney, NSW  2065, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW  2006, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW  2010, Australia; School of Medical Sciences, University of New South Wales, Sydney, NSW  2052, Australia; Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW  2052, Australia; Northern Clinical School, Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW  2065, Australia},\nabstract={Humans lack the capacity to produce the Galα1-3Galβ1-4GlcNAc (α-gal) glycan, and produce anti-α-gal antibodies upon exposure to the carbohydrate on a diverse set of immunogens, including commensal gut bacteria, malaria parasites, cetuximab, and tick proteins. Here we use X-ray crystallographic analysis of antibodies from α-gal knockout mice and humans in complex with the glycan to reveal a common binding motif, centered on a germline-encoded tryptophan residue at Kabat position 33 (W33) of the complementarity-determining region of the variable heavy chain (CDRH1). Immunoglobulin sequencing of anti-α-gal B cells in healthy humans and tick-induced mammalian meat anaphylaxis patients revealed preferential use of heavy chain germline IGHV3-7, encoding W33, among an otherwise highly polyclonal antibody response. Antigen binding was critically dependent on the presence of the germline-encoded W33 residue for all of the analyzed antibodies; moreover, introduction of the W33 motif into naive IGHV3-23 antibody phage libraries enabled the rapid selection of α-gal binders. Our results outline structural and genetic factors that shape the human anti-α-galactosyl antibody response, and provide a framework for future therapeutics development. Copyright © 2022 the Author(s).},\nauthor_keywords={alpha-galactose;  antibody;  germline restriction;  mammalian meat allergy},\nkeywords={alpha galactosyl antibody;  antibody;  galactose;  glycan;  immunoglobulin;  immunoglobulin antibody;  immunoglobulin heavy chain;  polyclonal antibody;  tryptophan;  unclassified drug, antibody library;  antibody response;  antibody structure;  antigen binding;  Article;  B lymphocyte;  bacteriophage;  clinical article;  cohort analysis;  controlled study;  germ line;  heredity;  human;  human cell;  human genetics;  knockout mouse;  protein binding;  protein motif;  red meat allergy;  structure analysis;  tick bite;  X ray crystallography;  anaphylaxis;  animal;  antibody production;  mammal;  meat;  mouse;  tick, Anaphylaxis;  Animals;  Antibody Formation;  Humans;  Mammals;  Meat;  Mice;  Mice, Knockout;  Ticks},\ncorrespondence_address1={Reed, J.H.; Garvan Institute of Medical ResearchAustralia; email: joanne.reed@sydney.edu.au; Christ, D.; Garvan Institute of Medical ResearchAustralia; email: d.christ@garvan.org.au},\npublisher={National Academy of Sciences},\nissn={00278424},\ncoden={PNASA},\npubmed_id={35867757},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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@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

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\n \n\n \n \n \n \n \n \n Binding and folding in transcriptional complexes.\n \n \n \n \n\n\n \n Smith, N.; Kuravsky, M.; Shammas, S.; and Matthews, J.\n\n\n \n\n\n\n Current Opinion in Structural Biology, 66: 156-162. 2021.\n cited By 2\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 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

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@ARTICLE{Smith2021156,\nauthor={Smith, N.C. and Kuravsky, M. and Shammas, S.L. and Matthews, J.M.},\ntitle={Binding and folding in transcriptional complexes},\njournal={Current Opinion in Structural Biology},\nyear={2021},\nvolume={66},\npages={156-162},\ndoi={10.1016/j.sbi.2020.10.026},\nnote={cited By 2},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85097395988&doi=10.1016%2fj.sbi.2020.10.026&partnerID=40&md5=54360060859b8e69880bb7319c8edd15},\naffiliation={School of Life and Environmental Sciences, The University of SydneyNSW  2006, Australia; Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX29 4JP, United Kingdom},\nabstract={Transcription factors are among the classes of proteins with the highest levels of disorder. Investigation of these regulatory proteins is uncovering not just the mechanisms that underlie gene regulation, but relationships that apply to all intrinsically disordered proteins. Recent studies confirm that binding does not necessarily induce folding but that when it does, it tends to follow induced fit mechanisms. Other work emphasises the importance of electrostatics to interactions involving intrinsically disordered proteins, and roles of intrinsic disorder in phase transitions. All these features help direct transcription factors to target sites in the genome to upregulate or downregulate transcription. © 2020},\nkeywords={CREB kinase inducible domain;  DNA;  E1A associated p300 protein;  forkhead box protein M1;  intrinsically disordered protein;  mediator complex;  octamer transcription factor 4;  phosphotransferase;  protein p53;  prothymosin alpha;  RNA polymerase II;  transcription factor FKHR;  unclassified drug;  intrinsically disordered protein;  protein binding;  transcription factor, alpha helix;  amino terminal sequence;  beta sheet;  binding affinity;  binding site;  carboxy terminal sequence;  DNA binding;  DNA sequence;  down regulation;  gene activation;  gene expression regulation;  heterodimerization;  homodimerization;  human;  hydrophobicity;  isomerization;  molecular dynamics;  priority journal;  protein binding;  protein conformation;  protein folding;  protein processing;  protein protein interaction;  protein stability;  Review;  static electricity;  tetramerization;  transcription initiation;  transcription regulation;  upregulation;  metabolism, Intrinsically Disordered Proteins;  Protein Binding;  Protein Folding;  Transcription Factors},\npublisher={Elsevier Ltd},\nissn={0959440X},\ncoden={COSBE},\npubmed_id={33248428},\nlanguage={English},\nabbrev_source_title={Curr. Opin. Struct. Biol.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Contrasting DNA-binding behaviour by ISL1 and LHX3 underpins differential gene targeting in neuronal cell specification.\n \n \n \n \n\n\n \n Smith, N.; Wilkinson-White, L.; Kwan, A.; Trewhella, J.; and Matthews, J.\n\n\n \n\n\n\n Journal of Structural Biology: X, 5. 2021.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Contrasting$ 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

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@ARTICLE{Smith2021,\nauthor={Smith, N.C. and Wilkinson-White, L.E. and Kwan, A.H.Y. and Trewhella, J. and Matthews, J.M.},\ntitle={Contrasting DNA-binding behaviour by ISL1 and LHX3 underpins differential gene targeting in neuronal cell specification},\njournal={Journal of Structural Biology: X},\nyear={2021},\nvolume={5},\ndoi={10.1016/j.yjsbx.2020.100043},\nart_number={100043},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85098961085&doi=10.1016%2fj.yjsbx.2020.100043&partnerID=40&md5=51b38e84695b31e42b87d79263ce8f5a},\naffiliation={School of Life and Environmental Sciences, University of SydneyNSW  2006, Australia; Sydney Analytical Core Research Facility, University of SydneyNSW  2006, Australia; The University of Sydney Nano Institute, University of SydneyNSW  2006, Australia},\nabstract={The roles of ISL1 and LHX3 in the development of spinal motor neurons have been well established. Whereas LHX3 triggers differentiation into interneurons, the additional expression of ISL1 in developing neuronal cells is sufficient to redirect their developmental trajectory towards spinal motor neurons. However, the underlying mechanism of this action by these transcription factors is less well understood. Here, we used electrophoretic mobility shift assays (EMSAs) and surface plasmon resonance (SPR) to probe the different DNA-binding behaviours of these two proteins, both alone and in complexes mimicking those found in developing neurons, and found that ISL1 shows markedly different binding properties to LHX3. We used small angle X-ray scattering (SAXS) to structurally characterise DNA-bound species containing ISL1 and LHX3. Taken together, these results have allowed us to develop a model of how these two DNA-binding modules coordinate to regulate gene expression and direct development of spinal motor neurons. © 2020 The Authors},\nauthor_keywords={DNA-binding specificity;  Homeodomain-DNA interaction;  LIM-homeodomain transcription factors;  SAXS;  Transcriptional complex},\nkeywords={Article;  controlled study;  DNA binding;  gel mobility shift assay;  gene;  gene control;  gene expression;  gene targeting;  in vivo study;  ISL1 gene;  LHX3 gene;  molecular weight;  nerve cell;  pH;  plasmid;  priority journal;  promoter region;  spinal cord motoneuron;  surface plasmon resonance;  X ray crystallography},\ncorrespondence_address1={Matthews, J.M.; School of Life and Environmental Sciences, Australia; email: jacqueline.matthews@sydney.edu.au},\npublisher={Academic Press Inc.},\nissn={25901524},\nlanguage={English},\nabbrev_source_title={J. Struct. Biol. X},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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@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

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\n \n\n \n \n \n \n \n \n Ip7-spx domain interaction controls fungal virulence by stabilizing phosphate signaling machinery.\n \n \n \n \n\n\n \n Desmarini, D.; Lev, S.; Furkert, D.; Crossett, B.; Saiardi, A.; Kaufman-Francis, K.; Li, C.; Sorrell, T.; Wilkinson-White, L.; Matthews, J.; Fiedler, D.; and Teresa Djordjevic, J.\n\n\n \n\n\n\n mBio, 11(5): 1-20. 2020.\n cited By 10\n\n\n\n
\n\n\n\n \n \n $\"Ip7-spx$ 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

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@ARTICLE{Desmarini20201,\nauthor={Desmarini, D. and Lev, S. and Furkert, D. and Crossett, B. and Saiardi, A. and Kaufman-Francis, K. and Li, C. and Sorrell, T.C. and Wilkinson-White, L. and Matthews, J. and Fiedler, D. and Teresa Djordjevic, J.},\ntitle={Ip7-spx domain interaction controls fungal virulence by stabilizing phosphate signaling machinery},\njournal={mBio},\nyear={2020},\nvolume={11},\nnumber={5},\npages={1-20},\ndoi={10.1128/mBio.01920-20},\nart_number={e01920-20},\nnote={cited By 10},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85094147536&doi=10.1128%2fmBio.01920-20&partnerID=40&md5=c282b72be9a639f775c5f8c9115a1f1c},\naffiliation={Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, NSW, Australia; Sydney Medical School-Westmead, University of Sydney, Sydney, NSW, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia; Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany; Sydney Mass Spectrometry, University of Sydney, Sydney, NSW, Australia; Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia},\nabstract={In the human-pathogenic fungus Cryptococcus neoformans, the inositol polyphosphate signaling pathway is critical for virulence. We recently demonstrated the key role of the inositol pyrophosphate IP7 (isomer 5-PP-IP5) in driving fungal virulence; however, the mechanism of action remains elusive. Using genetic and biochemical approaches, and mouse infection models, we show that IP7 synthesized by Kcs1 regulates fungal virulence by binding to a conserved lysine surface cluster in the SPX domain of Pho81. Pho81 is the cyclin-dependent kinase (CDK) inhibitor of the phosphate signaling (PHO) pathway. We also provide novel mechanistic insight into the role of IP7 in PHO pathway regulation by demonstrating that IP7 functions as an intermolecular “glue” to stabilize Pho81 association with Pho85/Pho80 and, hence, promote PHO pathway activation and phosphate acquisition. Blocking IP7-Pho81 interaction using site-directed mutagenesis led to a dramatic loss of fungal virulence in a mouse infection model, and the effect was similar to that observed following PHO81 gene deletion, highlighting the key importance of Pho81 in fungal virulence. Furthermore, our findings provide additional evidence of evolutionary divergence in PHO pathway regulation in fungi by demonstrating that IP7 isomers have evolved different roles in PHO pathway control in C. neoformans and nonpathogenic yeast. IMPORTANCE Invasive fungal diseases pose a serious threat to human health globally with _1.5 million deaths occurring annually, 180,000 of which are attributable to the AIDS-related pathogen, Cryptococcus neoformans. Here, we demonstrate that interaction of the inositol pyrophosphate, IP7, with the CDK inhibitor protein, Pho81, is instrumental in promoting fungal virulence. IP7-Pho81 interaction stabilizes Pho81 association with other CDK complex components to promote PHO pathway activation and phosphate acquisition. Our data demonstrating that blocking IP7-Pho81 interaction or preventing Pho81 production leads to a dramatic loss in fungal virulence, coupled with Pho81 having no homologue in humans, highlights Pho81 function as a potential target for the development of urgently needed antifungal drugs. © 2020 Desmarini et al.},\nauthor_keywords={Cryptococcus neoformans;  Cyclindependent kinase inhibitor;  Fungal virulence;  Inositol polyphosphate;  Inositol pyrophosphate;  IP7;  PHO pathway;  Pho81;  SPX domain},\nkeywords={inositol derivative;  inositol pyrophosphate IP7;  pyrophosphoric acid derivative;  unclassified drug;  inorganic pyrophosphatase;  inositol phosphate;  phosphotransferase;  repressor protein, animal experiment;  animal model;  animal tissue;  Article;  chemical interaction;  controlled study;  cryptococcosis;  evolution;  female;  fungal virulence;  gene;  gene deletion;  mouse;  nonhuman;  PHO81 gene;  priority journal;  protein binding;  protein domain;  signal transduction;  site directed mutagenesis;  animal;  C57BL mouse;  Cryptococcus neoformans;  genetics;  human;  metabolism;  pathogenicity;  signal transduction;  virulence, Animals;  Cryptococcus neoformans;  Female;  Humans;  Inositol Phosphates;  Mice, Inbred C57BL;  Mutagenesis, Site-Directed;  Phosphotransferases (Phosphate Group Acceptor);  Pyrophosphatases;  Repressor Proteins;  Signal Transduction;  Virulence},\ncorrespondence_address1={Teresa Djordjevic, J.; Centre for Infectious Diseases and Microbiology, Australia; email: julianne.djordjevic@sydney.edu.au; Teresa Djordjevic, J.; Sydney Medical School-Westmead, Australia; email: julianne.djordjevic@sydney.edu.au; Teresa Djordjevic, J.; Marie Bashir Institute for Infectious Diseases and Biosecurity, Australia; email: julianne.djordjevic@sydney.edu.au},\npublisher={American Society for Microbiology},\nissn={21612129},\npubmed_id={33082258},\nlanguage={English},\nabbrev_source_title={mBio},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n In the human-pathogenic fungus Cryptococcus neoformans, the inositol polyphosphate signaling pathway is critical for virulence. We recently demonstrated the key role of the inositol pyrophosphate IP7 (isomer 5-PP-IP5) in driving fungal virulence; however, the mechanism of action remains elusive. Using genetic and biochemical approaches, and mouse infection models, we show that IP7 synthesized by Kcs1 regulates fungal virulence by binding to a conserved lysine surface cluster in the SPX domain of Pho81. Pho81 is the cyclin-dependent kinase (CDK) inhibitor of the phosphate signaling (PHO) pathway. We also provide novel mechanistic insight into the role of IP7 in PHO pathway regulation by demonstrating that IP7 functions as an intermolecular “glue” to stabilize Pho81 association with Pho85/Pho80 and, hence, promote PHO pathway activation and phosphate acquisition. Blocking IP7-Pho81 interaction using site-directed mutagenesis led to a dramatic loss of fungal virulence in a mouse infection model, and the effect was similar to that observed following PHO81 gene deletion, highlighting the key importance of Pho81 in fungal virulence. Furthermore, our findings provide additional evidence of evolutionary divergence in PHO pathway regulation in fungi by demonstrating that IP7 isomers have evolved different roles in PHO pathway control in C. neoformans and nonpathogenic yeast. IMPORTANCE Invasive fungal diseases pose a serious threat to human health globally with _1.5 million deaths occurring annually, 180,000 of which are attributable to the AIDS-related pathogen, Cryptococcus neoformans. Here, we demonstrate that interaction of the inositol pyrophosphate, IP7, with the CDK inhibitor protein, Pho81, is instrumental in promoting fungal virulence. IP7-Pho81 interaction stabilizes Pho81 association with other CDK complex components to promote PHO pathway activation and phosphate acquisition. Our data demonstrating that blocking IP7-Pho81 interaction or preventing Pho81 production leads to a dramatic loss in fungal virulence, coupled with Pho81 having no homologue in humans, highlights Pho81 function as a potential target for the development of urgently needed antifungal drugs. © 2020 Desmarini et al.\n

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\n \n 2019\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n Mutation in a flexible linker modulates binding affinity for modular complexes.\n \n \n \n \n\n\n \n Stokes, P.; Robertson, N.; Silva, A.; Estephan, T.; Trewhella, J.; Guss, J.; and Matthews, J.\n\n\n \n\n\n\n Proteins: Structure, Function and Bioinformatics, 87(5): 425-429. 2019.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Mutation$ 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

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@ARTICLE{Stokes2019425,\nauthor={Stokes, P.H. and Robertson, N.O. and Silva, A.P.G. and Estephan, T. and Trewhella, J. and Guss, J.M. and Matthews, J.M.},\ntitle={Mutation in a flexible linker modulates binding affinity for modular complexes},\njournal={Proteins: Structure, Function and Bioinformatics},\nyear={2019},\nvolume={87},\nnumber={5},\npages={425-429},\ndoi={10.1002/prot.25675},\nnote={cited By 1},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85062710586&doi=10.1002%2fprot.25675&partnerID=40&md5=e05ac04d4b6ea969378065dbb4a2ff4d},\naffiliation={School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia; Cancer Biology and Genetics Program, Memorial Soon Kettering Cancer Center, New York, NY  10065, United States; Teva Pharmaceuticals, 37 Epping Road, Macquarie Park, NSW  2113, Australia},\nabstract={Tandem beta zippers are modular complexes formed between repeated linear motifs and tandemly arrayed domains of partner proteins in which β-strands form upon binding. Studies of such complexes, formed by LIM domain proteins and linear motifs in their intrinsically disordered partners, revealed spacer regions between the linear motifs that are relatively flexible but may affect the overall orientation of the binding modules. We demonstrate that mutation of a solvent exposed side chain in the spacer region of an LHX4–ISL2 complex has no significant effect on the structure of the complex, but decreases binding affinity, apparently by increasing flexibility of the linker. © 2019 Wiley Periodicals, Inc.},\nauthor_keywords={intrinsically disordered region;  modular binding;  mutation;  protein complex;  protein–protein interaction},\nkeywords={homeodomain protein;  LIM protein;  protein ISL2;  protein LHX4;  unclassified drug;  DNA binding protein;  Isl2 protein, mouse;  Lhx4 protein, mouse;  LIM homeodomain protein;  multiprotein complex;  protein binding;  spacer DNA;  transcription factor, amino acid sequence;  Article;  binding affinity;  nonhuman;  priority journal;  protein analysis;  protein protein interaction;  protein stability;  protein structure;  animal;  binding site;  chemistry;  genetics;  molecular model;  mouse;  mutation;  protein secondary structure;  protein tertiary structure;  sequence homology;  ultrastructure, Amino Acid Sequence;  Animals;  Binding Sites;  DNA, Intergenic;  DNA-Binding Proteins;  LIM-Homeodomain Proteins;  Mice;  Models, Molecular;  Multiprotein Complexes;  Mutation;  Protein Binding;  Protein Structure, Secondary;  Protein Structure, Tertiary;  Sequence Homology, Amino Acid;  Transcription Factors},\ncorrespondence_address1={Matthews, J.M.; School of Life and Environmental Sciences, Australia; email: jacqueline.matthews@sydney.edu.au},\npublisher={John Wiley and Sons Inc.},\nissn={08873585},\npubmed_id={30788856},\nlanguage={English},\nabbrev_source_title={Proteins Struct. Funct. Bioinformatics},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Correction: Mutations in MITF and PAX3 Cause \"splashed White\" and Other White Spotting Phenotypes in Horses(PLoS Genet (2012) 8:4 (e1002653) DOI:10.1371/journal.pgen.1002653).\n \n \n \n \n\n\n \n Hauswirth, R.; Haase, B.; Blatter, M.; Brooks, S.; Burger, D.; Drögemüller, C.; Gerber, V.; Henke, D.; Janda, J.; Jude, R.; Gary Magdesian, K.; Matthews, J.; Poncet, P.; lmurSvansson , V.; Tozaki, T.; Wilkinson-White, L.; Penedo, M.; Rieder, S.; and Leeb, T.\n\n\n \n\n\n\n PLoS Genetics, 15(8). 2019.\n cited By 1\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

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@ARTICLE{Hauswirth2019,\nauthor={Hauswirth, R. and Haase, B. and Blatter, M. and Brooks, S.A. and Burger, D. and Drögemüller, C. and Gerber, V. and Henke, D. and Janda, J. and Jude, R. and Gary Magdesian, K. and Matthews, J.M. and Poncet, P.-A. and lmurSvansson, V. and Tozaki, T. and Wilkinson-White, L. and Penedo, M.C.T. and Rieder, S. and Leeb, T.},\ntitle={Correction: Mutations in MITF and PAX3 Cause "splashed White" and Other White Spotting Phenotypes in Horses(PLoS Genet (2012) 8:4 (e1002653) DOI:10.1371/journal.pgen.1002653)},\njournal={PLoS Genetics},\nyear={2019},\nvolume={15},\nnumber={8},\ndoi={10.1371/journal.pgen.1008321},\nart_number={e1008321},\nnote={cited By 1},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85071195975&doi=10.1371%2fjournal.pgen.1008321&partnerID=40&md5=68a0f79022f086ee406fd30f9b8cb6ef},\nabstract={There are errors in the identification of an allele, PAX3C70Y, arising by a de novo mutation event in a Quarter Horse mare born in 1987. The authors discovered a sample mix-up concerning the erroneously claimed Quarter Horse founder mare, labeled QH095 and genotyped PAX3+/+. Through analysis of an independent sample of QH095, the authors identified the genotype PAX3C70Y/+ in the new sample. Therefore, QH095 is not the founder animal for the PAX3C70Y allele. © 2019 Hauswirth et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},\nkeywords={erratum;  error},\npublisher={Public Library of Science},\nissn={15537390},\npubmed_id={31374075},\nlanguage={English},\nabbrev_source_title={PLoS Genet.},\ndocument_type={Erratum},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n 1D Self-Assembly and Ice Recrystallization Inhibition Activity of Antifreeze Glycopeptide-Functionalized Perylene Bisimides.\n \n \n \n \n\n\n \n Adam, M.; Jarrett-Wilkins, C.; Beards, M.; Staykov, E.; MacFarlane, L.; Bell, T.; Matthews, J.; Manners, I.; Faul, C.; Moens, P.; Ben, R.; and Wilkinson, B.\n\n\n \n\n\n\n Chemistry - A European Journal, 24(31): 7834-7839. 2018.\n cited By 12\n\n\n\n
\n\n\n\n \n \n $\"1D$ 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

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@ARTICLE{Adam20187834,\nauthor={Adam, M.K. and Jarrett-Wilkins, C. and Beards, M. and Staykov, E. and MacFarlane, L.R. and Bell, T.D.M. and Matthews, J.M. and Manners, I. and Faul, C.F.J. and Moens, P.D.J. and Ben, R.N. and Wilkinson, B.L.},\ntitle={1D Self-Assembly and Ice Recrystallization Inhibition Activity of Antifreeze Glycopeptide-Functionalized Perylene Bisimides},\njournal={Chemistry - A European Journal},\nyear={2018},\nvolume={24},\nnumber={31},\npages={7834-7839},\ndoi={10.1002/chem.201800857},\nnote={cited By 12},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85046535469&doi=10.1002%2fchem.201800857&partnerID=40&md5=d4c761762d0923c4fc973945293792d4},\naffiliation={School of Science and Technology, University of New England, Armidale, 2351, Australia; Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, K1N 6N5, Canada; School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom; School of Chemistry, Monash University, Melbourne, 3800, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, 2006, Australia},\nabstract={Antifreeze glycoproteins (AFGPs) are polymeric natural products that have drawn considerable interest in diverse research fields owing to their potent ice recrystallization inhibition (IRI) activity. Self-assembled materials have emerged as a promising class of biomimetic ice growth inhibitor, yet the development of AFGP-based supramolecular materials that emulate the aggregative behavior of AFGPs have not yet been reported. This work reports the first example of the 1D self-assembly and IRI activity of AFGP-functionalized perylene bisimides (AFGP-PBIs). Glycopeptide-functionalized PBIs underwent 1D self-assembly in water and showed modest IRI activity, which could be tuned through substitution of the PBI core. This work presents essential proof-of-principle for the development of novel IRIs as potential supramolecular cryoprotectants and glycoprotein mimics. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim},\nauthor_keywords={1D self-assembly;  antifreeze glycopeptides;  perylene bisimides;  pi interactions;  soft matter},\nkeywords={Biomimetic materials;  Biomimetics;  Glycoproteins;  Peptides;  Polycyclic aromatic hydrocarbons;  Recrystallization (metallurgy);  Self assembly;  Supramolecular chemistry, Antifreeze glycoprotein;  Glycopeptides;  Perylene bisimides;  Pi interactions;  Proof of principles;  Self assembled material;  Soft matter;  Supramolecular materials, Ice, antifreeze protein;  glycopeptide;  ice;  imide;  perylene;  perylene bisimide;  water, analogs and derivatives;  chemistry;  crystallization;  protein multimerization;  thermodynamics, Antifreeze Proteins;  Crystallization;  Glycopeptides;  Ice;  Imides;  Perylene;  Protein Multimerization;  Thermodynamics;  Water},\ncorrespondence_address1={Wilkinson, B.L.; School of Science and Technology, Australia; email: Brendan.wilkinson@une.edu.au},\npublisher={Wiley-VCH Verlag},\nissn={09476539},\ncoden={CEUJE},\npubmed_id={29644728},\nlanguage={English},\nabbrev_source_title={Chem. Eur. J.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Disparate binding kinetics by an intrinsically disordered domain enables temporal regulation of transcriptional complex formation.\n \n \n \n \n\n\n \n Robertson, N.; Smith, N.; Manakas, A.; Mahjoub, M.; McDonald, G.; Kwan, A.; and Matthews, J.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 115(18): 4643-4648. 2018.\n cited By 8\n\n\n\n
\n\n\n\n \n \n $\"Disparate$ 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

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@ARTICLE{Robertson20184643,\nauthor={Robertson, N.O. and Smith, N.C. and Manakas, A. and Mahjoub, M. and McDonald, G. and Kwan, A.H. and Matthews, J.M.},\ntitle={Disparate binding kinetics by an intrinsically disordered domain enables temporal regulation of transcriptional complex formation},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2018},\nvolume={115},\nnumber={18},\npages={4643-4648},\ndoi={10.1073/pnas.1714646115},\nnote={cited By 8},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85046285915&doi=10.1073%2fpnas.1714646115&partnerID=40&md5=f6f820be6ab3b58bfa84d398adf8fd14},\naffiliation={School of Life and Environmental Sciences, University of Sydney, Sydney, NSW  2006, Australia; Centre for Translational Data Science, University of Sydney, Sydney, NSW  2006, Australia},\nabstract={Intrinsically disordered regions are highly represented among mammalian transcription factors, where they often contribute to the formation of multiprotein complexes that regulate gene expression. An example of this occurs with LIM-homeodomain (LIM-HD) proteins in the developing spinal cord. The LIM-HD protein LHX3 and the LIM-HD cofactor LDB1 form a binary complex that gives rise to interneurons, whereas in adjacent cell populations, LHX3 and LDB1 form a rearranged ternary complex with the LIM-HD protein ISL1, resulting in motor neurons. The protein–protein interactions within these complexes are mediated by ordered LIM domains in the LIM-HD proteins and intrinsically disordered LIM interaction domains (LIDs) in LDB1 and ISL1; however, little is known about how the strength or rates of binding contribute to complex assemblies. We have measured the interactions of LIM:LID complexes using FRET-based protein–protein interaction studies and EMSAs and used these data to model population distributions of complexes. The protein–protein interactions within the ternary complexes are much weaker than those in the binary complex, yet surprisingly slow LDB1: ISL1 dissociation kinetics and a substantial increase in DNA binding affinity promote formation of the ternary complex over the binary complex in motor neurons. We have used mutational and protein engineering approaches to show that allostery and modular binding by tandem LIM domains contribute to the LDB1LID binding kinetics. The data indicate that a single intrinsically disordered region can achieve highly disparate binding kinetics, which may provide a mechanism to regulate the timing of transcriptional complex assembly. © 2018 National Academy of Sciences. All rights reserved.},\nauthor_keywords={Binding kinetics;  Intrinsically disordered proteins;  Protein–DNA interactions;  Protein–protein interactions;  Transcriptional regulation},\nkeywords={homeodomain protein;  protein ISL1;  protein LDB1;  transcription factor LHX3;  unclassified drug;  DNA;  DNA binding protein;  insulin gene enhancer binding protein Isl-1;  intrinsically disordered protein;  Ldb1 protein, mouse;  LIM homeodomain protein;  LIM protein;  multiprotein complex;  protein binding;  transcription factor, allosterism;  Article;  binding affinity;  binding kinetics;  complex formation;  controlled study;  fluorescence resonance energy transfer;  gel mobility shift assay;  interneuron;  intrinsically disordered domain;  motoneuron;  priority journal;  protein DNA binding;  protein domain;  protein protein interaction;  animal;  chemistry;  genetics;  kinetics;  metabolism;  mouse;  protein domain;  transcription initiation, Animals;  DNA;  DNA-Binding Proteins;  Intrinsically Disordered Proteins;  Kinetics;  LIM Domain Proteins;  LIM-Homeodomain Proteins;  Mice;  Multiprotein Complexes;  Protein Binding;  Protein Domains;  Transcription Factors;  Transcription Initiation, Genetic},\ncorrespondence_address1={Matthews, J.M.; School of Life and Environmental Sciences, Australia; email: jacqui.matthews@sydney.edu.au},\npublisher={National Academy of Sciences},\nissn={00278424},\ncoden={PNASA},\npubmed_id={29666277},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Differential effects on gene transcription and hematopoietic differentiation correlate with GATA2 mutant disease phenotypes.\n \n \n \n \n\n\n \n Chong, C.; Venugopal, P.; Stokes, P.; Lee, Y.; Brautigan, P.; Yeung, D.; Babic, M.; Engler, G.; Lane, S.; Klingler-Hoffmann, M.; Matthews, J.; D'Andrea, R.; Brown, A.; Hahn, C.; and Scott, H.\n\n\n \n\n\n\n Leukemia, 32(1): 194-202. 2018.\n cited By 39\n\n\n\n
\n\n\n\n \n \n $\"Differential$ 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

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@ARTICLE{Chong2018194,\nauthor={Chong, C.-E. and Venugopal, P. and Stokes, P.H. and Lee, Y.K. and Brautigan, P.J. and Yeung, D.T.O. and Babic, M. and Engler, G.A. and Lane, S.W. and Klingler-Hoffmann, M. and Matthews, J.M. and D'Andrea, R.J. and Brown, A.L. and Hahn, C.N. and Scott, H.S.},\ntitle={Differential effects on gene transcription and hematopoietic differentiation correlate with GATA2 mutant disease phenotypes},\njournal={Leukemia},\nyear={2018},\nvolume={32},\nnumber={1},\npages={194-202},\ndoi={10.1038/leu.2017.196},\nnote={cited By 39},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028566824&doi=10.1038%2fleu.2017.196&partnerID=40&md5=4fe0e21caa1549d1469940ea4dcf7d4f},\naffiliation={Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, University of South Australia Alliance, Frome Road, Adelaide, SA  5000, Australia; Cancer Genomics Facility, Australian Cancer Research Foundation, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia; Division of Hematology, SA Pathology, Adelaide, SA, Australia; School of Medicine, University of Adelaide, Adelaide, SA, Australia; QIMR Berghofer Medical Research Institute, University of Queensland, Brisbane, QLD, Australia; School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia},\nabstract={Heterozygous GATA2 mutations underlie an array of complex hematopoietic and lymphatic diseases. Analysis of the literature reporting three recurrent GATA2 germline (g) mutations (gT354M, gR396Q and gR398W) revealed different phenotype tendencies. Although all three mutants differentially predispose to myeloid malignancies, there was no difference in leukemia-free survival for GATA2 patients. Despite intense interest, the molecular pathogenesis of GATA2 mutation is poorly understood. We functionally characterized a GATA2 mutant allelic series representing major disease phenotypes caused by germline and somatic (s) mutations in zinc finger 2 (ZF2). All GATA2 mutants, except for sL359V, displayed reduced DNA-binding affinity and transactivation compared with wild type (WT), which could be attributed to mutations of arginines critical for DNA binding or amino acids required for ZF2 domain structural integrity. Two GATA2 mutants (gT354M and gC373R) bound the key hematopoietic differentiation factor PU.1 more strongly than WT potentially perturbing differentiation via sequestration of PU.1. Unlike WT, all mutants failed to suppress colony formation and some mutants skewed cell fate to granulocytes, consistent with the monocytopenia phenotype seen in GATA2-related immunodeficiency disorders. These findings implicate perturbations of GATA2 function shaping the course of development of myeloid malignancy subtypes and strengthen complete or nearly complete haploinsufficiency for predisposition to lymphedema. © The Author(s) 2018.},\nkeywords={DNA fragment;  transcription factor GATA 2;  transcription factor PU 1;  unclassified drug;  zinc finger protein;  zinc finger protein 2;  GATA2 protein, human;  transcription factor GATA 2, acute myeloid leukemia;  adult;  amino acid substitution;  animal cell;  Article;  binding affinity;  cancer prognosis;  cancer susceptibility;  cell differentiation;  cell fate;  cellular distribution;  controlled study;  disease free survival;  DNA binding;  female;  GATA2 gene;  gene expression;  genetic transcription;  genotype phenotype correlation;  germline mutation;  granulocyte;  haploinsufficiency;  hematopoietic cell;  leukemogenesis;  mouse;  myelodysplastic syndrome;  nonhuman;  nuclear localization signal;  phenotype;  priority journal;  protein function;  somatic mutation;  transactivation;  transcription initiation;  animal;  C57BL mouse;  cell differentiation;  Chlorocebus aethiops;  CV-1 cell line;  genetic predisposition;  genetic transcription;  genetics;  genotype;  HEK293 cell line;  hematopoietic system;  human;  male;  mutation;  pathology;  phenotype, Animals;  Cell Differentiation;  Cercopithecus aethiops;  COS Cells;  Female;  GATA2 Transcription Factor;  Genetic Predisposition to Disease;  Genotype;  Haploinsufficiency;  HEK293 Cells;  Hematopoietic System;  Humans;  Male;  Mice;  Mice, Inbred C57BL;  Mutation;  Phenotype;  Transcription, Genetic},\ncorrespondence_address1={Hahn, C.N.; Department of Genetics and Molecular Pathology, Frome Road, Australia; email: chris.hahn@sa.gov.au},\npublisher={Nature Publishing Group},\nissn={08876924},\ncoden={LEUKE},\npubmed_id={28642594},\nlanguage={English},\nabbrev_source_title={Leukemia},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

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

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\n \n 2017\n \n \n (1)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Interactions between LHX3-And ISL1-family LIM-homeodomain transcription factors are conserved in Caenorhabditis elegans.\n \n \n \n \n\n\n \n Bhati, M.; Llamosas, E.; Jacques, D.; Jeffries, C.; Dastmalchi, S.; Ripin, N.; Nicholas, H.; and Matthews, J.\n\n\n \n\n\n\n Scientific Reports, 7(1). 2017.\n cited By 4\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 \n \n \n \n \n \n\n\n\n

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@ARTICLE{Bhati2017,\nauthor={Bhati, M. and Llamosas, E. and Jacques, D.A. and Jeffries, C.M. and Dastmalchi, S. and Ripin, N. and Nicholas, H.R. and Matthews, J.M.},\ntitle={Interactions between LHX3-And ISL1-family LIM-homeodomain transcription factors are conserved in Caenorhabditis elegans},\njournal={Scientific Reports},\nyear={2017},\nvolume={7},\nnumber={1},\ndoi={10.1038/s41598-017-04587-8},\nart_number={4579},\nnote={cited By 4},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021762731&doi=10.1038%2fs41598-017-04587-8&partnerID=40&md5=b08cee9fe67cf309db0a296384ed0fd0},\naffiliation={School of Life and Environmental Sciences, University of SydneyNSW  2006, Australia; Teva Pharmaceuticals Australia Pty Ltd, Macquarie ParkNSW  2113, Australia; School of Women's and Children's Health, University of New South Wales, NSW, Australia; Department of Biology, ETH, Zurich, 8093, Switzerland; IThree Institute, University of Technology, NSW, 2007, Australia; European Molecular Biology Laboratory (EMBL) Hamburg Outstation, c/o DESY Notkestrasse 85, Hamburg, 22607, Germany; Biotechnology Research Center and School of Pharmacy, Tabritz Univeristy of Medical Science, Tabritz, Iran},\nabstract={LIM-Homeodomain (LIM-HD) transcription factors are highly conserved in animals where they are thought to act in a transcriptional 'LIM code' that specifies cell types, particularly in the central nervous system. In chick and mammals the interaction between two LIM-HD proteins, LHX3 and Islet1 (ISL1), is essential for the development of motor neurons. Using yeast two-hybrid analysis we showed that the Caenorhabditis elegans orthologs of LHX3 and ISL1, CEH-14 and LIM-7 can physically interact. Structural characterisation of a complex comprising the LIM domains from CEH-14 and a LIM-interaction domain from LIM-7 showed that these nematode proteins assemble to form a structure that closely resembles that of their vertebrate counterparts. However, mutagenic analysis across the interface indicates some differences in the mechanisms of binding. We also demonstrate, using fluorescent reporter constructs, that the two C. elegans proteins are co-expressed in a small subset of neurons. These data show that the propensity for LHX3 and Islet proteins to interact is conserved from C. elegans to mammals, raising the possibility that orthologous cell specific LIM-HD-containing transcription factor complexes play similar roles in the development of neuronal cells across diverse species. © 2017 The Author(s).},\nkeywords={insulin gene enhancer binding protein Isl-1;  LIM homeodomain protein;  multiprotein complex;  protein binding;  transcription factor;  transcription factor LHX3, alternative RNA splicing;  animal;  binding site;  Caenorhabditis elegans;  chemistry;  conserved sequence;  gene expression regulation;  genetics;  metabolism;  molecular evolution;  molecular model;  multigene family;  protein analysis;  protein conformation;  protein domain;  solution and solubility, Alternative Splicing;  Animals;  Binding Sites;  Caenorhabditis elegans;  Conserved Sequence;  Evolution, Molecular;  Gene Expression Regulation;  LIM-Homeodomain Proteins;  Models, Molecular;  Multigene Family;  Multiprotein Complexes;  Protein Binding;  Protein Conformation;  Protein Interaction Domains and Motifs;  Protein Interaction Mapping;  Solutions;  Transcription Factors},\ncorrespondence_address1={Nicholas, H.R.; School of Life and Environmental Sciences, Australia; email: hannah.nicholas@sydney.edu.au},\npublisher={Nature Publishing Group},\nissn={20452322},\npubmed_id={28676648},\nlanguage={English},\nabbrev_source_title={Sci. Rep.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n 2016\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n A Quantitative Fluorescence-Based Assay for Assessing LIM Domain–Peptide Interactions.\n \n \n \n \n\n\n \n Robertson, N.; Shah, M.; and Matthews, J.\n\n\n \n\n\n\n Angewandte Chemie - International Edition, 55(42): 13236-13239. 2016.\n cited By 3\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

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@ARTICLE{Robertson201613236,\nauthor={Robertson, N.O. and Shah, M. and Matthews, J.M.},\ntitle={A Quantitative Fluorescence-Based Assay for Assessing LIM Domain–Peptide Interactions},\njournal={Angewandte Chemie - International Edition},\nyear={2016},\nvolume={55},\nnumber={42},\npages={13236-13239},\ndoi={10.1002/anie.201605964},\nnote={cited By 3},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84992075200&doi=10.1002%2fanie.201605964&partnerID=40&md5=a5bd0b6cbc36d411cd35f9791692dd6e},\naffiliation={School of Life and Environmental Sciences, The University of SydneyNSW  2006, Australia},\nabstract={We have developed Förster resonance energy transfer (FRET)-based experiments for measuring the binding affinity, off-rates, and inferred on-rates for interactions between a family of transcriptional regulators and their intrinsically disordered binding partners. It was difficult to evaluate these interactions previously, as the transcriptional regulators are obligate binding proteins that aggregate in the absence of a binding partner. The assays rely on fusion constructs where binding domains are linked by a flexible tether containing a specific protease site, with fluorescent proteins at either end that display FRET when the complex is formed. Loss of FRET is monitored after cutting the tether followed by dilution or competition with a non-fluorescent peptide. These methods allowed a wide range of binding affinities (10−9–10−5m) to be determined. Our data indicate that interactions of closely related proteins can have surprisingly different binding properties. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim},\nauthor_keywords={fluorescence;  FRET;  kinetics;  protein engineering;  protein–protein interactions},\nkeywords={Energy transfer;  Enzyme kinetics;  Flexible displays;  Fluorescence;  Forster resonance energy transfer;  Peptides;  Tetherlines, Binding properties;  Fluorescent peptides;  Fluorescent protein;  FRET;  Protein engineering;  Protein interaction;  Resonance energy transfer;  Transcriptional regulator, Binding energy, LIM protein;  peptide, chemistry;  fluorescence resonance energy transfer;  molecular model, Fluorescence Resonance Energy Transfer;  LIM Domain Proteins;  Models, Molecular;  Peptides},\ncorrespondence_address1={Matthews, J.M.; School of Life and Environmental Sciences, Australia; email: jacqui.matthews@sydney.edu.au},\npublisher={Wiley-VCH Verlag},\nissn={14337851},\ncoden={ACIEF},\npubmed_id={27647681},\nlanguage={English},\nabbrev_source_title={Angew. Chem. Int. Ed.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors.\n \n \n \n \n\n\n \n Smith, N.; and Matthews, J.\n\n\n \n\n\n\n Current Opinion in Structural Biology, 38: 68-74. 2016.\n cited By 37\n\n\n\n
\n\n\n\n \n \n $\"Mechanisms$ 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

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@ARTICLE{Smith201668,\nauthor={Smith, N.C. and Matthews, J.M.},\ntitle={Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors},\njournal={Current Opinion in Structural Biology},\nyear={2016},\nvolume={38},\npages={68-74},\ndoi={10.1016/j.sbi.2016.05.006},\nnote={cited By 37},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84973494701&doi=10.1016%2fj.sbi.2016.05.006&partnerID=40&md5=55b7f116a7038124ee739e32dd3fd870},\naffiliation={School of Life and Environmental Science, The University of SydneyNSW  2006, Australia},\nabstract={Eukaryotic transcription factors up-regulate and down-regulate the expression of genes in a very controlled manner. The DNA-binding domains of these proteins have quite well established mechanisms for binding to DNA, but a surprisingly poor intrinsic ability to discriminate target and variant non-target DNA sequences. Here, we summarise established mechanisms of protein-DNA recognition, as specified by both macromolecules. We also review recent advances in the fields of genome binding, molecular dynamics and biomolecular interaction studies that bring us close to a full understanding of how eukaryotic transcription factors find and target DNA in vivo to form functional centres of gene regulation through networks of protein-protein and protein-DNA interactions. © 2016 Elsevier Ltd.},\nkeywords={transcription factor;  DNA;  transcription factor, amino terminal sequence;  binding site;  epigenetics;  gene control;  gene expression;  human;  in vitro study;  in vivo study;  molecular dynamics;  molecular recognition;  priority journal;  protein DNA binding;  protein expression;  protein protein interaction;  protein targeting;  Review;  structure analysis;  animal;  chemistry;  enzyme specificity;  gene expression regulation;  genetics;  metabolism, Animals;  Binding Sites;  DNA;  Gene Expression Regulation;  Humans;  Substrate Specificity;  Transcription Factors},\ncorrespondence_address1={Matthews, J.M.; School of Life and Environmental Science, Australia; email: jacqui.matthews@sydney.edu.au},\npublisher={Elsevier Ltd},\nissn={0959440X},\ncoden={COSBE},\npubmed_id={27295424},\nlanguage={English},\nabbrev_source_title={Curr. Opin. Struct. Biol.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Discovery, characterization and in vivo activity of pyocin SD2, a protein antibiotic from Pseudomonas aeruginosa.\n \n \n \n \n\n\n \n McCaughey, L.; Josts, I.; Grinter, R.; White, P.; Byron, O.; Tucker, N.; Matthews, J.; Kleanthous, C.; Whitchurch, C.; and Walker, D.\n\n\n \n\n\n\n Biochemical Journal, 473(15): 2345-2358. 2016.\n cited By 32\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

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@ARTICLE{McCaughey20162345,\nauthor={McCaughey, L.C. and Josts, I. and Grinter, R. and White, P. and Byron, O. and Tucker, N.P. and Matthews, J.M. and Kleanthous, C. and Whitchurch, C.B. and Walker, D.},\ntitle={Discovery, characterization and in vivo activity of pyocin SD2, a protein antibiotic from Pseudomonas aeruginosa},\njournal={Biochemical Journal},\nyear={2016},\nvolume={473},\nnumber={15},\npages={2345-2358},\ndoi={10.1042/BCJ20160470},\nnote={cited By 32},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85009349962&doi=10.1042%2fBCJ20160470&partnerID=40&md5=a398954fdca3edbb2c9d3c144dd7c4f0},\naffiliation={Ithree Institute, University of Technology Sydney, Ultimo, NSW  2007, Australia; Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom; Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom; School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom; Strathclyde Institute for Pharmaceutical and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, United Kingdom; School of Molecular Bioscience, University of SydneyNSW  2008, Australia},\nabstract={Increasing rates of antibiotic resistance among Gram-negative pathogens such as Pseudomonas aeruginosa means alternative approaches to antibiotic development are urgently required. Pyocins, produced by P. aeruginosa for intraspecies competition, are highly potent protein antibiotics known to actively translocate across the outer membrane of P. aeruginosa. Understanding and exploiting the mechanisms by which pyocins target, penetrate and kill P. aeruginosa is a promising approach to antibiotic development. In this work we show the therapeutic potential of a newly identified tRNase pyocin, pyocin SD2, by demonstrating its activity in vivo in a murine model of P. aeruginosa lung infection. In addition, we propose a mechanism of cell targeting and translocation for pyocin SD2 across the P. aeruginosa outer membrane. Pyocin SD2 is concentrated at the cell surface, via binding to the common polysaccharide antigen (CPA) of P. aeruginosa lipopolysaccharide (LPS), from where it can efficiently locate its outer membrane receptor FpvAI. This strategy of utilizing both the CPA and a protein receptor for cell targeting is common among pyocins as we show that pyocins S2, S5 and SD3 also bind to the CPA. Additional data indicate a key role for an unstructured N-terminal region of pyocin SD2 in the subsequent translocation of the pyocin into the cell. These results greatly improve our understanding of how pyocins target and translocate across the outer membrane of P. aeruginosa. This knowledge could be useful for the development of novel antipseudomonal therapeutics and will also support the development of pyocin SD2 as a therapeutic in its own right. © 2016 The Author(s).},\nauthor_keywords={Antibiotics;  Bacteriocins;  Common polysaccharide antigen;  Outer membrane;  Pseudomonas aeruginosa;  Pyocins},\nkeywords={antibiotic agent;  bacterial protein;  outer membrane protein;  polysaccharide;  pyocin SD1;  pyocin SD2;  pyosin SD3;  unclassified drug;  antiinfective agent;  pyocin, amino terminal sequence;  animal experiment;  animal model;  Article;  bacterial genome;  bactericidal activity;  cell surface;  female;  in vivo study;  mouse;  nonhuman;  priority journal;  protein purification;  protein secondary structure;  Pseudomonas aeruginosa;  Pseudomonas pneumonia;  site directed mutagenesis;  animal;  chemistry;  circular dichroism;  isolation and purification;  Lung Diseases;  molecular cloning;  Pseudomonas aeruginosa;  small angle scattering;  ultraviolet spectrophotometry;  X ray diffraction, Animals;  Anti-Bacterial Agents;  Circular Dichroism;  Cloning, Molecular;  Lung Diseases;  Mice;  Pseudomonas aeruginosa;  Pyocins;  Scattering, Small Angle;  Spectrophotometry, Ultraviolet;  X-Ray Diffraction},\ncorrespondence_address1={McCaughey, L.C.; Ithree Institute, Australia; email: Laura.mccaughey@uts.edu.au},\npublisher={Portland Press Ltd},\nissn={02646021},\ncoden={BIJOA},\npubmed_id={27252387},\nlanguage={English},\nabbrev_source_title={Biochem. J.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n 2015\n \n \n (6)\n \n \n

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\n \n\n \n \n \n \n \n \n GATA1 directly mediates interactions with closely spaced pseudopalindromic but not distantly spaced double GATA sites on DNA.\n \n \n \n \n\n\n \n Wilkinson-White, L.; Lester, K.; Ripin, N.; Jacques, D.; Mitchell Guss, J.; and Matthews, J.\n\n\n \n\n\n\n Protein Science, 24(10): 1649-1659. 2015.\n cited By 7\n\n\n\n
\n\n\n\n \n \n $\"GATA1$ 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

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@ARTICLE{Wilkinson-White20151649,\nauthor={Wilkinson-White, L. and Lester, K.L. and Ripin, N. and Jacques, D.A. and Mitchell Guss, J. and Matthews, J.M.},\ntitle={GATA1 directly mediates interactions with closely spaced pseudopalindromic but not distantly spaced double GATA sites on DNA},\njournal={Protein Science},\nyear={2015},\nvolume={24},\nnumber={10},\npages={1649-1659},\ndoi={10.1002/pro.2760},\nnote={cited By 7},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84957091411&doi=10.1002%2fpro.2760&partnerID=40&md5=c213197f1ecc78176e2529a21630c534},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW  2042, Australia; Institute of Molecular Biology and Biophysics, ETH Hönggerberg, Zürich, 8093, Switzerland; MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom},\nabstract={The transcription factor GATA1 helps regulate the expression of thousands of genes involved in blood development, by binding to single or double GATA sites on DNA. An important part of gene activation is chromatin looping, the bringing together of DNA elements that lie up to many thousands of basepairs apart in the genome. It was recently suggested, based on studies of the closely related protein GATA3, that GATA-mediated looping may involve interactions of each of two zinc fingers (ZF) with distantly spaced DNA elements. Here we present a structure of the GATA1 ZF region bound to pseudopalindromic double GATA site DNA, which is structurally equivalent to a recently-solved GATA3-DNA complex. However, extensive analysis of GATA1-DNA binding indicates that although the N-terminal ZF (NF) can modulate GATA1-DNA binding, under physiological conditions the NF binds DNA so poorly that it cannot play a direct role in DNA-looping. Rather, the ability of the NF to stabilize transcriptional complexes through protein-protein interactions, and thereby recruit looping factors such as Ldb1, provides a more compelling model for GATA-mediated looping. © 2015 The Protein Society.},\nauthor_keywords={chromatin looping;  DNA binding;  GATA1;  protein-DNA structure;  transcription factor complex},\nkeywords={DNA;  LIM domain binding protein 1;  nucleic acid binding protein;  pseudopalindromic dna;  transcription factor GATA 1;  unclassified drug;  DNA;  DNA binding protein;  LDB1 protein, human;  LIM protein;  transcription factor;  transcription factor GATA 1, amino terminal sequence;  Article;  binding site;  dna looping;  DNA protein complex;  DNA structure;  mouse;  nonhuman;  priority journal;  protein DNA binding;  protein protein interaction;  protein stability;  transcription regulation;  zinc finger motif;  biological model;  chemistry;  metabolism;  nucleotide sequence;  X ray crystallography, Base Sequence;  Binding Sites;  Crystallography, X-Ray;  DNA;  DNA-Binding Proteins;  GATA1 Transcription Factor;  LIM Domain Proteins;  Models, Biological;  Transcription Factors},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, Australia; email: jacqui.matthews@sydney.edu.au},\npublisher={Blackwell Publishing Ltd},\nissn={09618368},\ncoden={PRCIE},\npubmed_id={26234528},\nlanguage={English},\nabbrev_source_title={Protein Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n GATA2 is required for lymphatic vessel valve development and maintenance.\n \n \n \n \n\n\n \n Kazenwadel, J.; Betterman, K.; Chong, C.; Stokes, P.; Lee, Y.; Secker, G.; Agalarov, Y.; Demir, C.; Lawrence, D.; Sutton, D.; Tabruyn, S.; Miura, N.; Salminen, M.; Petrova, T.; Matthews, J.; Hahn, C.; Scott, H.; and Harvey, N.\n\n\n \n\n\n\n Journal of Clinical Investigation, 125(8): 2879-2994. 2015.\n cited By 140\n\n\n\n
\n\n\n\n \n \n $\"GATA2$ 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

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@ARTICLE{Kazenwadel20152879,\nauthor={Kazenwadel, J. and Betterman, K.L. and Chong, C.-E. and Stokes, P.H. and Lee, Y.K. and Secker, G.A. and Agalarov, Y. and Demir, C.S. and Lawrence, D.M. and Sutton, D.L. and Tabruyn, S.P. and Miura, N. and Salminen, M. and Petrova, T.V. and Matthews, J.M. and Hahn, C.N. and Scott, H.S. and Harvey, N.L.},\ntitle={GATA2 is required for lymphatic vessel valve development and maintenance},\njournal={Journal of Clinical Investigation},\nyear={2015},\nvolume={125},\nnumber={8},\npages={2879-2994},\ndoi={10.1172/JCI78888},\nnote={cited By 140},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84939243994&doi=10.1172%2fJCI78888&partnerID=40&md5=28a1b01e2bd5131004f9707a1b2c9955},\naffiliation={Centre for Cancer Biology, University of South Australia, SA Pathology, PO Box 14, Rundle Mall, Adelaide, SA  5000, Australia; Centre for Cancer Biology, University of South Australia, Department of Molecular Pathology, Adelaide, SA, Australia; School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia; Department of Oncology, University Hospital of Lausanne, University of Lausanne, Lausanne, Switzerland; Australian Cancer Research Foundation (ACRF) Cancer Genomics Facility, University of South Australia, SA Pathology, Adelaide, SA, Australia; School of Molecular and Biomedical Bioscience, University of Adelaide, Adelaide, SA, Australia; Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan; Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland; École Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland; School of Medicine, University of Adelaide, Adelaide, SA, Australia},\nabstract={Heterozygous germline mutations in the zinc finger transcription factor GATA2 have recently been shown to underlie a range of clinical phenotypes, including Emberger syndrome, a disorder characterized by lymphedema and predisposition to myelodysplastic syndrome/acute myeloid leukemia (MDS/AML). Despite well-defined roles in hematopoiesis, the functions of GATA2 in the lymphatic vasculature and the mechanisms by which GATA2 mutations result in lymphedema have not been characterized. Here, we have provided a molecular explanation for lymphedema predisposition in a subset of patients with germline GATA2 mutations. Specifically, we demonstrated that Emberger-associated GATA2 missense mutations result in complete loss of GATA2 function, with respect to the capacity to regulate the transcription of genes that are important for lymphatic vessel valve development. We identified a putative enhancer element upstream of the key lymphatic transcriptional regulator PROX1 that is bound by GATA2, and the transcription factors FOXC2 and NFATC1. Emberger GATA2 missense mutants had a profoundly reduced capacity to bind this element. Conditional Gata2 deletion in mice revealed that GATA2 is required for both development and maintenance of lymphovenous and lymphatic vessel valves. Together, our data unveil essential roles for GATA2 in the lymphatic vasculature and explain why a select catalogue of human GATA2 mutations results in lymphedema. © 2015, American Society for Clinical Investigation. All rights reserved.},\nkeywords={beta galactosidase;  protein PROX1;  transcription factor FOXC2;  transcription factor GATA 1;  transcription factor GATA 2;  transcription factor GATA 3;  transcription factor NFATC1;  unclassified drug;  forkhead transcription factor;  GATA2 protein, human;  Gata2 protein, mouse;  homeodomain protein;  NFATC1 protein, human;  Nfatc1 protein, mouse;  prospero-related homeobox 1 protein;  transcription factor FOXC2;  transcription factor GATA 2;  transcription factor NFAT;  tumor suppressor protein, adult;  Article;  binding affinity;  capillary endothelial cell;  carboxy terminal sequence;  controlled study;  embryo;  enhancer region;  gene deletion;  gene locus;  genetic transcription;  germline mutation;  haploinsufficiency;  heart valve;  hematopoiesis;  human;  human cell;  loss of function mutation;  lymphangiogenesis;  lymphedema;  missense mutation;  mouse;  nonhuman;  oscillation;  priority journal;  protein DNA binding;  protein domain;  protein folding;  protein protein interaction;  reporter gene;  transcription initiation site;  transcription regulation;  animal;  embryology;  genetics;  K562 cell line;  lymph vessel;  metabolism;  mutation;  pathology, Animals;  Enhancer Elements, Genetic;  Forkhead Transcription Factors;  GATA2 Transcription Factor;  Gene Deletion;  Homeodomain Proteins;  Humans;  K562 Cells;  Lymphatic Vessels;  Lymphedema;  Mice;  Mutation;  NFATC Transcription Factors;  Tumor Suppressor Proteins},\ncorrespondence_address1={Harvey, N.L.; Centre for Cancer Biology, PO Box 14, Rundle Mall, Australia; email: Natasha.harvey@unisa.edu.au},\npublisher={American Society for Clinical Investigation},\nissn={00219738},\ncoden={JCINA},\npubmed_id={26214525},\nlanguage={English},\nabbrev_source_title={J. Clin. Invest.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Biochemical and biophysical characterisation of haloalkane dehalogenases DmrA and DmrB in Mycobacterium strain JS60 and their role in growth on haloalkanes.\n \n \n \n \n\n\n \n Fung, H.; Gadd, M.; Drury, T.; Cheung, S.; Guss, J.; Coleman, N.; and Matthews, J.\n\n\n \n\n\n\n Molecular Microbiology, 97(3): 439-453. 2015.\n cited By 18\n\n\n\n
\n\n\n\n \n \n $\"Biochemical$ 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

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@ARTICLE{Fung2015439,\nauthor={Fung, H.K.H. and Gadd, M.S. and Drury, T.A. and Cheung, S. and Guss, J.M. and Coleman, N.V. and Matthews, J.M.},\ntitle={Biochemical and biophysical characterisation of haloalkane dehalogenases DmrA and DmrB in Mycobacterium strain JS60 and their role in growth on haloalkanes},\njournal={Molecular Microbiology},\nyear={2015},\nvolume={97},\nnumber={3},\npages={439-453},\ndoi={10.1111/mmi.13039},\nnote={cited By 18},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84937972083&doi=10.1111%2fmmi.13039&partnerID=40&md5=8a597bc56bf22f77b6ea682cdc8bac28},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW  2006, Australia; Department of Biology, University of York, United Kingdom; College of Life Sciences, University of Dundee, United Kingdom; Department of Biochemistry, University of Cambridge, United Kingdom},\nabstract={Haloalkane dehalogenases (HLDs) catalyse the hydrolysis of haloalkanes to alcohols, offering a biological solution for toxic haloalkane industrial wastes. Hundreds of putative HLD genes have been identified in bacterial genomes, but relatively few enzymes have been characterised. We identified two novel HLDs in the genome of Mycobacterium rhodesiae strain JS60, an isolate from an organochlorine-contaminated site: DmrA and DmrB. Both recombinant enzymes were active against C2-C6 haloalkanes, with a preference for brominated linear substrates. However, DmrA had higher activity against a wider range of substrates. The kinetic parameters of DmrA with 4-bromobutyronitrile as a substrate were Km=1.9±0.2mM, kcat=3.1±0.2s-1. DmrB showed the highest activity against 1-bromohexane. DmrA is monomeric, whereas DmrB is tetrameric. We determined the crystal structure of selenomethionyl DmrA to 1.7Å resolution. A spacious active site and alternate conformations of a methionine side-chain in the slot access tunnel may contribute to the broad substrate activity of DmrA. We show that M.rhodesiaeJS60 can utilise 1-iodopropane, 1-iodobutane and 1-bromobutane as sole carbon and energy sources. This ability appears to be conferred predominantly through DmrA, which shows significantly higher levels of upregulation in response to haloalkanes than DmrB. © 2015 John Wiley & Sons Ltd.},\nkeywords={4 brombutyronitrile;  bromobutane;  bromohexane;  butane;  butyronitrile;  carbon;  haloalkane dehalogenase;  hexane;  hydrolase;  iodobutane;  iodopropane;  methionine;  organochlorine derivative;  propane;  selenomethionine;  unclassified drug;  alkane;  bacterial DNA;  haloalkane dehalogenase;  halogenated hydrocarbon;  hydrolase, Article;  bacterial genome;  bacterial growth;  bacterial strain;  biochemistry;  biophysics;  carbon source;  controlled study;  crystal structure;  DmrA gene;  DmrB gene;  energy resource;  enzyme active site;  enzyme activity;  enzyme conformation;  enzyme kinetics;  enzyme substrate;  gene identification;  Mycobacterium;  Mycobacterium rhodesiae;  nonhuman;  phylogeny;  priority journal;  proton nuclear magnetic resonance;  sequence alignment;  soil pollution;  upregulation;  chemistry;  DNA sequence;  energy metabolism;  enzyme specificity;  enzymology;  genetics;  growth, development and aging;  hydrolysis;  isolation and purification;  kinetics;  metabolism;  microbiology;  molecular genetics;  Mycobacterium;  protein conformation;  X ray crystallography, Bacteria (microorganisms);  Mycobacterium;  Mycobacterium rhodesiae, Alkanes;  Carbon;  Catalytic Domain;  Crystallography, X-Ray;  DNA, Bacterial;  Energy Metabolism;  Environmental Microbiology;  Hydrocarbons, Halogenated;  Hydrolases;  Hydrolysis;  Kinetics;  Molecular Sequence Data;  Mycobacterium;  Protein Conformation;  Sequence Analysis, DNA;  Substrate Specificity},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, Australia; email: jacqui.matthews@sydney.edu.au},\npublisher={Blackwell Publishing Ltd},\nissn={0950382X},\ncoden={MOMIE},\npubmed_id={25899475},\nlanguage={English},\nabbrev_source_title={Mol. Microbiol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Editing the genome to introduce a beneficial naturally occurring mutation associated with increased fetal globin.\n \n \n \n \n\n\n \n Wienert, B.; Funnell, A.; Norton, L.; Pearson, R.; Wilkinson-White, L.; Lester, K.; Vadolas, J.; Porteus, M.; Matthews, J.; Quinlan, K.; and Crossley, M.\n\n\n \n\n\n\n Nature Communications, 6. 2015.\n cited By 83\n\n\n\n
\n\n\n\n \n \n $\"Editing$ 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

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@ARTICLE{Wienert2015,\nauthor={Wienert, B. and Funnell, A.P.W. and Norton, L.J. and Pearson, R.C.M. and Wilkinson-White, L.E. and Lester, K. and Vadolas, J. and Porteus, M.H. and Matthews, J.M. and Quinlan, K.G.R. and Crossley, M.},\ntitle={Editing the genome to introduce a beneficial naturally occurring mutation associated with increased fetal globin},\njournal={Nature Communications},\nyear={2015},\nvolume={6},\ndoi={10.1038/ncomms8085},\nart_number={7085},\nnote={cited By 83},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84929630294&doi=10.1038%2fncomms8085&partnerID=40&md5=712825834eed9fb2f4ec7593235abbfd},\naffiliation={School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW  2052, Australia; School of Molecular Bioscience, University of Sydney, Sydney, NSW  2006, Australia; Cell and Gene Therapy Research Group, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC  3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC  3052, Australia; Department of Pediatrics, Stanford University, Stanford, CA  94304, United States},\nabstract={Genetic disorders resulting from defects in the adult globin genes are among the most common inherited diseases. Symptoms worsen from birth as fetal γ-globin expression is silenced. Genome editing could permit the introduction of beneficial single-nucleotide variants to ameliorate symptoms. Here, as proof of concept, we introduce the naturally occurring Hereditary Persistance of Fetal Haemoglobin (HPFH)-175T>C point mutation associated with elevated fetal γ-globin into erythroid cell lines. We show that this mutation increases fetal globin expression through de novo recruitment of the activator TAL1 to promote chromatin looping of distal enhancers to the modified γ-globin promoter. © 2015 Macmillan Publishers Limited. All rights reserved.},\nkeywords={fetoprotein;  globin;  hemoglobin F;  hemoglobin gamma chain;  transcription activator like effector nuclease;  transcription factor TAL1;  basic helix loop helix transcription factor;  chromatin;  hemoglobin F;  oncoprotein;  TAL1 protein, human;  Tal1 protein, mouse, gene expression;  genome;  mutation;  symptom, animal cell;  Article;  chromatin;  controlled study;  erythroid cell;  gene expression;  gene mutation;  genetic engineering;  genome;  genome editing;  globin gene;  human;  human cell;  K562 cell line;  nonhuman;  point mutation;  promoter region;  protein expression;  animal;  binding site;  dimerization;  gene silencing;  genetics;  molecular genetics;  mouse;  mutation;  nucleotide sequence;  single nucleotide polymorphism;  site directed mutagenesis;  transgenic mouse, Animals;  Base Sequence;  Basic Helix-Loop-Helix Transcription Factors;  Binding Sites;  Chromatin;  Dimerization;  Fetal Hemoglobin;  Gene Silencing;  Genome;  Humans;  K562 Cells;  Mice;  Mice, Transgenic;  Molecular Sequence Data;  Mutagenesis, Site-Directed;  Mutation;  Point Mutation;  Polymorphism, Single Nucleotide;  Promoter Regions, Genetic;  Proto-Oncogene Proteins},\ncorrespondence_address1={Crossley, M.; School of Biotechnology and Biomolecular Sciences, University of New South WalesAustralia},\npublisher={Nature Publishing Group},\nissn={20411723},\npubmed_id={25971621},\nlanguage={English},\nabbrev_source_title={Nat. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers.\n \n \n \n \n\n\n \n Harten, S.; Oey, H.; Bourke, L.; Bharti, V.; Isbel, L.; Daxinger, L.; Faou, P.; Robertson, N.; Matthews, J.; and Whitelaw, E.\n\n\n \n\n\n\n BMC Biology, 13(1). 2015.\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\n\n\n

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@ARTICLE{Harten2015,\nauthor={Harten, S.K. and Oey, H. and Bourke, L.M. and Bharti, V. and Isbel, L. and Daxinger, L. and Faou, P. and Robertson, N. and Matthews, J.M. and Whitelaw, E.},\ntitle={The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers},\njournal={BMC Biology},\nyear={2015},\nvolume={13},\nnumber={1},\ndoi={10.1186/s12915-015-0128-2},\nart_number={21},\nnote={cited By 14},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84925852266&doi=10.1186%2fs12915-015-0128-2&partnerID=40&md5=9101711db23a95af6fe0df9fca436a39},\naffiliation={Epigenetics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD  4006, Australia; Department of Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC  3086, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia; Department of Biochemistry, La Trobe University, Melbourne, VIC  3086, Australia; School of Molecular Bioscience, University of Sydney, Sydney, NSW  2006, Australia; Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands},\nabstract={Background: We recently identified a novel protein, Rearranged L-myc fusion (Rlf), that is required for DNA hypomethylation and transcriptional activity at two specific regions of the genome known to be sensitive to epigenetic gene silencing. To identify other loci affected by the absence of Rlf, we have now analysed 12 whole genome bisulphite sequencing datasets across three different embryonic tissues/stages from mice wild-type or null for Rlf. Results: Here we show that the absence of Rlf results in an increase in DNA methylation at thousands of elements involved in transcriptional regulation and many of the changes occur at enhancers and CpG island shores. ChIP-seq for H3K4me1, a mark generally found at regulatory elements, revealed associated changes at many of the regions that are differentially methylated in the Rlf mutants. RNA-seq showed that the numerous effects of the absence of Rlf on the epigenome are associated with relatively subtle effects on the mRNA population. In vitro studies suggest that Rlf's zinc fingers have the capacity to bind DNA and that the protein interacts with other known epigenetic modifiers. Conclusion: This study provides the first evidence that the epigenetic modifier Rlf is involved in the maintenance of DNA methylation at enhancers and CGI shores across the genome. © Harten et al.; licensee BioMed Central.},\nauthor_keywords={Bisulphite;  DNA methylation;  Enhancers;  Rearranged L-Myc Fusion;  Rlf},\nkeywords={Murinae;  Mus, chromatin;  DNA;  histone;  lysine;  protein binding;  Rgl2 protein, mouse;  transcription factor, allele;  animal;  antibody specificity;  chromatin;  CpG island;  DNA methylation;  DNA replication;  embryology;  enhancer region;  exon;  gene expression regulation;  gene locus;  genetic epigenesis;  genetic transcription;  genetics;  HEK293 cell line;  homozygote;  human;  liver;  metabolism;  modifier gene;  mouse;  mutation, Alleles;  Animals;  Chromatin;  CpG Islands;  DNA;  DNA Methylation;  DNA Replication;  Enhancer Elements, Genetic;  Epigenesis, Genetic;  Exons;  Gene Expression Regulation, Developmental;  Genes, Modifier;  Genetic Loci;  HEK293 Cells;  Histones;  Homozygote;  Humans;  Liver;  Lysine;  Mice;  Mutation;  Organ Specificity;  Protein Binding;  Transcription Factors;  Transcription, Genetic},\ncorrespondence_address1={Whitelaw, E.; Department of Genetics, La Trobe Institute for Molecular Science, La Trobe UniversityAustralia},\npublisher={BioMed Central Ltd.},\nissn={17417007},\npubmed_id={25857663},\nlanguage={English},\nabbrev_source_title={BMC Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Protein complex hierarchy and translocation gene products.\n \n \n \n \n\n\n \n Matthews, J.\n\n\n \n\n\n\n Springer International Publishing, 2015.\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 abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@BOOK{Matthews2015447,\nauthor={Matthews, J.M.},\ntitle={Protein complex hierarchy and translocation gene products},\njournal={Chromosomal Translocations and Genome Rearrangements in Cancer},\nyear={2015},\npages={447-466},\ndoi={10.1007/978-3-319-19983-2_21},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85016813521&doi=10.1007%2f978-3-319-19983-2_21&partnerID=40&md5=2a4e8d3246bfdb8807394318eff74f56},\naffiliation={School of Molecular Bioscience, The University of Sydney, Sydney, Australia},\nabstract={Disease-causing chromosomal translocations tend to cause the upregulated expression of proteins, or result in fusion proteins with altered functionality. Four sets of chromosomal translocations are presented as case studies to illustrate how the protein products of chromosomal translocations disrupt normal cellular processes through a range of different mechanisms. For translocations affecting LMO2 and MYC expression, alterations to transcriptional regulation ultimately cause disease. In the case of the Philadelphia Chromosome, BCR-ABL1 disrupts cell signalling and cell cycle regulation by generating an always active form of the ABL1 tyrosine kinase. Upregulation of BCL2 blocks apoptosis. In each case the molecular basis of activity, and strategies for inhibition by directly targeting the disease causing proteins are summarized. © Springer International Publishing Switzerland 2015.},\nauthor_keywords={Apoptosis;  Fusion proteins;  Kinases;  Protein over-expression;  Transcriptional regulation},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, Australia; email: jacqueline.matthews@sydney.edu.au},\npublisher={Springer International Publishing},\nisbn={9783319199832; 9783319199825},\nlanguage={English},\nabbrev_source_title={Chromosomal Translocations and Genome Rearrangements in Cancer},\ndocument_type={Book Chapter},\nsource={Scopus},\n}\n\n

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\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

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@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

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\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

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@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

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\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

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@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

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\n \n\n \n \n \n \n \n \n The PA207 peptide inhibitor of LIM-only protein 2 (Lmo2) targets zinc finger domains in a non-specific manner.\n \n \n \n \n\n\n \n Wilkinson-White, L.; and Matthews, J.\n\n\n \n\n\n\n Protein and Peptide Letters, 21(2): 132-139. 2014.\n cited By 2\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

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@ARTICLE{Wilkinson-White2014132,\nauthor={Wilkinson-White, L. and Matthews, J.M.},\ntitle={The PA207 peptide inhibitor of LIM-only protein 2 (Lmo2) targets zinc finger domains in a non-specific manner},\njournal={Protein and Peptide Letters},\nyear={2014},\nvolume={21},\nnumber={2},\npages={132-139},\ndoi={10.2174/09298665113206660116},\nnote={cited By 2},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84893293805&doi=10.2174%2f09298665113206660116&partnerID=40&md5=104c0e6889bfe39742117f92032dd445},\naffiliation={School of Molecular Bioscience, University of Sydney, NSW 2006, Australia},\nabstract={Peptide aptamers of LIM-only protein 2 (Lmo2) were previously used to successfully treat Lmo2-induced tumours in a mouse model of leukaemia. Here we show that the Lmo2 aptamer PA207, either as a free peptide or fused to thioredoxin Trx-PA207, causes purified Lmo2 to precipitate rather than binding to a defined surface on the protein. Stabilisation of Lmo2 through interaction with LIM domain binding protein 1 (Ldb1), a normal binding partner of Lmo2, abrogates this effect. The addition of free zinc causes Trx-PA207 to self associate, suggesting that PA207 destabilises Lmo2 by modulating normal zinc-coordination in the LIM domains. GST-pulldown experiments with other Lmo and Gata proteins indicates that PA207 can bind to a range of zinc finger proteins. Thus, PA207 and other cysteine-containing peptide aptamers for Lmo2 may form a class of general zinc finger inhibitors. © 2014 Bentham Science Publishers.},\nauthor_keywords={Chemical shift perturbation experiments;  Lmo2;  Peptide aptamer;  Peptide-protein interaction;  Protein destabilisation;  Zinc co-ordination},\nkeywords={basic helix loop helix transcription factor;  glutathione transferase;  LIM domain binding protein 1;  LIM only protein 2;  pa 207;  peptide aptamer;  regulator protein;  thioredoxin;  unclassified drug;  zinc finger protein, amino terminal sequence;  article;  carboxy terminal sequence;  controlled study;  drug protein binding;  in vitro study;  molecular interaction;  molecular weight;  nuclear magnetic resonance;  protein binding;  protein domain;  protein protein interaction;  protein purification;  protein stability;  protein targeting;  protein unfolding, DNA-Binding Proteins;  Peptides;  Protein Multimerization;  Protein Stability;  Protein Structure, Tertiary;  Protein Unfolding;  Substrate Specificity;  Transcription Factors;  Zinc;  Zinc Fingers},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, , NSW 2006, Australia; email: jacqui.matthews@sydney.edu.au},\npublisher={Bentham Science Publishers},\nissn={09298665},\ncoden={PPELE},\npubmed_id={24188027},\nlanguage={English},\nabbrev_source_title={Protein Pept. Lett.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n 2013\n \n \n (11)\n \n \n

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\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

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@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

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\n \n\n \n \n \n \n \n \n A structural basis for the regulation of the LIM-homeodomain protein islet 1 (Isl1) by intra- and intermolecular interactions.\n \n \n \n \n\n\n \n Gadd, M.; Jacques, D.; Nisevic, I.; Craig, V.; Kwan, A.; Guss, J.; and Matthews, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 288(30): 21924-21935. 2013.\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

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@ARTICLE{Gadd201321924,\nauthor={Gadd, M.S. and Jacques, D.A. and Nisevic, I. and Craig, V.J. and Kwan, A.H. and Guss, J.M. and Matthews, J.M.},\ntitle={A structural basis for the regulation of the LIM-homeodomain protein islet 1 (Isl1) by intra- and intermolecular interactions},\njournal={Journal of Biological Chemistry},\nyear={2013},\nvolume={288},\nnumber={30},\npages={21924-21935},\ndoi={10.1074/jbc.M113.478586},\nnote={cited By 18},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84881241858&doi=10.1074%2fjbc.M113.478586&partnerID=40&md5=cfc9fa9ab03999ad0f1b50be0b2d6883},\naffiliation={School of Molecular Bioscience, Building G08, University of Sydney, NSW 2006, Australia; Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Ave., Cambridge CB2 0QH, United Kingdom; Novartis Insts. for BioMedical Research, Klybeckstr. 141, 4057 Basel, Switzerland},\nabstract={Background: A putative intramolecular interaction in the Islet 1 (Isl1) transcription factor inhibits DNA binding. Results: An intramolecular interaction between the LIM domains and LIM homeobox 3 (Lhx3)-binding domain in Isl1 was characterized. Conclusion: The intramolecular interaction within Isl1 is weak but specific. Significance: This interaction likely prevents unproductive binding in the absence of cofactor proteins. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Binding domain;  Cofactors;  DNA binding;  Intermolecular interactions;  Intramolecular interactions;  LIM domain;  Structural basis, Biochemistry;  Biology, Proteins, binding protein;  DNA;  LIM domain binding protein 1;  LIM homeodomain protein;  LIM homeodomain protein Islet 1;  transcription factor LHX3;  unclassified drug, amino acid composition;  amino acid sequence;  amino acid substitution;  article;  binding affinity;  controlled study;  crystal structure;  DNA binding;  genetic complementation;  inhibition kinetics;  molecular cloning;  molecular interaction;  mouse;  nonhuman;  nuclear magnetic resonance spectroscopy;  nucleotide sequence;  priority journal;  protein aggregation;  protein binding;  protein domain;  protein expression;  protein structure;  structural homology;  two hybrid system, Competitive Binding;  LIM-Homeodomain Transcription Factors;  Protein-Nucleic Acid Interaction;  Protein-Protein Interactions;  Structural Biology;  Tissue-specific Transcription Factors;  Transcription Regulation, Amino Acid Sequence;  Animals;  Binding Sites;  Crystallography, X-Ray;  LIM-Homeodomain Proteins;  Mice;  Models, Molecular;  Molecular Sequence Data;  Mutation;  Protein Binding;  Protein Structure, Tertiary;  Saccharomyces cerevisiae;  Transcription Factors;  Two-Hybrid System Techniques},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, , NSW 2006, Australia; email: jacqui.matthews@sydney.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={23750000},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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@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

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\n \n\n \n \n \n \n \n \n Synthesis of peptides and glycopeptides with polyproline II helical topology as potential antifreeze molecules.\n \n \n \n \n\n\n \n Corcilius, L.; Santhakumar, G.; Stone, R.; Capicciotti, C.; Joseph, S.; Matthews, J.; Ben, R.; and Payne, R.\n\n\n \n\n\n\n Bioorganic and Medicinal Chemistry, 21(12): 3569-3581. 2013.\n cited By 20\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

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@ARTICLE{Corcilius20133569,\nauthor={Corcilius, L. and Santhakumar, G. and Stone, R.S. and Capicciotti, C.J. and Joseph, S. and Matthews, J.M. and Ben, R.N. and Payne, R.J.},\ntitle={Synthesis of peptides and glycopeptides with polyproline II helical topology as potential antifreeze molecules},\njournal={Bioorganic and Medicinal Chemistry},\nyear={2013},\nvolume={21},\nnumber={12},\npages={3569-3581},\ndoi={10.1016/j.bmc.2013.02.025},\nnote={cited By 20},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84878231115&doi=10.1016%2fj.bmc.2013.02.025&partnerID=40&md5=bdbe2a81552ce6384d57365da1bcc7d1},\naffiliation={School of Chemistry, University of Sydney, NSW 2006, Australia; Department of Chemistry, University of Ottawa, Ottawa, K1N 6N5, Canada; School of Molecular Bioscience, University of Sydney, NSW 2006, Australia},\nabstract={A library of peptides and glycopeptides containing (4R)-hydroxy-l-proline (Hyp) residues were designed with a view to providing stable polyproline II (PPII) helical molecules with antifreeze activity. A library of dodecapeptides containing contiguous Hyp residues or an Ala-Hyp-Ala tripeptide repeat sequence were synthesized with and without α-O-linked N-acetylgalactosamine and α-O-linked galactose-β-(1→3)-N-acetylgalactosamine appended to the peptide backbone. All (glyco)peptides possessed PPII helical secondary structure with some showing significant thermal stability. The majority of the (glyco)peptides did not exhibit thermal hysteresis (TH) activity and were not capable of modifying the morphology of ice crystals. However, an unglycosylated Ala-Hyp-Ala repeat peptide did show significant TH and ice crystal re-shaping activity suggesting that it was capable of binding to the surface of ice. All (glyco)peptides synthesized displayed some ice recrystallization inhibition (IRI) activity with unglycosylated peptides containing the Ala-Hyp-Ala motif exhibiting the most potent inhibitory activity. Interestingly, although glycosylation is critical to the activity of native antifreeze glycoproteins (AFGPs) that possess an Ala-Thr-Ala tripeptide repeat, this same structural modification is detrimental to the antifreeze activity of the Ala-Hyp-Ala repeat peptides studied here. © 2013 Elsevier Ltd. All rights reserved.},\nauthor_keywords={Antifreeze glycoprotein;  Carbohydrate;  Glycopeptides;  Hydroxyproline;  Polyproline II helix},\nkeywords={antifreeze protein;  glycopeptide;  hydroxyproline;  polyproline II;  unclassified drug, alpha helix;  amino acid sequence;  article;  controlled study;  crystal structure;  crystallization;  hysteresis;  peptide library;  peptide synthesis;  protein glycosylation;  protein localization;  protein secondary structure;  structure activity relation;  structure analysis;  thermostability, Antifreeze Proteins;  Molecular Structure;  Peptide Library;  Peptides},\ncorrespondence_address1={Payne, R.J.; School of Chemistry, , NSW 2006, Australia; email: richard.payne@sydney.edu.au},\nissn={09680896},\ncoden={BMECE},\npubmed_id={23523384},\nlanguage={English},\nabbrev_source_title={Bioorg. Med. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n No evidence for cumulative effects in a Dnmt3b hypomorph across multiple generations.\n \n \n \n \n\n\n \n Youngson, N.; Epp, T.; Roberts, A.; Daxinger, L.; Ashe, A.; Huang, E.; Lester, K.; Harten, S.; Kay, G.; Cox, T.; Matthews, J.; Chong, S.; and Whitelaw, E.\n\n\n \n\n\n\n Mammalian Genome, 24(5-6): 206-217. 2013.\n cited By 9\n\n\n\n
\n\n\n\n \n \n $\"No$ 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

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@ARTICLE{Youngson2013206,\nauthor={Youngson, N.A. and Epp, T. and Roberts, A.R. and Daxinger, L. and Ashe, A. and Huang, E. and Lester, K.L. and Harten, S.K. and Kay, G.F. and Cox, T. and Matthews, J.M. and Chong, S. and Whitelaw, E.},\ntitle={No evidence for cumulative effects in a Dnmt3b hypomorph across multiple generations},\njournal={Mammalian Genome},\nyear={2013},\nvolume={24},\nnumber={5-6},\npages={206-217},\ndoi={10.1007/s00335-013-9451-5},\nnote={cited By 9},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84879549776&doi=10.1007%2fs00335-013-9451-5&partnerID=40&md5=93e0748bce289c2ff2dfe5e04c3eb2c9},\naffiliation={Queensland Institute of Medical Research, Brisbane, QLD 4006, Australia; Department of Pharmacology, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Institute of Molecular Genetics of the ASCR V. V. I., Vídeňská 1083, 142 20 Prague 4, Czech Republic; School of Biomolecular and Physical Sciences, Griffith University, Nathan, QLD 4111, Australia; School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia; Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, United States; Mater Research TRI, 37 Kent Street, Woolloongabba, QLD 4102, Australia; School of Molecular Sciences, Department of Genetics, La Trobe Institute for Molecular Science, Melbourne, VIC 3086, Australia},\nabstract={Observations of inherited phenotypes that cannot be explained solely through genetic inheritance are increasing. Evidence points to transmission of non-DNA molecules in the gamete as mediators of the phenotypes. However, in most cases it is unclear what the molecules are, with DNA methylation, chromatin proteins, and small RNAs being the most prominent candidates. From a screen to generate novel mouse mutants of genes involved in epigenetic reprogramming, we produced a DNA methyltransferase 3b allele that is missing exon 13. Mice that are homozygous for the mutant allele have smaller stature and reduced viability, with particularly high levels of female post-natal death. Reduced DNA methylation was also detected at telocentric repeats and the X-linked Hprt gene. However, none of the abnormal phenotypes or DNA methylation changes worsened with multiple generations of homozygous mutant inbreeding. This suggests that in our model the abnormalities are reset each generation and the processes of transgenerational epigenetic reprogramming are effective in preventing their inheritance. © 2013 Springer Science+Business Media New York.},\nkeywords={DNA methyltransferase 3B, allele;  animal experiment;  animal genetics;  animal model;  article;  controlled study;  death;  DNA methylation;  DNMT3B gene;  embryo;  epigenetics;  exon;  female;  gene;  gene deletion;  gene function;  gene synthesis;  genetic analysis;  genetic disorder;  genetic line;  genetic screening;  heredity;  homozygote;  Hprt gene;  inbreeding;  male;  mouse;  mouse mutant;  nonhuman;  nuclear reprogramming;  postnatal death;  sex difference;  short stature, Alleles;  Animals;  Base Sequence;  DNA (Cytosine-5-)-Methyltransferase;  DNA Methylation;  Epigenesis, Genetic;  Exons;  Female;  Homozygote;  Male;  Mice;  Mice, Transgenic;  Molecular Sequence Data;  Pedigree, Mus},\ncorrespondence_address1={Whitelaw, E.; Queensland Institute of Medical Research, Brisbane, QLD 4006, Australia; email: e.whitelaw@latrobe.edu.au},\nissn={09388990},\ncoden={MAMGE},\npubmed_id={23636699},\nlanguage={English},\nabbrev_source_title={Mamm. Genome},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n The tandem β-zipper: Modular binding of tandem domains and linear motifs.\n \n \n \n \n\n\n \n Matthews, J.; and Potts, J.\n\n\n \n\n\n\n FEBS Letters, 587(8): 1164-1171. 2013.\n cited By 19\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

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@ARTICLE{Matthews20131164,\nauthor={Matthews, J.M. and Potts, J.R.},\ntitle={The tandem β-zipper: Modular binding of tandem domains and linear motifs},\njournal={FEBS Letters},\nyear={2013},\nvolume={587},\nnumber={8},\npages={1164-1171},\ndoi={10.1016/j.febslet.2013.01.002},\nnote={cited By 19},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84876018623&doi=10.1016%2fj.febslet.2013.01.002&partnerID=40&md5=04acd8a8d05c49cac908b68bf92d6632},\naffiliation={School of Molecular Bioscience, University of Sydney, NSW 2006, Australia; Department of Biology, University of York, York YO10 5DD, United Kingdom},\nabstract={The tandem β-zipper protein-protein binding interface involves an intrinsically disordered protein (IDP) binding two or more globular domains through β-sheet-augmentation in a modular fashion, and represents a paradigm in IDP-mediated protein-protein interactions. While characterised tandem β-zippers are rare, known examples are associated with diverse biological processes. A combination of their advantages (binding specificity and the ability to generate high affinity binding sites by linking multiple lower affinity motifs) and the prevalence of both tandem domains and IDPs points to the existence of many more β-zippers in nature. The characterisation of these interactions has greatly enhanced the understanding of the biological systems involved but given their apparent tolerance to mutation, detecting other tandem β-zipper interactions using bioinformatics may be challenging. © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.},\nauthor_keywords={Binding specificity;  Protein-protein interaction;  Short linear motif;  Tandem β-zipper;  Tandem binding},\nkeywords={binding protein;  fibronectin binding protein;  LIM protein;  tandem beta zipper protein;  unclassified drug, beta sheet;  binding affinity;  binding kinetics;  binding site;  binding specificity;  bioinformatics;  human;  mutation;  nonhuman;  prevalence;  priority journal;  protein binding;  protein domain;  protein function;  protein motif;  protein protein interaction;  protein structure;  review, Amino Acid Motifs;  Amino Acid Sequence;  Models, Molecular;  Molecular Sequence Data;  Mutation;  Protein Binding;  Protein Conformation;  Protein Folding;  Protein Structure, Secondary;  Protein Structure, Tertiary;  Proteins;  Sequence Homology, Amino Acid},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, , NSW 2006, Australia; email: jacqui.matthews@sydney.edu.au},\nissn={00145793},\ncoden={FEBLA},\npubmed_id={23333654},\nlanguage={English},\nabbrev_source_title={FEBS Lett.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

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\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

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@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

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\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

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@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

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\n \n\n \n \n \n \n \n \n LIM-domain Proteins.\n \n \n \n \n\n\n \n Matthews, J.\n\n\n \n\n\n\n Elsevier Inc., 2013.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"LIM-domain$ 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

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@BOOK{Matthews2013242,\nauthor={Matthews, J.M.},\ntitle={LIM-domain Proteins},\njournal={Brenner's Encyclopedia of Genetics: Second Edition},\nyear={2013},\npages={242-245},\ndoi={10.1016/B978-0-12-374984-0.00867-6},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85043279943&doi=10.1016%2fB978-0-12-374984-0.00867-6&partnerID=40&md5=8648948a1d5ce86099ca7ce887db98ff},\naffiliation={The University of Sydney, Sydney, NSW, Australia},\nabstract={LIM domains are zinc fingers that coordinate two zinc ions and that mediate protein-protein interactions. They are found in arrays of 1-5 LIM domains in a wide variety of proteins inside the cell, and may be accompanied by one or more other types of protein-protein interaction domains and catalytic domains. LIM proteins tend to function by regulating transcriptional events through recruitment of transcription factors (or in the case of LIM-homeodomain proteins by binding directly to DNA through the homeodomain) and/or are involved in remodeling of the cytoskeleton. Many LIM domain proteins have both of these activities and appear to shuttle in and out of the nucleus in response to stimuli, mediating communication between the major compartments of the cell. © 2013 Elsevier Inc. All rights reserved.},\nauthor_keywords={Cell-type specification;  Cysteine/histidine-rich proteins;  Cytoskeletal organization;  Focal adhesion complexes;  Four-and-a-half LIM domain proteins;  Intracellular signaling;  LIM domain;  LIM-homeodomain transcription factors;  LIM-only proteins;  Neural development;  Protein-protein interactions;  Transcription complexes;  Transcriptional regulation;  Zinc finger},\ncorrespondence_address1={Matthews, J.M.; The University of SydneyAustralia},\npublisher={Elsevier Inc.},\nisbn={9780080961569; 9780123749840},\nlanguage={English},\nabbrev_source_title={Brenner's Encycl. of Genet.: Second Ed.},\ndocument_type={Book Chapter},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n LIM-domain-only proteins in cancer.\n \n \n \n \n\n\n \n Matthews, J.; Lester, K.; Joseph, S.; and Curtis, D.\n\n\n \n\n\n\n Nature Reviews Cancer, 13(2): 111-122. 2013.\n cited By 88\n\n\n\n
\n\n\n\n \n \n $\"LIM-domain-only$ 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

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@ARTICLE{Matthews2013111,\nauthor={Matthews, J.M. and Lester, K. and Joseph, S. and Curtis, D.J.},\ntitle={LIM-domain-only proteins in cancer},\njournal={Nature Reviews Cancer},\nyear={2013},\nvolume={13},\nnumber={2},\npages={111-122},\ndoi={10.1038/nrc3418},\nnote={cited By 88},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84873058654&doi=10.1038%2fnrc3418&partnerID=40&md5=8ce16e67b94331b40e345148bae1136a},\naffiliation={School of Molecular Bioscience, University of Sydney, NSW 2006, Australia; Australian Centre for Blood Diseases, Central Clinical School, Monash University, VIC 3004, Australia},\nabstract={LIM-domain proteins are a large family of proteins that are emerging as key molecules in a wide variety of human cancers. In particular, all members of the human LIM-domain-only (LMO) proteins, LMO1-4, which are required for many developmental processes, are implicated in the onset or the progression of several cancers, including T cell leukaemia, breast cancer and neuroblastoma. These small proteins contain two protein-interacting LIM domains but little additional sequence, and they seem to function by nucleating the formation of new transcriptional complexes and/or by disrupting existing transcriptional complexes to modulate gene expression programmes. Through these activities, the LMO proteins have important cellular roles in processes that are relevant to cancer such as self-renewal, cell cycle regulation and metastasis. These functions highlight the therapeutic potential of targeting these proteins in cancer. © 2013 Macmillan Publishers Limited. All rights reserved.},\nkeywords={antineoplastic agent;  autoantigen;  gene therapy agent;  LIM domain only protein 1;  LIM domain only protein 2;  LIM domain only protein 3;  LIM domain only protein 4;  LIM domain only protein 4 inhibitor;  LIM protein;  protein inhibitor;  unclassified drug;  zinc finger protein, acute lymphoblastic leukemia;  B cell leukemia;  breast cancer;  cancer gene therapy;  cancer growth;  cancer stem cell;  carcinogenesis;  cell cycle regulation;  cell renewal;  chromosome translocation;  complex formation;  gene mutation;  gene overexpression;  human;  large cell lymphoma;  metastasis;  neoplasm;  neuroblastoma;  nonhuman;  priority journal;  prostate cancer;  protein domain;  protein function;  protein structure;  review;  solid tumor;  T cell leukemia;  transcription regulation;  X linked severe combined immunodeficiency, Animals;  Disease Progression;  Gene Expression Regulation, Neoplastic;  Humans;  LIM Domain Proteins;  Neoplasms;  Protein Interaction Domains and Motifs},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, , NSW 2006, Australia; email: jacqui.matthews@sydney.edu.au},\nissn={1474175X},\ncoden={NRCAC},\npubmed_id={23303138},\nlanguage={English},\nabbrev_source_title={Nat. Rev. Cancer},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

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\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

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@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

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

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\n \n\n \n \n \n \n \n \n Preface.\n \n \n \n \n\n\n \n Matthews, J.\n\n\n \n\n\n\n Advances in Experimental Medicine and Biology, 747: v-vi. 2012.\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\n\n\n

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@ARTICLE{Matthews2012,\nauthor={Matthews, J.M.},\ntitle={Preface},\njournal={Advances in Experimental Medicine and Biology},\nyear={2012},\nvolume={747},\npages={v-vi},\nnote={cited By 0},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84868673468&partnerID=40&md5=7c8f766f6eca8b528c07dc1d27463609},\nkeywords={polypeptide;  potassium channel, cell function;  dimerization;  editorial;  enzyme activity;  oligomerization;  priority journal;  protein analysis;  protein domain;  protein folding;  protein function;  protein protein interaction;  stoichiometry;  structure analysis;  transcription regulation},\ncorrespondence_address1={Matthews, J.M.},\neditor={Matthews J.M.},\nissn={00652598},\nisbn={9781461432289},\ncoden={AEMBA},\nlanguage={English},\nabbrev_source_title={Adv. Exp. Med. Biol.},\ndocument_type={Editorial},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Crystallization and diffraction of an Isl1-Ldb1 complex.\n \n \n \n \n\n\n \n Gadd, M.; Jacques, D.; Guss, J.; and Matthews, J.\n\n\n \n\n\n\n Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 68(11): 1398-1401. 2012.\n cited By 1\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

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@ARTICLE{Gadd20121398,\nauthor={Gadd, M.S. and Jacques, D.A. and Guss, J.M. and Matthews, J.M.},\ntitle={Crystallization and diffraction of an Isl1-Ldb1 complex},\njournal={Acta Crystallographica Section F: Structural Biology and Crystallization Communications},\nyear={2012},\nvolume={68},\nnumber={11},\npages={1398-1401},\ndoi={10.1107/S1744309112040031},\nnote={cited By 1},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84869012180&doi=10.1107%2fS1744309112040031&partnerID=40&md5=e2872c76944ba99f5274062e81a0e18a},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={A stable intramolecular complex comprising the LIM domains of the LIM-homeodomain protein Isl1 tethered to a peptide region of Ldb1 has been engineered, purified and crystallized. The orthorhombic crystals belonged to space group P2221, with unit-cell parameters a = 57.2, b = 56.7, c = 179.8 Å, and diffracted to 3.10 Å resolution. © 2012 International Union of Crystallography All rights reserved.},\nauthor_keywords={Isl1-Ldb1 complex;  LIM domains},\nkeywords={DNA binding protein;  insulin gene enhancer binding protein Isl 1;  insulin gene enhancer binding protein Isl-1;  Ldb1 protein, mouse;  LIM homeodomain protein;  LIM protein;  multiprotein complex;  transcription factor;  zinc, animal;  article;  chemistry;  crystallization;  mouse;  protein tertiary structure;  X ray crystallography, Animals;  Crystallization;  Crystallography, X-Ray;  DNA-Binding Proteins;  LIM Domain Proteins;  LIM-Homeodomain Proteins;  Mice;  Multiprotein Complexes;  Protein Structure, Tertiary;  Transcription Factors;  Zinc},\ncorrespondence_address1={Gadd, M.S.; School of Molecular Bioscience, , Sydney, NSW 2006, Australia; email: mgad4240@uni.sydney.edu.au},\nissn={17443091},\npubmed_id={23143258},\nlanguage={English},\nabbrev_source_title={Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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@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

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\n \n\n \n \n \n \n \n \n Protein-protein interactions. Preface.\n \n \n \n \n\n\n \n Matthews, J.\n\n\n \n\n\n\n Advances in experimental medicine and biology, 747: v-vi. 2012.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Protein-protein$ 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 \n \n\n\n\n

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@ARTICLE{Matthews2012,\nauthor={Matthews, J.M.},\ntitle={Protein-protein interactions. Preface.},\njournal={Advances in experimental medicine and biology},\nyear={2012},\nvolume={747},\npages={v-vi},\nnote={cited By 1},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84866793167&partnerID=40&md5=053b4f085adc32fc9a44b9bb14d2ba00},\nkeywords={protein, chemistry;  editorial;  genetics;  metabolism;  protein multimerization;  protein subunit, Protein Multimerization;  Protein Subunits;  Proteins},\ncorrespondence_address1={Matthews, J.M.},\nissn={00652598},\npubmed_id={22977895},\nlanguage={English},\nabbrev_source_title={Adv. Exp. Med. Biol.},\ndocument_type={Editorial},\nsource={Scopus},\n}\n\n

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\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

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@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

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\n \n\n \n \n \n \n \n \n Contribution of DEAF1 structural domains to the interaction with the breast cancer oncogene LMO4.\n \n \n \n \n\n\n \n Cubeddu, L.; Joseph, S.; Richard, D.; and Matthews, J.\n\n\n \n\n\n\n PLoS ONE, 7(6). 2012.\n cited By 16\n\n\n\n
\n\n\n\n \n \n $\"Contribution$ 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

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@ARTICLE{Cubeddu2012,\nauthor={Cubeddu, L. and Joseph, S. and Richard, D.J. and Matthews, J.M.},\ntitle={Contribution of DEAF1 structural domains to the interaction with the breast cancer oncogene LMO4},\njournal={PLoS ONE},\nyear={2012},\nvolume={7},\nnumber={6},\ndoi={10.1371/journal.pone.0039218},\nart_number={e39218},\nnote={cited By 16},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84862562783&doi=10.1371%2fjournal.pone.0039218&partnerID=40&md5=e80dcaeac042dc231c5617cc3d87a0a7},\naffiliation={School of Molecular Bioscience, The University of Sydney, Sydney, NSW, Australia; Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia; School of Science and Health, University of Western Sydney, Penrith, NSW, Australia},\nabstract={The proteins LMO4 and DEAF1 contribute to the proliferation of mammary epithelial cells. During breast cancer LMO4 is upregulated, affecting its interaction with other protein partners. This may set cells on a path to tumour formation. LMO4 and DEAF1 interact, but it is unknown how they cooperate to regulate cell proliferation. In this study, we identify a specific LMO4-binding domain in DEAF1. This domain contains an unstructured region that directly contacts LMO4, and a coiled coil that contains the DEAF1 nuclear export signal (NES). The coiled coil region can form tetramers and has the typical properties of a coiled coil domain. Using a simple cell-based assay, we show that LMO4 modulates the activity of the DEAF NES, causing nuclear accumulation of a construct containing the LMO4-interaction region of DEAF1. © 2012 Cubeddu et al.},\nkeywords={protein DEAF1;  protein LMO4;  tetramer;  transcription factor;  unclassified drug, article;  cell assay;  cell nucleus;  controlled study;  human;  human cell;  nuclear export signal;  nucleotide sequence;  protein binding;  protein domain;  protein function;  protein protein interaction, Active Transport, Cell Nucleus;  Adaptor Proteins, Signal Transducing;  Animals;  Breast Neoplasms;  Cell Nucleus;  Female;  LIM Domain Proteins;  Mice;  Protein Binding;  Protein Interaction Domains and Motifs;  Transcription Factors},\ncorrespondence_address1={Cubeddu, L.; School of Science and Health, , Penrith, NSW, Australia; email: liza.cubeddu@sydney.edu.au},\nissn={19326203},\npubmed_id={22723967},\nlanguage={English},\nabbrev_source_title={PLoS ONE},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Total synthesis of homogeneous antifreeze glycopeptides and glycoproteins.\n \n \n \n \n\n\n \n Wilkinson, B.; Stone, R.; Capicciotti, C.; Thaysen-Andersen, M.; Matthews, J.; Packer, N.; Ben, R.; and Payne, R.\n\n\n \n\n\n\n Angewandte Chemie - International Edition, 51(15): 3606-3610. 2012.\n cited By 96\n\n\n\n
\n\n\n\n \n \n $\"Total$ 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

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@ARTICLE{Wilkinson20123606,\nauthor={Wilkinson, B.L. and Stone, R.S. and Capicciotti, C.J. and Thaysen-Andersen, M. and Matthews, J.M. and Packer, N.H. and Ben, R.N. and Payne, R.J.},\ntitle={Total synthesis of homogeneous antifreeze glycopeptides and glycoproteins},\njournal={Angewandte Chemie - International Edition},\nyear={2012},\nvolume={51},\nnumber={15},\npages={3606-3610},\ndoi={10.1002/anie.201108682},\nnote={cited By 96},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84859540284&doi=10.1002%2fanie.201108682&partnerID=40&md5=a82ea05abf08fe889211d067006299b6},\naffiliation={School of Chemistry, University of Sydney, NSW 2006, Australia; Department of Chemistry, University of Ottawa, Ottawa K1N 6N5, Canada; Biomolecular Frontiers Research Centre, Macquarie University, NSW 2109, Australia; School of Molecular Bioscience, University of Sydney, NSW 2006, Australia},\nabstract={Don't freeze! A native chemical ligation-desulfurization strategy has been employed for the convergent synthesis of a library of defined antifreeze glycopeptides and glycoproteins (AFGPs) ranging in size from 1.2 to 19.5 kDa (see picture). These AFGPs possessed the secondary structure of a polyproline type II helix and exhibited significant ice recrystallization inhibition and thermal hysteresis activity. © 2012 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.},\nauthor_keywords={antifreeze proteins;  chemical ligation;  glycopeptides;  glycoproteins;  thermal hysteresis},\nkeywords={Antifreeze protein;  chemical ligation;  Convergent synthesis;  Glycopeptides;  Polyproline;  Secondary structures;  Thermal hysteresis;  Total synthesis;  Type II, Desulfurization;  Glycoproteins;  Hysteresis, Peptides, antifreeze protein;  glycopeptide;  glycoprotein, article;  chemistry;  synthesis, Antifreeze Proteins;  Glycopeptides;  Glycoproteins},\ncorrespondence_address1={Payne, R.J.; School of Chemistry, , NSW 2006, Australia; email: richard.payne@sydney.edu.au},\nissn={14337851},\ncoden={ACIEF},\npubmed_id={22389168},\nlanguage={English},\nabbrev_source_title={Angew. Chem. Int. Ed.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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@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

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\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

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@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

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\n \n\n \n \n \n \n \n \n Tropoelastin bridge region positions the cell-interactive C terminus and contributes to elastic fiber assembly.\n \n \n \n \n\n\n \n Yeo, G.; Baldock, C.; Tuukkanen, A.; Roessle, M.; Dyksterhuis, L.; Wise, S.; Matthews, J.; Mithieux, S.; and Weiss, A.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 109(8): 2878-2883. 2012.\n cited By 48\n\n\n\n
\n\n\n\n \n \n $\"Tropoelastin$ 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

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@ARTICLE{Yeo20122878,\nauthor={Yeo, G.C. and Baldock, C. and Tuukkanen, A. and Roessle, M. and Dyksterhuis, L.B. and Wise, S.G. and Matthews, J. and Mithieux, S.M. and Weiss, A.S.},\ntitle={Tropoelastin bridge region positions the cell-interactive C terminus and contributes to elastic fiber assembly},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2012},\nvolume={109},\nnumber={8},\npages={2878-2883},\ndoi={10.1073/pnas.1111615108},\nnote={cited By 48},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84857428645&doi=10.1073%2fpnas.1111615108&partnerID=40&md5=020b2f694c9c09df545585b35e034646},\naffiliation={School of Molecular Bioscience, University of Sydney, NSW 2006, Australia; Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom; Biological Small Angle X-ray Scattering Group, European Molecular Biology Laboratory Outstation Hamburg, D-22603 Hamburg, Germany; Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia},\nabstract={The tropoelastin monomer undergoes stages of association by coacervation, deposition onto microfibrils, and cross-linking to form elastic fibers. Tropoelastin consists of an elastic N-terminal coil region and a cell-interactive C-terminal foot region linked together by a highly exposed bridge region. The bridge region is conveniently positioned to modulate elastic fiber assembly through association by coacervation and its proximity to dominant cross-linking domains. Tropoelastin constructs that either modify or remove the entire bridge and downstream regions were assessed for elastogenesis. These constructs focused on a single alanine substitution (R515A) and a truncation (M155n) at the highly conserved arginine 515 site that borders the bridge. Each form displayed less efficient coacervation, impaired hydrogel formation, and decreased dermal fibroblast attachment compared to wild-type tropoelastin. The R515A mutant protein additionally showed reduced elastic fiber formation upon addition to human retinal pigmented epithelium cells and dermal fibroblasts. The small-angle X-ray scattering nanostructure of the R515A mutant protein revealed greater conformational flexibility around the bridge and C-terminal regions. This increased flexibility of the R515A mutant suggests that the tropoelastin R515 residue stabilizes the structure of the bridge region, which is critical for elastic fiber assembly.},\nauthor_keywords={Protease resistance;  Tropoelastin assembly},\nkeywords={alanine;  arginine;  nanomaterial;  tropoelastin, article;  carboxy terminal sequence;  cell interaction;  controlled study;  elastic fiber;  fibroblast;  hydrogel;  nonhuman;  particle size;  pigment epithelium;  priority journal;  protein degradation;  radiation scattering;  scanning electron microscopy, Cell Adhesion;  Cell Communication;  Cells, Cultured;  Elastic Tissue;  Fibroblasts;  Humans;  Hydrogels;  Microscopy, Confocal;  Models, Molecular;  Mutant Proteins;  Particle Size;  Protein Structure, Tertiary;  Proteolysis;  Solutions;  Structure-Activity Relationship;  Temperature;  Tropoelastin},\ncorrespondence_address1={Weiss, A.S.; School of Molecular Bioscience, , NSW 2006, Australia; email: tony.weiss@sydney.edu.au},\nissn={00278424},\ncoden={PNASA},\npubmed_id={22328151},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Dimers, oligomers, everywhere.\n \n \n \n \n\n\n \n Matthews, J.; and Sunde, M.\n\n\n \n\n\n\n Advances in Experimental Medicine and Biology, 747: 1-18. 2012.\n cited By 60\n\n\n\n
\n\n\n\n \n \n $\"Dimers,$ 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

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@ARTICLE{Matthews20121,\nauthor={Matthews, J.M. and Sunde, M.},\ntitle={Dimers, oligomers, everywhere},\njournal={Advances in Experimental Medicine and Biology},\nyear={2012},\nvolume={747},\npages={1-18},\ndoi={10.1007/978-1-4614-3229-6_1},\nnote={cited By 60},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84934439604&doi=10.1007%2f978-1-4614-3229-6_1&partnerID=40&md5=d360742451519ca83fab0095879873ce},\naffiliation={School of Molecular Bioscience, University of Sydney, Sydney, Australia; Discipline of Pharmacology, University of Sydney, Sydney, Australia},\nabstract={The specific self-association of proteins to form homodimers and higher order oligomers is an extremely common event in biological systems. In this chapter we review the prevalence of protein oligomerization and discuss the likely origins of this phenomenon. We also outline many of the functional advantages conferred by the dimerization or oligomerization of a wide range of different proteins and in a variety of biological roles, that are likely to have placed a selective pressure on biological systems to evolve and maintain homodimerization/oligomerization interfaces. © 2012 Springer Science+Business Media, LLC.},\nkeywords={dimer;  DNA;  G protein coupled receptor;  growth hormone;  Janus kinase;  LIM protein;  oligomer;  prealbumin;  proteasome;  Rad50 protein;  receptor for activated C kinase 1;  retinol binding protein;  STAT protein;  tetramer;  tumor necrosis factor;  protein, allosterism;  binding affinity;  binding site;  complex formation;  cytokine production;  dimerization;  gene targeting;  human;  molecular dynamics;  molecular evolution;  nonhuman;  oligomerization;  priority journal;  protein assembly;  protein determination;  protein DNA binding;  protein folding;  protein function;  protein protein interaction;  protein transport;  review;  signal transduction;  archaeon;  chemical structure;  chemistry;  dimerization;  genetics;  metabolism;  protein binding;  protein conformation;  protein multimerization;  protein subunit;  virus;  yeast, Archaea;  Dimerization;  Evolution, Molecular;  Humans;  Models, Molecular;  Protein Binding;  Protein Conformation;  Protein Folding;  Protein Multimerization;  Protein Subunits;  Proteins;  Viruses;  Yeasts},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, University of Sydney, Sydney, Australia; email: jacqui.matthews@sydney.edu.au},\npublisher={Springer New York LLC},\nissn={00652598},\nisbn={9781461432289},\ncoden={AEMBA},\npubmed_id={22949108},\nlanguage={English},\nabbrev_source_title={Adv. Exp. Med. Biol.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Mutations in MITF and PAX3 cause \"splashed white\" and other white spotting phenotypes in horses.\n \n \n \n \n\n\n \n Hauswirth, R.; Haase, B.; Blatter, M.; Brooks, S.; Burger, D.; Drögemüller, C.; Gerber, V.; Henke, D.; Janda, J.; Jude, R.; Magdesian, K.; Matthews, J.; Poncet, P.; Svansson, V.; Tozaki, T.; Wilkinson-White, L.; Penedo, M.; Rieder, S.; and Leeb, T.\n\n\n \n\n\n\n PLoS Genetics, 8(4). 2012.\n cited By 114\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

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@ARTICLE{Hauswirth2012,\nauthor={Hauswirth, R. and Haase, B. and Blatter, M. and Brooks, S.A. and Burger, D. and Drögemüller, C. and Gerber, V. and Henke, D. and Janda, J. and Jude, R. and Magdesian, K.G. and Matthews, J.M. and Poncet, P.-A. and Svansson, V. and Tozaki, T. and Wilkinson-White, L. and Penedo, M.C.T. and Rieder, S. and Leeb, T.},\ntitle={Mutations in MITF and PAX3 cause "splashed white" and other white spotting phenotypes in horses},\njournal={PLoS Genetics},\nyear={2012},\nvolume={8},\nnumber={4},\ndoi={10.1371/journal.pgen.1002653},\nart_number={e1002653},\nnote={cited By 114},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84860546946&doi=10.1371%2fjournal.pgen.1002653&partnerID=40&md5=b4423f48f4d7bf7428ea626d0b68eccd},\naffiliation={Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland; DermFocus, University of Bern, Bern, Switzerland; Faculty of Veterinary Science, University of Sydney, Sydney, Australia; Swiss National Stud, ALP-Haras, Avenches, Switzerland; Department of Animal Science, Cornell University, Ithaca, NY, United States; Swiss Institute of Equine Medicine, Vetsuisse Faculty, ALP-Haras and University of Bern, Avenches, Switzerland; Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern and ALP-Haras, Bern, Switzerland; Division of Neurology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Division of Experimental Clinical Research, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Certagen GmbH, Rheinbach, Germany; Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA, United States; School of Molecular Bioscience, University of Sydney, Sydney, Australia; Institute for Experimental Pathology, University of Iceland, Reykjavík, Iceland; Department of Molecular Genetics, Laboratory of Racing Chemistry, Utsunomiya, Japan; Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California Davis, Davis, CA, United States},\nabstract={During fetal development neural-crest-derived melanoblasts migrate across the entire body surface and differentiate into melanocytes, the pigment-producing cells. Alterations in this precisely regulated process can lead to white spotting patterns. White spotting patterns in horses are a complex trait with a large phenotypic variance ranging from minimal white markings up to completely white horses. The "splashed white" pattern is primarily characterized by an extremely large blaze, often accompanied by extended white markings at the distal limbs and blue eyes. Some, but not all, splashed white horses are deaf. We analyzed a Quarter Horse family segregating for the splashed white coat color. Genome-wide linkage analysis in 31 horses gave a positive LOD score of 1.6 in a region on chromosome 6 containing the PAX3 gene. However, the linkage data were not in agreement with a monogenic inheritance of a single fully penetrant mutation. We sequenced the PAX3 gene and identified a missense mutation in some, but not all, splashed white Quarter Horses. Genome-wide association analysis indicated a potential second signal near MITF. We therefore sequenced the MITF gene and found a 10 bp insertion in the melanocyte-specific promoter. The MITF promoter variant was present in some splashed white Quarter Horses from the studied family, but also in splashed white horses from other horse breeds. Finally, we identified two additional non-synonymous mutations in the MITF gene in unrelated horses with white spotting phenotypes. Thus, several independent mutations in MITF and PAX3 together with known variants in the EDNRB and KIT genes explain a large proportion of horses with the more extreme white spotting phenotypes. © 2012 Hauswirth et al.},\nkeywords={article;  chromosome 6;  gene;  gene function;  gene insertion;  gene sequence;  genetic association;  genetic heterogeneity;  genetic variability;  horse;  missense mutation;  MITF gene;  mutational analysis;  nonhuman;  pathogenesis;  PAX3 gene;  phenotypic variation;  pigment disorder;  sequence analysis;  single nucleotide polymorphism;  skin color;  animal;  chromosome map;  color;  genetic linkage;  genetics;  genome;  hair color;  horse;  melanocyte;  metabolism;  molecular genetics;  mutation;  nucleotide sequence;  phenotype;  pigmentation;  promoter region, Equidae;  Nemophila;  Pseudomugilidae, microphthalmia associated transcription factor;  paired box transcription factor, Animals;  Base Sequence;  Chromosome Mapping;  Color;  Genetic Linkage;  Genome;  Genome-Wide Association Study;  Hair Color;  Horses;  Lod Score;  Melanocytes;  Microphthalmia-Associated Transcription Factor;  Molecular Sequence Data;  Mutation;  Paired Box Transcription Factors;  Phenotype;  Pigmentation;  Promoter Regions, Genetic},\ncorrespondence_address1={Leeb, T.; Institute of Genetics, , Bern, Switzerland; email: Tosso.Leeb@vetsuisse.unibe.ch},\npublisher={Public Library of Science},\nissn={15537390},\npubmed_id={22511888},\nlanguage={English},\nabbrev_source_title={PLoS Genet.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n 2011\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Structural basis for partial redundancy in a class of transcription factors, the LIM homeodomain proteins, in neural cell type specification.\n \n \n \n \n\n\n \n Gadd, M.; Bhati, M.; Jeffries, C.; Langley, D.; Trewhella, J.; Guss, J.; and Matthews, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 286(50): 42971-42980. 2011.\n cited By 30\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

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@ARTICLE{Gadd201142971,\nauthor={Gadd, M.S. and Bhati, M. and Jeffries, C.M. and Langley, D.B. and Trewhella, J. and Guss, J.M. and Matthews, J.M.},\ntitle={Structural basis for partial redundancy in a class of transcription factors, the LIM homeodomain proteins, in neural cell type specification},\njournal={Journal of Biological Chemistry},\nyear={2011},\nvolume={286},\nnumber={50},\npages={42971-42980},\ndoi={10.1074/jbc.M111.248559},\nnote={cited By 30},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-83355166918&doi=10.1074%2fjbc.M111.248559&partnerID=40&md5=c618ad7a4f22ffac5d4a015bb2727ac3},\naffiliation={Bldg. G08, School of Molecular Bioscience, University of Sydney, NSW 2006, Australia; School of Biomedical Sciences, Monash University, VIC 3800, Australia; Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia},\nabstract={Combinations of LIM homeodomain proteins form a transcriptional "LIM code" to direct the specification of neural cell types. Two paralogous pairs of LIM homeodomain proteins, LIM homeobox protein 3/4 (Lhx3/Lhx4) and Islet-1/2 (Isl1/Isl2), are expressed in developing ventral motor neurons. Lhx3 and Isl1 interact within a well characterized transcriptional complex that triggers motor neuron development, but it was not known whether Lhx4 and Isl2 could participate in equivalent complexes. We have identified an Lhx3-binding domain (LBD) in Isl2 based on sequence homology with the Isl1 LBD and show that both Isl2 LBD and Isl1 LBD can bind each of Lhx3 and Lhx4. X-ray crystal- and small-angle x-ray scattering-derived solution structures of an Lhx4•Isl2 complex exhibit many similarities with that of Lhx3•Isl1; however, structural differences supported by mutagenic studies reveal differences in the mechanisms of binding. Differences in binding have implications for the mode of exchange of protein partners in transcriptional complexes and indicate a divergence in functions of Lhx3/4 and Isl1/2. The formation of weaker Lhx•Isl complexes would likely be masked by the availability of the other Lhx•Isl complexes in postmitotic motor neurons. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Binding domain;  Homeodomain proteins;  Motor neurons;  Neural cells;  Sequence homology;  Small-angle x-rays;  Solution structures;  Structural basis;  Structural differences;  Transcriptional complexes;  X ray crystals, Brain;  Neurons;  Transcription factors;  X ray scattering, Specifications, cell protein;  protein Isl1;  protein Isl2;  transcription factor;  transcription factor LHX3;  transcription factor LHX4;  unclassified drug, amino acid sequence;  article;  binding affinity;  cell specificity;  complex formation;  controlled study;  crystal structure;  mitosis;  motoneuron;  mutagenesis;  nerve cell;  nerve cell differentiation;  nonhuman;  nucleotide sequence;  priority journal;  protein analysis;  protein binding;  protein domain;  protein expression;  protein folding;  protein function;  protein motif;  protein protein interaction;  protein structure;  sequence homology;  X ray crystallography, Animals;  Crystallography, X-Ray;  DNA-Binding Proteins;  LIM Domain Proteins;  LIM-Homeodomain Proteins;  Mice;  Mutagenesis;  Protein Binding;  Protein Structure, Secondary;  Protein Structure, Tertiary;  Recombinant Proteins;  Transcription Factors;  Two-Hybrid System Techniques},\ncorrespondence_address1={Matthews, J.M.; Bldg. G08, , NSW 2006, Australia; email: jacqui.matthews@sydney.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={22025611},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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@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

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\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

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@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

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\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

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@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

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\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

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@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

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\n \n\n \n \n \n \n \n \n LIM Domain binding proteins 1 and 2 have different oligomeric states.\n \n \n \n \n\n\n \n Cross, A.; Jeffries, C.; Trewhella, J.; and Matthews, J.\n\n\n \n\n\n\n Journal of Molecular Biology, 399(1): 133-144. 2010.\n cited By 34\n\n\n\n
\n\n\n\n \n \n $\"LIM$ 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

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@ARTICLE{Cross2010133,\nauthor={Cross, A.J. and Jeffries, C.M. and Trewhella, J. and Matthews, J.M.},\ntitle={LIM Domain binding proteins 1 and 2 have different oligomeric states},\njournal={Journal of Molecular Biology},\nyear={2010},\nvolume={399},\nnumber={1},\npages={133-144},\ndoi={10.1016/j.jmb.2010.04.006},\nnote={cited By 34},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77953082257&doi=10.1016%2fj.jmb.2010.04.006&partnerID=40&md5=2cdab3b5d68483d5d9fb14bc3d180477},\naffiliation={School of Molecular Bioscience, The University of Sydney, Building G08, NSW 2006, Australia},\nabstract={LIM domain binding (Ldb) proteins are important regulators of LIM homeodomain and LIM-only proteins that specify cell fate in many different tissues. An essential feature of these proteins is the ability to self-associate, but there have been no studies that characterise the nature of this self-association. We have used deletion mutagenesis with yeast two-hybrid analysis to define the minimal self-association domains of Ldb1 and Ldb2 as residues 14-200 and 21-197, respectively. We then used a range of different biophysical methods, including sedimentation equilibrium and small-angle X-ray scattering to show that Ldb114-200 forms a trimer and Ldb221-197 undergoes a monomer-tetramer-octamer equilibrium, where the association in each case is of moderate affinity (~105 M-1). These modes of association represent a clear physical difference between these two proteins that otherwise appear to have very similar properties. The levels of association are more complex than previously assumed and emphasise roles of avidity and DNA looping in transcriptional regulation by Ldb1/LIM protein complexes. The abilities of Ldb1 and Ldb2 to form trimers and higher oligomers, respectively, should be considered in models of transcriptional regulation by Ldb1-containing complexes in a wide range of biological processes. © 2010 Elsevier Ltd.},\nauthor_keywords={Ldb/CLIM/NLI;  Sedimentation equilibrium;  Self-association;  Small-angle X-ray scattering;  Transcriptional regulation},\nkeywords={LIM domain binding protein 1;  LIM domain binding protein 2;  LIM protein;  unclassified drug, article;  circular dichroism;  controlled study;  mutagenesis;  nonhuman;  oligomerization;  priority journal;  protein analysis;  protein expression;  protein folding;  protein function;  protein secondary structure;  protein structure;  radiation scattering;  sedimentation;  transcription regulation},\ncorrespondence_address1={Matthews, J.M.; School of Molecular Bioscience, Building G08, NSW 2006, Australia; email: jacqui.matthews@sydney.edu.au},\npublisher={Academic Press},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={20382157},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n 2009\n \n \n (4)\n \n \n

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\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

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@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

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\n \n\n \n \n \n \n \n \n The importance of pH in regulating the function of the Fasciola hepatica cathepsin L1 cysteine protease.\n \n \n \n \n\n\n \n Lowther, J.; Robinson, M.; Donnelly, S.; Xu, W.; Stack, C.; Matthews, J.; and Dalton, J.\n\n\n \n\n\n\n PLoS Neglected Tropical Diseases, 3(1). 2009.\n cited By 65\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

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@ARTICLE{Lowther2009,\nauthor={Lowther, J. and Robinson, M.W. and Donnelly, S.M. and Xu, W. and Stack, C.M. and Matthews, J.M. and Dalton, J.P.},\ntitle={The importance of pH in regulating the function of the Fasciola hepatica cathepsin L1 cysteine protease},\njournal={PLoS Neglected Tropical Diseases},\nyear={2009},\nvolume={3},\nnumber={1},\ndoi={10.1371/journal.pntd.0000369},\nart_number={e369},\nnote={cited By 65},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-65549085704&doi=10.1371%2fjournal.pntd.0000369&partnerID=40&md5=11a33428cfc92f3715c9984b899f6e38},\naffiliation={Institute for the Biotechnology of Infectious Diseases (IBID), University of Technology Sydney (UTS), Sydney, NSW, Australia; School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW, Australia; Department of Medical Microbiology, University of Western Sydney (UWS), Narellan Road, Campbelltown, NSW, Australia},\nabstract={The helminth parasite Fasciola hepatica secretes cathepsin L cysteine proteases to invade its host, migrate through tissues and digest haemoglobin, its main source of amino acids. Here we investigated the importance of pH in regulating the activity and functions of the major cathepsin L protease FheCL1. The slightly acidic pH of the parasite gut facilitates the auto-catalytic activation of FheCL1 from its inactive proFheCL1 zymogen; this process was ∼40-fold faster at pH 4.5 than at pH 7.0. Active mature FheCL1 is very stable at acidic and neutral conditions (the enzyme retained ∼45% activity when incubated at 37°C and pH 4.5 for 10 days) and displayed a broad pH range for activity peptide substrates and the protein ovalbumin, peaking between pH 5.5 and pH 7.0. This pH profile likely reflects the need for FheCL1 to function both in the parasite gut and in the host tissues. FheCL1, however, could not cleave its natural substrate Hb in the pH range pH 5.5 and pH 7.0; digestion occurred only at pH ≤4.5, which coincided with pH-induced dissociation of the Hb tetramer. Our studies indicate that the acidic pH of the parasite relaxes the Hb structure, making it susceptible to proteolysis by FheCL1. This process is enhanced by glutathione (GSH), the main reducing agent contained in red blood cells. Using mass spectrometry, we show that FheCL1 can degrade Hb to small peptides, predominantly of 4-14 residues, but cannot release free amino acids. Therefore, we suggest that Hb degradation is not completed in the gut lumen but that the resulting peptides are absorbed by the gut epithelial cells for further processing by intracellular di- and amino-peptidases to free amino acids that are distributed through the parasite tissue for protein anabolism. © 2009 Lowther et al.},\nkeywords={amino acid;  aminopeptidase;  cathepsin L;  cysteine proteinase;  dipeptidase;  enzyme precursor;  glutathione;  hemoglobin;  ovalbumin;  tetramer;  cathepsin;  cathepsin L1, Fasciola hepatica;  hemoglobin, animal cell;  animal tissue;  article;  controlled study;  dissociation;  enzyme activation;  enzyme activity;  enzyme degradation;  enzyme substrate;  erythrocyte;  Fasciola hepatica;  incubation time;  intestine absorption;  intestine epithelium cell;  mass spectrometry;  nonhuman;  pH;  protein degradation;  protein secretion;  protein synthesis;  regulatory mechanism;  animal;  enzymology;  Fasciola hepatica;  metabolism, Animals;  Cathepsins;  Fasciola hepatica;  Hemoglobins;  Hydrogen-Ion Concentration},\ncorrespondence_address1={Lowther, J.; Institute for the Biotechnology of Infectious Diseases (IBID), , Sydney, NSW, Australia},\npubmed_id={19172172},\nlanguage={English},\nabbrev_source_title={PLoS. Negl. Trop. Dis.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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@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

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\n \n\n \n \n \n \n \n \n Crystallization and diffraction of an Lhx4-Isl2 complex.\n \n \n \n \n\n\n \n Gadd, M.; Langley, D.; Guss, J.; and Matthews, J.\n\n\n \n\n\n\n Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 65(2): 151-153. 2009.\n cited By 5\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

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@ARTICLE{Gadd2009151,\nauthor={Gadd, M.S. and Langley, D.B. and Guss, J.M. and Matthews, J.M.},\ntitle={Crystallization and diffraction of an Lhx4-Isl2 complex},\njournal={Acta Crystallographica Section F: Structural Biology and Crystallization Communications},\nyear={2009},\nvolume={65},\nnumber={2},\npages={151-153},\ndoi={10.1107/S1744309108043431},\nnote={cited By 5},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-59749083097&doi=10.1107%2fS1744309108043431&partnerID=40&md5=d34848842bad97d5751ef67a8356913b},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Australia},\nabstract={A stable intramolecular complex comprising the LIM domains of the LIM-homeodomain protein Lhx4 tethered to a peptide region of Isl2 has been engineered, purified and crystallized. The monoclinic crystals belonged to space group P21, with unit-cell parameters a = 46.8, b = 88.7, c = 49.9 Å, β = 111.9°, and diffracted to 2.16 Å resolution. © International Union of Crystallography 2009.},\nauthor_keywords={Isl2;  Lhx4;  Lim domains;  Lim-homeodomain transcription factors},\nkeywords={homeodomain protein;  insulin gene enhancer binding protein Isl 1;  insulin gene enhancer binding protein Isl-1;  Lhx4 protein, mouse;  nerve protein;  transcription factor, animal;  article;  chemistry;  comparative study;  crystallization;  metabolism;  methodology;  motoneuron;  mouse;  physiology;  protein binding;  protein engineering;  X ray diffraction, Animals;  Crystallization;  Homeodomain Proteins;  Mice;  Motor Neurons;  Nerve Tissue Proteins;  Protein Binding;  Protein Engineering;  Transcription Factors;  X-Ray Diffraction},\ncorrespondence_address1={Matthews, J. M.; School of Molecular and Microbial Biosciences, Australia; email: j.matthews@usyd.edu.au},\nissn={17443091},\npubmed_id={19194008},\nlanguage={English},\nabbrev_source_title={Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n 2008\n \n \n (8)\n \n \n

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\n \n\n \n \n \n \n \n \n ATP binding equilibria of the Na+,K+-ATPase.\n \n \n \n \n\n\n \n Pilotelle-Bunner, A.; Matthews, J.; Cornelius, F.; Apell, H.; Sebban, P.; and Clarke, R.\n\n\n \n\n\n\n Biochemistry, 47(49): 13103-13114. 2008.\n cited By 12\n\n\n\n
\n\n\n\n \n \n $\"ATP$ 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

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@ARTICLE{Pilotelle-Bunner200813103,\nauthor={Pilotelle-Bunner, A. and Matthews, J.M. and Cornelius, F. and Apell, H.-J. and Sebban, P. and Clarke, R.J.},\ntitle={ATP binding equilibria of the Na+,K+-ATPase},\njournal={Biochemistry},\nyear={2008},\nvolume={47},\nnumber={49},\npages={13103-13114},\ndoi={10.1021/bi801593g},\nnote={cited By 12},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-57449083633&doi=10.1021%2fbi801593g&partnerID=40&md5=e04912de6f98e3a6a683e6fc21d9b068},\naffiliation={School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia; School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Department of Physiology and Biophysics, University of Aarhus, DK-8000 Aarhus C, Denmark; Faculty of Biology, University of Konstanz, D-78435 Konstanz, Germany; Laboratoire de Chimie-Physique, Université Paris-Sud, CNRS, F-91405 Orsay, France},\nabstract={Reported values of the dissociation constant, Kd, of ATP with the E1 conformation of the Na+,K+-ATPase fall in two distinct ranges depending on how it is measured. Equilibrium binding studies yield values of 0.1-0.6 μM, whereas presteady-state kinetic studies yield values of 3-14 μM. It is unacceptable that Kd varies with the experimental method of its determination. Using simulations of the expected equilibrium behavior for different binding models based on thermodynamic data obtained from isothermal titration calorimetry we show that this apparent discrepancy can be explained in part by the presence in presteady-state kinetic studies of excess Mg2+ ions, which compete with the enzyme for the available ATP. Another important contributing factor is an inaccurate assumption in the majority of presteady-state kinetic studies of a rapid relaxation of the ATP binding reaction on the time scale of the subsequent phosphorylation. However, these two factors alone are insufficient to explain the previously observed presteady-state kinetic behavior. In addition one must assume that there are two E1-ATP binding equilibria. Because crystal structures of P-type ATPases indicate only a single bound ATP per α-subunit, the only explanation consistent with both crystal structural and kinetic data is that the enzyme exists as an (αβ)2 diprotomer, with protein - protein interactions between adjacent α-subunits producing two ATP affinities. We propose that in equilibrium measurements the measured K d is due to binding of ATP to one α-subunit, whereas in presteady-state kinetic studies, the measured apparent Kd is due to the binding of ATP to both α-subunits within the diprotomer. © 2008 American Chemical Society.},\nkeywords={Data structures;  Dissociation;  Enzymes;  Volumetric analysis, Atp bindings;  ATPases;  Binding models;  Contributing factors;  Dissociation constants;  Equilibrium behaviors;  Equilibrium bindings;  Equilibrium measurements;  Excess mg;  Experimental methods;  Isothermal titration calorimetries;  Kinetic behaviors;  Kinetic datums;  Kinetic studies;  Protein interactions;  Rapid relaxations;  Time scales;  Yield values, Kinetic theory, adenosine triphosphatase (potassium sodium);  adenosine triphosphate, article;  crystal structure;  dissociation constant;  enzyme analysis;  enzyme binding;  enzyme kinetics;  enzyme phosphorylation;  enzyme structure;  isothermal titration calorimetry;  priority journal;  thermodynamics, Adenosine Triphosphate;  Animals;  Calorimetry;  Computer Simulation;  Kinetics;  Protein Binding;  Protein Subunits;  Sharks;  Sodium-Potassium-Exchanging ATPase;  Thermodynamics},\ncorrespondence_address1={Clarke, R. J.; School of Chemistry, , Sydney, NSW 2006, Australia; email: r.clarke@chem.usyd.edu.au},\nissn={00062960},\ncoden={BICHA},\npubmed_id={19006328},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Competition between LIM-binding domains.\n \n \n \n \n\n\n \n Matthews, J.; Bhati, M.; Craig, V.; Deane, J.; Jeffries, C.; Lee, C.; Nancarrow, A.; Ryan, D.; and Sunde, M.\n\n\n \n\n\n\n Biochemical Society Transactions, 36(6): 1393-1397. 2008.\n cited By 23\n\n\n\n
\n\n\n\n \n \n $\"Competition$ 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

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@ARTICLE{Matthews20081393,\nauthor={Matthews, J.M. and Bhati, M. and Craig, V.J. and Deane, J.E. and Jeffries, C. and Lee, C. and Nancarrow, A.L. and Ryan, D.P. and Sunde, M.},\ntitle={Competition between LIM-binding domains},\njournal={Biochemical Society Transactions},\nyear={2008},\nvolume={36},\nnumber={6},\npages={1393-1397},\ndoi={10.1042/BST0361393},\nnote={cited By 23},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-59149084489&doi=10.1042%2fBST0361393&partnerID=40&md5=1f95d64c2575672d6438c453a42579a9},\naffiliation={School of Molecular and Microbial Biosciences, The University of Sydney, Sydney, NSW 2006, Australia},\nabstract={LMO (LIM-only) and LIM-HD (LIM-homeodomain) proteins form a family of proteins that is required for myriad developmental processes and which can contribute to diseases such as T-cell leukaemia and breast cancer. The four LMO and 12 LIM-HD proteins in mammals are expressed in a combinatorial manner in many cell types, forming a transcriptional 'LIM code'. The proteins all contain a pair of closely spaced LIM domains near their N-termini that mediate protein-protein interactions, including binding to the ∼30-residue LID (LIM interaction domain) of the essential co-factor protein Ldb1 (LIM domain-binding protein 1). In an attempt to understand the molecular mechanisms behind the LIM code, we have determined the molecular basis of binding of LMO and LIM-HD proteins for Ldb1LID through a series of structural, mutagenic and biophysical studies. These studies provide an explanation for why Ldb1 binds the LIM domains of the LMO/LIM-HD family, but not LIM domains from other proteins. The LMO/LIM-HD family exhibit a range of affinities for Ldb1, which influences the formation of specific functional complexes within cells. We have also identified an additional LIM interaction domain in one of the LIM-HD proteins, Isl1. Despite low sequence similarity to Ldb1LID, this domain binds another LIM-HD protein, Lhx3, in an identical manner to Ldb1LID. Through our and other studies, it is emerging that the multiple layers of competitive binding involving LMO and LIM-HD proteins and their partner proteins contribute significantly to cell fate specification and development. © 2008 Biochemical Society.},\nauthor_keywords={Apterous;  Competitive binding;  LIM domain-binding protein 1 (Ldb1);  LIM interaction domain (LID);  LIM-homeodomain (LIM-HD);  LIM-only (LMO)},\nkeywords={LIM protein;  transcription factor LHX3;  homeodomain protein;  protein, amino acid sequence;  binding competition;  binding site;  blood cell;  carcinogenesis;  cell fate;  cell maturation;  complex formation;  conference paper;  gene mutation;  human;  priority journal;  protein domain;  protein family;  protein protein interaction;  sequence homology;  T cell leukemia;  animal;  antibody specificity;  binding competition;  chemical structure;  chemistry;  metabolism;  molecular genetics;  protein tertiary structure;  review, Mammalia, Amino Acid Sequence;  Animals;  Binding, Competitive;  Homeodomain Proteins;  Humans;  Models, Molecular;  Molecular Sequence Data;  Organ Specificity;  Protein Structure, Tertiary;  Proteins},\ncorrespondence_address1={Matthews, J.M.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.matthews@usyd.edu.au},\nissn={03005127},\ncoden={BCSTB},\npubmed_id={19021562},\nlanguage={English},\nabbrev_source_title={Biochem. Soc. Trans.},\ndocument_type={Conference Paper},\nsource={Scopus},\n}\n\n

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\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

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@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

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\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

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@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

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\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

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@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

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\n \n\n \n \n \n \n \n \n Crystallization of an Lhx3-Isl1 complex.\n \n \n \n \n\n\n \n Bhati, M.; Lee, M.; Nancarrow, A.; Bach, I.; Guss, J.; and Matthews, J.\n\n\n \n\n\n\n Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 64(4): 297-299. 2008.\n cited By 14\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

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@ARTICLE{Bhati2008297,\nauthor={Bhati, M. and Lee, M. and Nancarrow, A.L. and Bach, I. and Guss, J.M. and Matthews, J.M.},\ntitle={Crystallization of an Lhx3-Isl1 complex},\njournal={Acta Crystallographica Section F: Structural Biology and Crystallization Communications},\nyear={2008},\nvolume={64},\nnumber={4},\npages={297-299},\ndoi={10.1107/S174430910800691X},\nnote={cited By 14},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-41949124179&doi=10.1107%2fS174430910800691X&partnerID=40&md5=d8d486fd90c00893414c79921d991b3a},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Australia; Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, United States},\nabstract={A stable intramolecular complex comprising the LIM domains of the LIM-homeodomain protein Lhx3 tethered to a peptide region of Isl1 has been engineered, purified and crystallized. The monoclinic crystals belong to space group C2, with unit-cell parameters a = 119, b = 62.2, c = 51.9 Å, β = 91.6°, and diffract to 2.05 Å resolution. © International Union of Crystallography 2008.},\nauthor_keywords={Isl1;  Lhx3;  LIM-homeodomain proteins;  Motor-neuron development;  Protein complex},\nkeywords={homeodomain protein;  transcription factor LHX3;  zinc finger protein, article;  biosynthesis;  chemistry;  comparative study;  crystallization;  gene vector;  genetics;  protein engineering;  synthesis, Crystallization;  Genetic Vectors;  Homeodomain Proteins;  Protein Engineering;  Zinc Fingers},\ncorrespondence_address1={Matthews, J. M.; School of Molecular and Microbial Biosciences, Australia; email: j.matthews@mmb.usyd.edu.au},\nissn={17443091},\npubmed_id={18391431},\nlanguage={English},\nabbrev_source_title={Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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@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

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\n \n\n \n \n \n \n \n \n Assembly of the oncogenic DNA-binding complex LMO2-Ldb1-TAL1-E12.\n \n \n \n \n\n\n \n Ryan, D.; Duncan, J.; Lee, C.; Kuchel, P.; and Matthews, J.\n\n\n \n\n\n\n Proteins: Structure, Function and Genetics, 70(4): 1461-1474. 2008.\n cited By 25\n\n\n\n
\n\n\n\n \n \n $\"Assembly$ 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

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@ARTICLE{Ryan20081461,\nauthor={Ryan, D.P. and Duncan, J.L. and Lee, C. and Kuchel, P.W. and Matthews, J.M.},\ntitle={Assembly of the oncogenic DNA-binding complex LMO2-Ldb1-TAL1-E12},\njournal={Proteins: Structure, Function and Genetics},\nyear={2008},\nvolume={70},\nnumber={4},\npages={1461-1474},\ndoi={10.1002/prot.21638},\nnote={cited By 25},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-39749171110&doi=10.1002%2fprot.21638&partnerID=40&md5=94a184abe78c39a610c1016b33e03602},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={The nuclear proteins TAL1 (T-cell acute leukaemia protein 1) and LMO2 (LIM-only protein 2) have critical roles in haematopoietic development, but are also often aberrantly activated in T-cell acute lymphoblastic leukaemia. TAL1 and LMO2 operate within multifactorial protein-DNA complexes that regulate gene expression in the developing blood cell. TAL1 is a tissue-specific basic helix-loop-helix (bHLH) protein that binds bHLH domains of ubiquitous E-proteins, (E12 and E47), to bind E-box (CANNTG) DNA motifs. TAL1 bHLH also interacts specifically with the LIM domains of LMO2, which in turn bind Ldb1 (LIM-domain binding protein 1). Here we used biophysical methods to characterize the assembly of a five-component complex containing TAL1, LMO2, Ldb1, E12, and DNA. The bHLH domains of TAL1 and E12 alone primarily formed helical homodimers, but together preferentially formed heterodimers, to which LMO2 bound with high affinity (KA ∼ 108 M -1). The resulting TAL1/E12/LMO2 complex formed in the presence or absence of DNA, but the different complexes preferentially bound different Ebox-sequences. Our data provide biophysical evidence for a mechanism, by which LMO2 and TAL1 both regulate transcription in normal blood cell development, and synergistically disrupt E2A function in T-cells to promote the onset of leukaemia. © 2007 Wiley-Liss, Inc.},\nauthor_keywords={LMO2;  Protein-DNA complex;  Protein/protein interactions;  T-cell leukaemia;  TAL1},\nkeywords={basic helix loop helix transcription factor;  DNA binding protein;  e protein 12;  homodimer;  lim domain binding protein 1;  lim only protein 2;  nuclear protein;  transcription factor TAL1;  unclassified drug, acute lymphoblastic leukemia;  amino acid sequence;  article;  binding affinity;  priority journal;  protein assembly;  protein binding;  protein DNA binding;  protein function;  protein protein interaction;  T cell leukemia},\ncorrespondence_address1={Matthews, J.M.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.matthews@mmb.usyd.edu.au},\npublisher={Wiley-Liss Inc.},\nissn={08873585},\ncoden={PSFGE},\npubmed_id={17910069},\nlanguage={English},\nabbrev_source_title={Proteins Struct. Funct. Genet.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n 2007\n \n \n (4)\n \n \n

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\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

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@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

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\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

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@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

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\n \n\n \n \n \n \n \n \n Modifiers of epigenetic reprogramming show paternal effects in the mouse.\n \n \n \n \n\n\n \n Chong, S.; Vickaryous, N.; Ashe, A.; Zamudio, N.; Youngson, N.; Hemley, S.; Stopka, T.; Skoultchi, A.; Matthews, J.; Scott, H.; De Kretser, D.; O'Bryan, M.; Blewitt, M.; and Whitelaw, E.\n\n\n \n\n\n\n Nature Genetics, 39(5): 614-622. 2007.\n cited By 141\n\n\n\n
\n\n\n\n \n \n $\"Modifiers$ 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

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@ARTICLE{Chong2007614,\nauthor={Chong, S. and Vickaryous, N. and Ashe, A. and Zamudio, N. and Youngson, N. and Hemley, S. and Stopka, T. and Skoultchi, A. and Matthews, J. and Scott, H.S. and De Kretser, D. and O'Bryan, M. and Blewitt, M. and Whitelaw, E.},\ntitle={Modifiers of epigenetic reprogramming show paternal effects in the mouse},\njournal={Nature Genetics},\nyear={2007},\nvolume={39},\nnumber={5},\npages={614-622},\ndoi={10.1038/ng2031},\nnote={cited By 141},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34247641746&doi=10.1038%2fng2031&partnerID=40&md5=86a87b1c6acb56d8032c3a3f22afa4fc},\naffiliation={Epigenetics Laboratory, Queensland Institute of Medical Research, 300 Herston Road, Brisbane, QLD 4006, Australia; Monash Institute of Medical Research, 27-31 Wright St., Clayton, Vic. 3168, Australia; School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Albert Einstein College of Medicine, Department of Cell Biology, 1300 Morris Park Avenue, Bronx, NY 10461, United States; Division of Molecular Medicine, Walter and Eliza Hall Institute of Medical Research, Genetics and Bioinformatics Division, 1G Royal Parade, Parkville, Vic. 3050, Australia},\nabstract={There is increasing evidence that epigenetic information can be inherited across generations in mammals, despite extensive reprogramming both in the gametes and in the early developing embryo. One corollary to this is that disrupting the establishment of epigenetic state in the gametes of a parent, as a result of heterozygosity for mutations in genes involved in reprogramming, could affect the phenotype of offspring that do not inherit the mutant allele. Here we show that such effects do occur following paternal inheritance in the mouse. We detected changes to transcription and chromosome ploidy in adult animals. Paternal effects of this type have not been reported previously in mammals and suggest that the untransmitted genotype of male parents can influence the phenotype of their offspring. © 2007 Nature Publishing Group.},\nkeywords={article;  controlled study;  DNA modification;  epigenetics;  female;  gamete;  gene mutation;  genetic transcription;  genotype;  male;  mouse;  nonhuman;  phenotype;  ploidy;  priority journal;  progeny;  sex chromosomal inheritance;  sex chromosome, Adenosine Triphosphatases;  Agouti Signaling Protein;  Amino Acid Sequence;  Animals;  Base Sequence;  Chromosomal Proteins, Non-Histone;  Crosses, Genetic;  DNA Methylation;  DNA Mutational Analysis;  Epigenesis, Genetic;  Flow Cytometry;  Gene Components;  Gene Expression Regulation, Developmental;  Immunohistochemistry;  Inheritance Patterns;  Male;  Mice;  Molecular Sequence Data;  Oligonucleotide Array Sequence Analysis;  Phenotype;  Point Mutation;  Sequence Alignment;  Spermatogenesis, Animalia;  Mammalia},\ncorrespondence_address1={Whitelaw, E.; Epigenetics Laboratory, 300 Herston Road, Brisbane, QLD 4006, Australia; email: emma.whitelaw@qimr.edu.au},\nissn={10614036},\ncoden={NGENE},\npubmed_id={17450140},\nlanguage={English},\nabbrev_source_title={Nat. Genet.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Dimerization of CtIP may stabilize in vivo interactions with the Retinoblastoma-pocket domain.\n \n \n \n \n\n\n \n Stokes, P.; Thompson, L.; Marianayagam, N.; and Matthews, J.\n\n\n \n\n\n\n Biochemical and Biophysical Research Communications, 354(1): 197-202. 2007.\n cited By 7\n\n\n\n
\n\n\n\n \n \n $\"Dimerization$ 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

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@ARTICLE{Stokes2007197,\nauthor={Stokes, P.H. and Thompson, L.S. and Marianayagam, N.J. and Matthews, J.M.},\ntitle={Dimerization of CtIP may stabilize in vivo interactions with the Retinoblastoma-pocket domain},\njournal={Biochemical and Biophysical Research Communications},\nyear={2007},\nvolume={354},\nnumber={1},\npages={197-202},\ndoi={10.1016/j.bbrc.2006.12.178},\nnote={cited By 7},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33846287511&doi=10.1016%2fj.bbrc.2006.12.178&partnerID=40&md5=7dedcb96a5b4591c722495b5961ff955},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia},\nabstract={CtIP is a tumor suppressor that interacts with Retinoblastoma protein (Rb) to regulate the G1/S-phase transition of the cell cycle. Despite its large size (897 residues) CtIP has few known structured regions. Rather it contains several linear motifs that interact with known binding partners, including an LXCXE motif that binds the pocket domain of Rb-family proteins. This LXCXE motif lies at the C-terminus of the only known structured domain, an N-terminal coiled-coil dimerization domain (DD; residues 45-160). Yeast two-hybrid (Y2H) and GST-pulldown analyses showed that CtIP requires the LXCXE motif to bind the Rb-pocket. Although isothermal titration calorimetry data indicates that the LXCXE motif is the sole determinant of binding affinity for the Rb-pocket domain (KA ∼ 106 M-1), Y2H data indicates that the DD is required to stabilize the interaction in vivo. Thus dimerization may increase the apparent stability of the proteins and/or the lifetime of the complexes. © 2006 Elsevier Inc. All rights reserved.},\nauthor_keywords={Auto-activation;  CtIP;  Protein dimerization;  Protein-protein interactions;  Retinoblastoma;  Stabilization},\nkeywords={glutathione transferase;  protein CtIP;  retinoblastoma protein;  tumor suppressor protein;  unclassified drug, amino terminal sequence;  article;  binding affinity;  cancer inhibition;  carboxy terminal sequence;  cell cycle G1 phase;  cell cycle regulation;  cell cycle S phase;  controlled study;  dimerization;  in vivo study;  isothermal titration calorimetry;  nonhuman;  priority journal;  protein binding;  protein domain;  protein motif;  protein protein interaction;  protein stability;  protein structure;  two hybrid system;  yeast, Amino Acid Motifs;  Amino Acid Sequence;  Binding Sites;  Carrier Proteins;  Dimerization;  Molecular Sequence Data;  Nuclear Proteins;  Protein Binding;  Protein Interaction Mapping;  Protein Structure, Tertiary;  Retinoblastoma Protein;  Structure-Activity Relationship},\ncorrespondence_address1={Matthews, J.M.; School of Molecular and Microbial Biosciences, , NSW 2006, Australia; email: j.matthews@mmb.usyd.edu.au},\nissn={0006291X},\ncoden={BBRCA},\npubmed_id={17214969},\nlanguage={English},\nabbrev_source_title={Biochem. Biophys. Res. Commun.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n 2006\n \n \n (6)\n \n \n

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\n \n\n \n \n \n \n \n \n Mechanism of allosteric regulation of transglutaminase 2 by GTP.\n \n \n \n \n\n\n \n Begg, G.; Carrington, L.; Stokes, P.; Matthews, J.; Wouters, M.; Husain, A.; Lorand, L.; Iismaa, S.; and Graham, R.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 103(52): 19683-19688. 2006.\n cited By 108\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 \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@ARTICLE{Begg200619683,\nauthor={Begg, G.E. and Carrington, L. and Stokes, P.H. and Matthews, J.M. and Wouters, M.A. and Husain, A. and Lorand, L. and Iismaa, S.E. and Graham, R.M.},\ntitle={Mechanism of allosteric regulation of transglutaminase 2 by GTP},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2006},\nvolume={103},\nnumber={52},\npages={19683-19688},\ndoi={10.1073/pnas.0609283103},\nnote={cited By 108},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33845926856&doi=10.1073%2fpnas.0609283103&partnerID=40&md5=2c680e7fca453b4a9caab8d5b8c247eb},\naffiliation={Victor Chang Cardiac Research Institute, University of New South Wales, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; University of Queensland, Brisbane, QLD 4072, Australia; University of Sydney, Sydney, NSW 2006, Australia; University of Alabama at Birmingham, Birmingham, AL 35294, United States; Northwestern University Medical School, Chicago, IL 60611, United States},\nabstract={Allosteric regulation is a fundamental mechanism of biological control. Here, we investigated the allosteric mechanism by which GTP inhibits cross-linking activity of transglutaminase 2 (TG2), a multifunctional protein, with postulated roles in receptor signaling, extracellular matrix assembly, and apoptosis. Our findings indicate that at least two components are involved in functionally coupling the allosteric site and active center of TG2, namely (i) GTP binding to mask a conformationally destabilizing switch residue, Arg-579, and to facilitate interdomain interactions that promote adoption of a compact, catalytically inactive conformation and (ii) stabilization of the inactive conformation by an uncommon H bond between a cysteine (Cys-277, an active center residue) and a tyrosine (Tyr-516, a residue located on a loop of the β-barrel 1 domain that harbors the GTP-binding site). Although not essential for GTP-mediated inhibition of cross-linking, this H bond enhances the rate of formation of the inactive conformer. © 2006 by The National Academy of Sciences of the USA.},\nauthor_keywords={GTP inhibition;  Protein conformation;  Transamidase activity},\nkeywords={arginine;  cysteine;  guanosine triphosphate;  protein glutamine gamma glutamyltransferase;  protein glutamine gamma glutamyltransferase 2;  tyrosine;  unclassified drug, allosterism;  apoptosis;  article;  beta chain;  binding site;  controlled study;  cross linking;  enzyme active site;  enzyme conformation;  enzyme regulation;  extracellular matrix;  hydrogen bond;  molecular interaction;  nonhuman;  priority journal;  regulatory mechanism;  signal transduction, Allosteric Regulation;  Animals;  Arginine;  Binding Sites;  Cysteine;  Disulfides;  GTP-Binding Proteins;  Guanosine Triphosphate;  Hydrogen Bonding;  Models, Molecular;  Mutation;  Protein Binding;  Protein Structure, Tertiary;  Rats;  Transglutaminases;  Tyrosine;  Water},\ncorrespondence_address1={Lorand, L.; Northwestern University Medical School, Chicago, IL 60611, United States; email: l-lorand@northwestern.edu},\nissn={00278424},\ncoden={PNASA},\npubmed_id={17179049},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Stabilization of a binary protein complex by intein-mediated cyclization.\n \n \n \n \n\n\n \n Jeffries, C.; Graham, S.; Stokes, P.; Collyer, C.; Guss, J.; and Matthews, J.\n\n\n \n\n\n\n Protein Science, 15(11): 2612-2618. 2006.\n cited By 29\n\n\n\n
\n\n\n\n \n \n $\"Stabilization$ 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

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@ARTICLE{Jeffries20062612,\nauthor={Jeffries, C.M. and Graham, S.C. and Stokes, P.H. and Collyer, C.A. and Guss, J.M. and Matthews, J.M.},\ntitle={Stabilization of a binary protein complex by intein-mediated cyclization},\njournal={Protein Science},\nyear={2006},\nvolume={15},\nnumber={11},\npages={2612-2618},\ndoi={10.1110/ps.062377006},\nnote={cited By 29},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33751073463&doi=10.1110%2fps.062377006&partnerID=40&md5=8be09ca0563ef53cf46194ef40179b70},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, United Kingdom},\nabstract={The study of protein-protein interactions can be hampered by the instability of one or more of the protein complex components. In this study, we showed that intein-mediated cyclization can be used to engineer an artificial intramolecular cyclic protein complex between two interacting proteins: the largely unstable LIM-only protein 4 (LMO4) and an unstructured domain of LIM domain binding protein 1 (ldb1). The X-ray structure of the cyclic complex is identical to noncyclized versions of the complex. Chemical and thermal denaturation assays using intrinsic tryptophan fluorescence and dynamic light scattering were used to compare the relative stabilities of the cyclized complex, the intermolecular (or free) complex, and two linear versions of the intramolecular complex (in which the interacting domains of LMO4 and ldb1 were fused, via a flexible linker, in either orientation). In terms of resistance to denaturation, the cyclic complex is the most stable variant and the intermolecular complex is the least stable; however, the two linear intramolecular variants show significant differences in stability. These differences appear to be related to the relative contact order (the average distance in sequence between residues that make contacts within a structure) of key binding residues at the interface of the two proteins. Thus, the restriction of the more stable component of a complex may enhance stability to a greater extent than restraining less stable components. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society.},\nauthor_keywords={Circular protein;  Fusion protein;  Intein;  LIM domain;  LMO4;  Protein cyclization;  Protein stability},\nkeywords={bacterial protein;  binding protein;  FLICE inhibitory protein;  intein;  LIM protein;  protein cz flinca4;  unclassified drug, article;  cyclization;  fluorescence;  light scattering;  priority journal;  protein degradation;  protein denaturation;  protein protein interaction;  protein stability;  protein structure;  X ray crystallography, Crystallography, X-Ray;  Cyclization;  DNA-Binding Proteins;  Homeodomain Proteins;  Inteins;  Models, Biological;  Models, Molecular;  Multiprotein Complexes;  Protein Binding;  Protein Conformation;  Protein Denaturation;  Protein Structure, Tertiary;  Recombinant Fusion Proteins;  Transcription Factors;  Trypsin},\ncorrespondence_address1={Matthews, J.M.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.matthews@mmb.usyd.edu.au},\nissn={09618368},\ncoden={PRCIE},\npubmed_id={17001033},\nlanguage={English},\nabbrev_source_title={Protein Sci.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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\n \n\n \n \n \n \n \n \n Mutation of a critical arginine in the GTP-binding site of transglutaminase 2 disinhibits intracellular cross-linking activity.\n \n \n \n \n\n\n \n Begg, G.; Holman, S.; Stokes, P.; Matthews, J.; Graham, R.; and Iismaa, S.\n\n\n \n\n\n\n Journal of Biological Chemistry, 281(18): 12603-12609. 2006.\n cited By 59\n\n\n\n
\n\n\n\n \n \n $\"Mutation$ 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{Begg200612603,\nauthor={Begg, G.E. and Holman, S.R. and Stokes, P.H. and Matthews, J.M. and Graham, R.M. and Iismaa, S.E.},\ntitle={Mutation of a critical arginine in the GTP-binding site of transglutaminase 2 disinhibits intracellular cross-linking activity},\njournal={Journal of Biological Chemistry},\nyear={2006},\nvolume={281},\nnumber={18},\npages={12603-12609},\ndoi={10.1074/jbc.M600146200},\nnote={cited By 59},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33744950386&doi=10.1074%2fjbc.M600146200&partnerID=40&md5=30f2b128e575dfe6044294e1d84b4239},\naffiliation={Molecular Cardiology Program, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; University of Sydney, NSW 2006, Australia; Molecular Cardiology Program, Victor Chang Cardiac Research Inst., 384 Victoria St., Darlinghurst, NSW 2010, Australia},\nabstract={Transglutaminase type 2 (TG2; also known as Gh) is a multifunctional protein involved in diverse cellular processes. It has two well characterized enzyme activities: receptor-stimulated signaling that requires GTP binding and calcium-activated transamidation or cross-linking that is inhibited by GTP. In addition to the GDP binding residues identified from the human TG2 crystal structure (Liu, S., Cerione, R. A., and Clardy, J. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 2743-2747), we have previously implicated Ser 171 in GTP binding, as binding is lost with glutamate substitution (Iismaa, S. E., Wu, M.-J., Nanda, N., Church, W. B., and Graham, R. M. (2000) J. Biol. Chem. 275, 18259-18265). Here, we have shown that alanine substitution of homologous residues in rat TG2 (Phe174 in the core domain or Arg476, Arg478, or Arg579 in barrel 1) does not affect TG activity but reduces or abolishes GTP binding and GTPγS inhibition of TG activity in vitro, indicating that these residues are important in GTP binding. Alanine substitution of Ser171 does not impair GTP binding, indicating this residue does not interact directly with GTP. Arg 579 is particularly important for GTP binding, as isothermal titration calorimetry demonstrated a 100-fold reduction in GTP binding affinity by the R579A mutant. Unlike wild-type TG2 or its S171E or F174A mutants, which are sensitive to both trypsin and μ-calpain digestion, R579A is inherently more resistant to μ-calpain, but not trypsin, digestion, indicating reduced accessibility and/or flexibility of this mutant in the region of the calpain cleavage site(s). Basal TG activity of intact R579A stable SH-SY5Y neuroblastoma cell transfectants was slightly increased relative to wild-type transfectants and, in contrast to the TG activity of the latter, was further stimulated by muscarinic receptor-activated calcium mobilization. Thus, loss of GTP binding sensitizes TG2 to intracellular calcium concentrations. These findings are consistent with the notion that intracellularly, under physiological conditions, TG2 is maintained largely as a latent enzyme, its calcium-activated crosslinking activity being suppressed allosterically by guanine nucleotide binding. © 2006 by The American Society for Biochemistry and Molecular Biology, Inc.},\nkeywords={Biochemistry;  Crosslinking;  Crystal structure;  Enzymes;  Human engineering;  Proteins, GTP-binding;  Isothermal titration calorimetry;  Transfectants;  Transglutaminase, Mutagens, arginine;  calcium;  calpain;  guanosine 5' o (3 thiotriphosphate);  guanosine diphosphate;  guanosine triphosphate;  mu calpain;  muscarinic receptor;  protein glutamine gamma glutamyltransferase;  serine;  transglutaminase 2;  unclassified drug, amino acid substitution;  article;  binding affinity;  binding site;  calcium mobilization;  controlled study;  cross linking;  enzyme activity;  enzyme inhibition;  enzyme regulation;  gene mutation;  human;  human cell;  in vitro study;  isothermal titration calorimetry;  priority journal;  protein folding;  wild type, Animals;  Arginine;  Binding Sites;  Calcium;  Cell Line, Tumor;  Cross-Linking Reagents;  GTP-Binding Proteins;  Guanosine Triphosphate;  Humans;  Models, Molecular;  Mutation;  Protein Processing, Post-Translational;  Rats;  Serine;  Transglutaminases;  Trypsin},\ncorrespondence_address1={Iismaa, S.E.; Molecular Cardiology Program, 384 Victoria St., Darlinghurst, NSW 2010, Australia; email: s.iismaa@victorchang.unsw.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={16522628},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n

\n Transglutaminase type 2 (TG2; also known as Gh) is a multifunctional protein involved in diverse cellular processes. It has two well characterized enzyme activities: receptor-stimulated signaling that requires GTP binding and calcium-activated transamidation or cross-linking that is inhibited by GTP. In addition to the GDP binding residues identified from the human TG2 crystal structure (Liu, S., Cerione, R. A., and Clardy, J. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 2743-2747), we have previously implicated Ser 171 in GTP binding, as binding is lost with glutamate substitution (Iismaa, S. E., Wu, M.-J., Nanda, N., Church, W. B., and Graham, R. M. (2000) J. Biol. Chem. 275, 18259-18265). Here, we have shown that alanine substitution of homologous residues in rat TG2 (Phe174 in the core domain or Arg476, Arg478, or Arg579 in barrel 1) does not affect TG activity but reduces or abolishes GTP binding and GTPγS inhibition of TG activity in vitro, indicating that these residues are important in GTP binding. Alanine substitution of Ser171 does not impair GTP binding, indicating this residue does not interact directly with GTP. Arg 579 is particularly important for GTP binding, as isothermal titration calorimetry demonstrated a 100-fold reduction in GTP binding affinity by the R579A mutant. Unlike wild-type TG2 or its S171E or F174A mutants, which are sensitive to both trypsin and μ-calpain digestion, R579A is inherently more resistant to μ-calpain, but not trypsin, digestion, indicating reduced accessibility and/or flexibility of this mutant in the region of the calpain cleavage site(s). Basal TG activity of intact R579A stable SH-SY5Y neuroblastoma cell transfectants was slightly increased relative to wild-type transfectants and, in contrast to the TG activity of the latter, was further stimulated by muscarinic receptor-activated calcium mobilization. Thus, loss of GTP binding sensitizes TG2 to intracellular calcium concentrations. These findings are consistent with the notion that intracellularly, under physiological conditions, TG2 is maintained largely as a latent enzyme, its calcium-activated crosslinking activity being suppressed allosterically by guanine nucleotide binding. © 2006 by The American Society for Biochemistry and Molecular Biology, Inc.\n

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\n \n\n \n \n \n \n \n \n Disparate thermodynamics governing T cell receptor-MHC-1 interactions implicate extrinsic factors in guiding MHC restriction.\n \n \n \n \n\n\n \n Ely, L.; Beddoe, T.; Clements, C.; Matthews, J.; Purcell, A.; Kjer-Nielsen, L.; McCluskey, J.; and Rossjohn, J.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 103(17): 6641-6646. 2006.\n cited By 48\n\n\n\n
\n\n\n\n \n \n $\"Disparate$ 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

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@ARTICLE{Ely20066641,\nauthor={Ely, L.K. and Beddoe, T. and Clements, C.S. and Matthews, J.M. and Purcell, A.W. and Kjer-Nielsen, L. and McCluskey, J. and Rossjohn, J.},\ntitle={Disparate thermodynamics governing T cell receptor-MHC-1 interactions implicate extrinsic factors in guiding MHC restriction},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={2006},\nvolume={103},\nnumber={17},\npages={6641-6646},\ndoi={10.1073/pnas.0600743103},\nnote={cited By 48},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33646240071&doi=10.1073%2fpnas.0600743103&partnerID=40&md5=1e80c1cdf1c74acfa0d5b8af83fac84b},\naffiliation={Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Vic. 3800, Australia; School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Vic. 3010, Australia; Department of Microbiology and Immunology, University of Melbourne, Parkville, Vic. 3010, Australia; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, United States},\nabstract={The underlying basis of major histocompatibility complex (MHC) restriction is unclear. Nevertheless, current data suggest that a common thermodynamic signature dictates αβ T cell receptor (TcR) ligation. To evaluate whether this thermodynamic signature defines MHC restriction, we have examined the thermodynamic basis of a highly characterized immunodominant TcR interacting with its cognate peptide-MHC-1 ligand. Surprisingly, we observed this interaction to be governed by favorable enthalpic and entropic forces, which is in contrast to the prevailing generality, namely, enthalpically driven interactions combined with markedly unfavorable entropic forces. We conclude that extrinsic molecular factors, such as coreceptor ligation, conformational adjustments involved in TcR signaling, or constraints dictated by higher-order arrangement of ligated TcRs, might play a greater role in guiding MHC restriction than appreciated previously. © 2006 by The National Academy of Sciences of the USA.},\nauthor_keywords={Cytotoxic T lymphocyte;  Energetics;  Epstein-Barr virus;  Immunodominance;  Microcalorimetry},\nkeywords={major histocompatibility antigen class 1;  T lymphocyte receptor;  T lymphocyte receptor alpha chain;  T lymphocyte receptor beta chain, article;  conformational transition;  cytotoxic T lymphocyte;  energy transfer;  enthalpy;  entropy;  Epstein Barr virus;  human;  major histocompatibility complex;  molecular interaction;  nonhuman;  priority journal;  signal transduction;  thermodynamics, Amino Acid Sequence;  beta 2-Microglobulin;  Binding Sites;  Entropy;  Epstein-Barr Virus Nuclear Antigens;  HLA-B Antigens;  Humans;  Hydrophobicity;  Ligands;  Models, Molecular;  Multiprotein Complexes;  Peptide Fragments;  Protein Conformation;  Receptors, Antigen, T-Cell, alpha-beta;  Recombinant Proteins;  Signal Transduction;  Surface Plasmon Resonance;  T-Lymphocytes, Cytotoxic;  Thermodynamics, Human herpesvirus 4},\ncorrespondence_address1={McCluskey, J.; Department of Microbiology and Immunology, , Parkville, Vic. 3010, Australia},\nissn={00278424},\ncoden={PNASA},\npubmed_id={16617112},\nlanguage={English},\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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@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

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\n \n 2005\n \n \n (6)\n \n \n

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\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

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@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

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\n \n\n \n \n \n \n \n \n Protein-protein interactions in human disease.\n \n \n \n \n\n\n \n Ryan, D.; and Matthews, J.\n\n\n \n\n\n\n Current Opinion in Structural Biology, 15(4): 441-446. 2005.\n cited By 242\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

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@ARTICLE{Ryan2005441,\nauthor={Ryan, D.P. and Matthews, J.M.},\ntitle={Protein-protein interactions in human disease},\njournal={Current Opinion in Structural Biology},\nyear={2005},\nvolume={15},\nnumber={4},\npages={441-446},\ndoi={10.1016/j.sbi.2005.06.001},\nnote={cited By 242},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-23044496736&doi=10.1016%2fj.sbi.2005.06.001&partnerID=40&md5=79ce2fbb098766cb0516fce29e31bbdd},\naffiliation={School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Many human diseases are the result of abnormal protein-protein interactions involving endogenous proteins, proteins from pathogens or both. The inhibition of these aberrant associations is of obvious clinical significance. Because of the diverse nature of protein-protein interactions, however, the successful design of therapeutics requires detailed knowledge of each system at a molecular and atomic level. Several recent studies have identified and/or characterised specific interactions from various disease systems, including cervical cancer, bacterial infection, leukaemia and neurodegenerative disease. A range of approaches are being developed to generate inhibitors of protein-protein interactions that may form useful therapeutics for human disease. © 2005 Elsevier Ltd. All rights reserved.},\nkeywords={glycoprotein E1;  protein;  protein inhibitor, amino terminal sequence;  atom;  bacterial infection;  carboxy terminal sequence;  degenerative disease;  general aspects of disease;  host;  host pathogen interaction;  human;  leukemia;  molecule;  nonhuman;  pathogenesis;  priority journal;  protein analysis;  protein domain;  protein protein interaction;  protein structure;  protein targeting;  review;  science;  structure analysis;  uterine cervix cancer, Disease;  Humans;  Models, Molecular;  Molecular Sequence Data;  Molecular Structure;  Protein Binding;  Protein Conformation;  Proteins},\ncorrespondence_address1={Matthews, J.M.; School of Molecular and Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.matthews@mmb.usyd.edu.au},\nissn={0959440X},\ncoden={COSBE},\npubmed_id={15993577},\nlanguage={English},\nabbrev_source_title={Curr. Opin. Struct. Biol.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

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\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

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@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

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\n \n\n \n \n \n \n \n \n Stabilization of native protein fold by intein-mediated covalent cyclization.\n \n \n \n \n\n\n \n Williams, N.; Liepinsh, E.; Watt, S.; Prosselkov, P.; Matthews, J.; Attard, P.; Beck, J.; Dixon, N.; and Otting, G.\n\n\n \n\n\n\n Journal of Molecular Biology, 346(4): 1095-1108. 2005.\n cited By 43\n\n\n\n
\n\n\n\n \n \n $\"Stabilization$ 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

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@ARTICLE{Williams20051095,\nauthor={Williams, N.K. and Liepinsh, E. and Watt, S.J. and Prosselkov, P. and Matthews, J.M. and Attard, P. and Beck, J.L. and Dixon, N.E. and Otting, G.},\ntitle={Stabilization of native protein fold by intein-mediated covalent cyclization},\njournal={Journal of Molecular Biology},\nyear={2005},\nvolume={346},\nnumber={4},\npages={1095-1108},\ndoi={10.1016/j.jmb.2004.12.037},\nnote={cited By 43},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-13444274403&doi=10.1016%2fj.jmb.2004.12.037&partnerID=40&md5=a5cecdf6aec9ec397f8c313f0feb7d26},\naffiliation={Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia; Dept. of Med. Biochem. and Biophys., Karolinska Institute, S-17177 Stockholm, Sweden; Chemistry Department, University of Wollongong, Wollongong, NSW 2522, Australia; Sch. of Molec. and Microbial Biosci., University of Sydney, NSW 2006, Australia; School of Chemistry, University of Sydney, NSW 2006, Australia},\nabstract={A mutant version of the N-terminal domain of Escherichia coli DnaB helicase was used as a model system to assess the stabilization against unfolding gained by covalent cyclization. Cyclization was achieved in vivo by formation of an amide bond between the N and C termini with the help of a split mini-intein. Linear and circular proteins were constructed to be identical in amino acid sequence. Mutagenesis of Phe102 to Glu rendered the protein monomeric even at high concentration. A difference in free energy of unfolding, ΔΔG, between circular and linear protein of 2.3(±0.5) kcal mol-1 was measured at 10°C by circular dichroism. A theoretical estimate of the difference in conformational entropy of linear and circular random chains in a three-dimensional cubic lattice model predicted ΔΔG=2.3 kcal mol-1, suggesting that stabilization by protein cyclization is driven by the reduced conformational entropy of the unfolded state. Amide-proton exchange rates measured by NMR spectroscopy and mass spectrometry showed a uniform, approximately tenfold decrease of the exchange rates of the most slowly exchanging amide protons, demonstrating that cyclization globally decreases the unfolding rate of the protein. The amide proton exchange was found to follow EX1 kinetics at near-neutral pH, in agreement with an unusually slow refolding rate of less than 4 min-1 measured by stopped-flow circular dichroism. The linear and circular proteins differed more in their unfolding than in their folding rates. Global unfolding of the N-terminal domain of E. coli DnaB is thus promoted strongly by spatial separation of the N and C termini, whereas their proximity is much less important for folding. © 2005 Elsevier Ltd. All rights reserved.},\nauthor_keywords={E. coli DnaB;  EX1 amide proton exchange;  NMR spectroscopy;  Protein cyclization;  Protein stability},\nkeywords={amide;  bacterial enzyme;  DNA B helicase;  helicase;  intein;  monomer;  proton;  unclassified drug, amino acid sequence;  amino terminal sequence;  article;  carboxy terminal sequence;  chemical bond;  circular dichroism;  controlled study;  cyclization;  energy;  entropy;  Escherichia coli;  in vivo study;  mass spectrometry;  molecular model;  mutagenesis;  nonhuman;  nuclear magnetic resonance spectroscopy;  pH;  priority journal;  protein conformation;  protein domain;  protein folding;  protein stability;  temperature dependence;  theoretical study, Escherichia coli},\ncorrespondence_address1={Otting, G.; Research School of Chemistry, , Canberra, ACT 0200, Australia; email: gottfried.otting@anu.edu.au},\npublisher={Academic Press},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={15701520},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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@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

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\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

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@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

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\n \n\n \n \n \n \n \n \n The power of two: Protein dimerization in biology.\n \n \n \n \n\n\n \n Marianayagam, N.; Sunde, M.; and Matthews, J.\n\n\n \n\n\n\n Trends in Biochemical Sciences, 29(11): 618-625. 2004.\n cited By 423\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

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@ARTICLE{Marianayagam2004618,\nauthor={Marianayagam, N.J. and Sunde, M. and Matthews, J.M.},\ntitle={The power of two: Protein dimerization in biology},\njournal={Trends in Biochemical Sciences},\nyear={2004},\nvolume={29},\nnumber={11},\npages={618-625},\ndoi={10.1016/j.tibs.2004.09.006},\nnote={cited By 423},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-6344260294&doi=10.1016%2fj.tibs.2004.09.006&partnerID=40&md5=202a8cbf65238d67917c143f719c6382},\naffiliation={Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW 2006, Australia, Australia},\nabstract={The self-association of proteins to form dimers and higher-order oligomers is a very common phenomenon. Recent structural and biophysical studies show that protein dimerization or oligomerization is a key factor in the regulation of proteins such as enzymes, ion channels, receptors and transcription factors. In addition, self-association can help to minimize genome size, while maintaining the advantages of modular complex formation. Oligomerization, however, can also have deleterious consequences when nonnative oligomers associated with pathogenic states are generated. Specific protein dimerization is integral to biological function, structure and control, and must be under substantial selection pressure to be maintained with such frequency throughout biology.},\nkeywords={dimer;  ion channel;  oligomer;  transcription factor, cell membrane transport;  crystal structure;  dimerization;  DNA binding;  enzyme activation;  enzyme regulation;  Escherichia coli;  gene expression;  gene frequency;  genome;  hydrogen bond;  nonhuman;  oligomerization;  priority journal;  protein structure;  review;  sickle cell anemia;  Streptomyces lividans;  X ray crystallography, Allosteric Regulation;  Amyloid;  Animals;  Cell Membrane;  Dimerization;  DNA-Binding Proteins;  Enzyme Activation;  Gene Expression Regulation;  Humans;  Models, Molecular;  Protein Structure, Quaternary;  Protein Transport;  Proteins, Escherichia coli;  Streptomyces;  Streptomyces lividans},\ncorrespondence_address1={Sch. of Molec. and Microbial Biosci., Australia},\nissn={09680004},\ncoden={TBSCD},\npubmed_id={15501681},\nlanguage={English},\nabbrev_source_title={Trends Biochem. Sci.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

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\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

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@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

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\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

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@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

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\n \n\n \n \n \n \n \n \n Tandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex.\n \n \n \n \n\n\n \n Deane, J.; Ryan, D.; Sunde, M.; Maher, M.; Guss, J.; Visvader, J.; and Matthews, J.\n\n\n \n\n\n\n EMBO Journal, 23(18): 3589-3598. 2004.\n cited By 79\n\n\n\n
\n\n\n\n \n \n $\"Tandem$ 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

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@ARTICLE{Deane20043589,\nauthor={Deane, J.E. and Ryan, D.P. and Sunde, M. and Maher, M.J. and Guss, J.M. and Visvader, J.E. and Matthews, J.M.},\ntitle={Tandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex},\njournal={EMBO Journal},\nyear={2004},\nvolume={23},\nnumber={18},\npages={3589-3598},\ndoi={10.1038/sj.emboj.7600376},\nnote={cited By 79},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-5044224710&doi=10.1038%2fsj.emboj.7600376&partnerID=40&md5=411ffd08d4d191c337d006b7d86e0843},\naffiliation={Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW 2006, Australia; Walter/Eliza Hall Inst. Med. Res., Parkville, Vic., Australia},\nabstract={Nuclear LIM-only (LMO) and LIM-homeodomain (LIM-HD) proteins have important roles in cell fate determination, organ development and oncogenesis. These proteins contain tandemly arrayed LIM domains that bind the LIM interaction domain (LID) of the nuclear adaptor protein LIM domain-binding protein-1 (Ldb1). We have determined a high-resolution X-ray crystal structure of LMO4, a putative breast oncoprotein, in complex with Ldb1-LID, providing the first example of a tandem LIM:Ldb1-LID complex and the first structure of a type-B LIM domain. The complex possesses a highly modular structure with Ldb1-LID binding in an extended manner across both LIM domains of LMO4. The interface contains extensive hydrophobic and electrostatic interactions and multiple backbone-backbone hydrogen bonds. A mutagenic screen of Ldb1-LID, assessed by yeast two-hybrid and competition ELISA analysis, identified key features at the interface and revealed that the interaction is tolerant to mutation. These combined properties provide a mechanism for the binding of Ldb1 to numerous LMO and LIM-HD proteins. Furthermore, the modular extended interface may form a general mode of binding to tandem LIM domains.},\nauthor_keywords={Ldb1;  LIM;  LMO4 domains;  Protein interactions;  Tandem binding},\nkeywords={adaptor protein;  binding protein;  homeodomain protein;  nuclear protein;  oncoprotein;  protein Ldb1;  protein LIM;  protein LIM HD;  protein lmo4;  unclassified drug, article;  carcinogenesis;  cell fate;  complex formation;  crystal structure;  enzyme linked immunosorbent assay;  hydrogen bond;  hydrophobicity;  molecular interaction;  mutation;  organogenesis;  priority journal;  protein domain;  protein protein interaction;  two hybrid system;  yeast, Amino Acid Sequence;  Animals;  Binding Sites;  Crystallography, X-Ray;  DNA-Binding Proteins;  Drug Synergism;  Factor Xa;  Homeodomain Proteins;  Magnetic Resonance Spectroscopy;  Mice;  Molecular Sequence Data;  Mutation;  Protein Binding;  Protein Conformation;  Protein Structure, Tertiary;  Recombinant Fusion Proteins;  Saccharomyces cerevisiae;  Sequence Homology, Amino Acid;  Tandem Repeat Sequences;  Transcription Factors;  Two-Hybrid System Techniques},\ncorrespondence_address1={Matthews, J.M.; Sch. of Molec. and Microbial Biosci., , Sydney, NSW 2006, Australia},\nissn={02614189},\ncoden={EMJOD},\npubmed_id={15343268},\nlanguage={English},\nabbrev_source_title={EMBO J.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Dimerization of CtIP, a BRCA1- and CtBP-interacting protein, is mediated by an N-terminal coiled-coil motif.\n \n \n \n \n\n\n \n Dubin, M.; Stokes, P.; Sum, E.; Williams, R.; Valova, V.; Robinson, P.; Lindeman, G.; Glover, J.; Visvader, J.; and Matthews, J.\n\n\n \n\n\n\n Journal of Biological Chemistry, 279(26): 26932-26938. 2004.\n cited By 44\n\n\n\n
\n\n\n\n \n \n $\"Dimerization$ 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

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@ARTICLE{Dubin200426932,\nauthor={Dubin, M.J. and Stokes, P.H. and Sum, E.Y.M. and Williams, R.S. and Valova, V.A. and Robinson, P.J. and Lindeman, G.J. and Glover, J.N.M. and Visvader, J.E. and Matthews, J.M.},\ntitle={Dimerization of CtIP, a BRCA1- and CtBP-interacting protein, is mediated by an N-terminal coiled-coil motif},\njournal={Journal of Biological Chemistry},\nyear={2004},\nvolume={279},\nnumber={26},\npages={26932-26938},\ndoi={10.1074/jbc.M313974200},\nnote={cited By 44},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-3042593642&doi=10.1074%2fjbc.M313974200&partnerID=40&md5=261effa637560e65acebff1bc1aa0ca8},\naffiliation={Sch. of Molec. and Microbial Biosci., University of Sydney, Australia; Walter/Eliza Hall Inst. of Med. Res., Bone Marrow Research Laboratories, Royal Melbourne Hospital, Parkville, Vic. 3050, Australia; Children's Med. Research Institute, Westmead, NSW 2145, Australia; Department of Biochemistry, University of Alberta, Edmonton, Alta. T6G 2H7, Canada; Sch. of Molec. and Microbial Biosci., Bldg. G08, University of Sydney, Australia},\nabstract={CtIP is a transcriptional co-regulator that binds a number of proteins involved in cell cycle control and cell development, such as CtBP (C terminus-binding protein), BRCA1 (breast cancer-associated protein-1), and LMO4 (LIM-only protein-4). The only recognizable structural motifs within CtIP are two putative coiled-coil domains located near the N and C termini of the protein. We now show that the N-terminal coiled coil (residues 45-160), but not the C-terminal coiled coil, mediates homodimerization of CtIP in mammalian 293T cells. The N-terminal coiled coil did not facilitate binding to LMO4 and BRCA1 proteins in these cells. A protease-resistant domain (residues 27-168) that minimally encompasses the putative N-terminal coiled coil was identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. This region is predicted to contain two smaller coiled-coil regions. The CtIP-(45-160) dimerization domain is helical and dimeric, indicating that the domain does form a coiled coil. The two smaller domains, CtIP-(45-92) and CtIP-(93-160), also formed dimers of lower binding affinity, but with less helical content than the longer peptide. The hydrodynamic radius of CtIP-(45-160) is the same as those of CtIP-(45-92) and CtIP-(93-160), implying that CtIP-(45-160) does not form a single long coiled coil, but a more compact structure involving homodimerization of the two smaller coiled coils, which fold back as a four-helix bundle or other compact structure. These results suggest a specific model for CtIP homodimerization via its N terminus and contribute to an improved understanding of how this protein might assemble other factors required for its role as a transcriptional corepressor.},\nkeywords={Cells;  Cytology;  Desorption;  Dimerization;  Ionization;  Mass spectrometry;  Tumors, Cell cycles;  Homodimerization, Proteins, binding protein;  BRCA1 protein;  LIM protein;  nuclear protein;  protein ctbp;  protein CtIP;  protein lmo4;  transcription factor;  unclassified drug, amino terminal sequence;  article;  binding affinity;  carboxy terminal sequence;  controlled study;  dimerization;  human;  human cell;  light scattering;  matrix assisted laser desorption ionization time of flight mass spectrometry;  peptide mapping;  priority journal;  protein degradation;  protein domain;  protein motif;  protein protein interaction;  transcription regulation;  ultracentrifugation;  ultraviolet spectrophotometry, Alcohol Oxidoreductases;  Amino Acid Motifs;  Amino Acid Sequence;  BRCA1 Protein;  Carrier Proteins;  Cell Line;  Chymotrypsin;  Circular Dichroism;  Dimerization;  DNA-Binding Proteins;  Escherichia coli;  Homeodomain Proteins;  Humans;  Models, Molecular;  Molecular Sequence Data;  Nuclear Proteins;  Peptide Fragments;  Phosphoproteins;  Protein Structure, Tertiary;  Recombinant Proteins;  Retinoblastoma Protein;  Transcription Factors;  Transfection;  Trypsin;  Ultracentrifugation, Mammalia},\ncorrespondence_address1={Sch. of Molec. and Microbial Biosci., Australia; email: j.matthews@mmb.usyd.edu.au},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={15084581},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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@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

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\n \n 2003\n \n \n (6)\n \n \n

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\n \n\n \n \n \n \n \n \n LIM-domain-binding protein 1: A multifunctional cofactor that interacts with diverse proteins.\n \n \n \n \n\n\n \n Matthews, J.; and Visvader, J.\n\n\n \n\n\n\n EMBO Reports, 4(12): 1132-1137. 2003.\n cited By 136\n\n\n\n
\n\n\n\n \n \n $\"LIM-domain-binding$ 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

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@ARTICLE{Matthews20031132,\nauthor={Matthews, J.M. and Visvader, J.E.},\ntitle={LIM-domain-binding protein 1: A multifunctional cofactor that interacts with diverse proteins},\njournal={EMBO Reports},\nyear={2003},\nvolume={4},\nnumber={12},\npages={1132-1137},\ndoi={10.1038/sj.embor.7400030},\nnote={cited By 136},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0347093483&doi=10.1038%2fsj.embor.7400030&partnerID=40&md5=c67a4f23cd7127c20f02fed39071d8bf},\naffiliation={School of Molec. Microbial Biosci., University of Sydney, Sydney, NSW 2006, Australia; W./E. Hall Inst. of Medical Research, Bone Marrow Research Laboratories, Parkville, Vic. 3050, Australia},\nabstract={The ubiquitous nuclear adaptor protein LIM-domain-binding protein 1 (Ldb1) was originally identified as a cofactor for LIM-homeodomain and LIM-only (LMO) proteins that have fundamental roles in development. In parallel, Ldb1 has been shown to have essential functions in diverse biological processes in different organisms. The recent targeting of this gene in mice has revealed roles for Ldb1 in neural patterning and development that have been conserved throughout evolution. Furthermore, the elucidation of the three-dimensional structures of LIM-Ldb1 complexes has provided insight into the molecular basis for the ability of Ldb1 to contact diverse LIM-domain proteins. It has become evident that Ldb1 is a multi-adaptor protein that mediates interactions between different classes of transcription factors and their co-regulators and that the nature of these complexes determines cell fate and differentiation.},\nkeywords={adaptor protein;  binding protein;  homeodomain protein;  LIM domain binding protein 1;  nuclear protein;  transcription factor;  unclassified drug, cell differentiation;  cell fate;  controlled study;  dimerization;  gene targeting;  genetic conservation;  human;  molecular evolution;  nonhuman;  priority journal;  protein analysis;  protein binding;  protein domain;  protein function;  protein protein interaction;  protein structure;  review;  transcription regulation, Amino Acid Sequence;  Animals;  Cell Differentiation;  Dimerization;  DNA-Binding Proteins;  Homeodomain Proteins;  Humans;  Models, Molecular;  Molecular Sequence Data;  Phylogeny;  Species Specificity;  Transcription Factors},\ncorrespondence_address1={Matthews, J.M.; School of Molec. Microbial Biosci., , Sydney, NSW 2006, Australia; email: j.matthews@mmb.usyd.edu.au},\nissn={1469221X},\ncoden={ERMEA},\npubmed_id={14647207},\nlanguage={English},\nabbrev_source_title={EMBO Rep.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Crystallization of FLINC4, an intramolecular LMO4-ldb1 complex.\n \n \n \n \n\n\n \n Deane, J.; Maher, M.; Langley, D.; Graham, S.; Visvader, J.; Guss, J.; and Matthews, J.\n\n\n \n\n\n\n Acta Crystallographica - Section D Biological Crystallography, 59(8): 1484-1486. 2003.\n cited By 11\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 \n \n\n\n\n

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@ARTICLE{Deane20031484,\nauthor={Deane, J.E. and Maher, M.J. and Langley, D.B. and Graham, S.C. and Visvader, J.E. and Guss, J.M. and Matthews, J.M.},\ntitle={Crystallization of FLINC4, an intramolecular LMO4-ldb1 complex},\njournal={Acta Crystallographica - Section D Biological Crystallography},\nyear={2003},\nvolume={59},\nnumber={8},\npages={1484-1486},\ndoi={10.1107/S0907444903011843},\nnote={cited By 11},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0041566740&doi=10.1107%2fS0907444903011843&partnerID=40&md5=081bdbe558c8cdb2a75adce99805e31a},\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={LMO4 is the most recently discovered member of a small family of nuclear transcriptional regulators that are important for both normal development and disease processes. LMO4 is comprised primarily of two tandemly repeated LIM domains and interacts with the ubiquitous nuclear adaptor protein ldb1. This interaction is mediated via the LIM domains of LMO4 and the LIM-interaction domain (LID) of ldb1. An intramolecular complex, termed FLINC4, consisting of the two LIM domains from LMO4 linked to the LID domain of ldb1 via a flexible linker has been engineered, purified and crystallized. The trigonal crystals, which belong to space group P312 with unit-cell parameters a = 61.3, c = 93.2 Å, diffract to 1.3 Å, resolution and contain one molecule of FLINC4 per asymmetric unit. Native and multiple-wavelength anomalous dispersion (MAD) data collected at the Zn X-ray absorption edge have been recorded to 1.3 and 1. 7 Å resolution, respectively. Anomalous Patterson maps calculated with data collected at the peak wavelength show strong peaks sufficient to determine the positions of four Zn atoms per asymmetric unit.},\nkeywords={DNA binding protein;  homeodomain protein;  hybrid protein;  LDB1 protein, human;  LMO4 protein, human;  Lmo4 protein, mouse;  transcription factor;  zinc, animal;  article;  cell nucleus;  chemistry;  human;  metabolism;  protein binding;  protein conformation;  protein tertiary structure;  X ray crystallography, Animals;  Cell Nucleus;  Crystallography, X-Ray;  DNA-Binding Proteins;  Homeodomain Proteins;  Humans;  Protein Binding;  Protein Conformation;  Protein Structure, Tertiary;  Recombinant Fusion Proteins;  Transcription Factors;  Zinc, Animalia},\ncorrespondence_address1={Matthews, J.M.; Sch. of Molec./Microbial Biosciences, , Sydney, NSW 2006, Australia; email: j.matthews@mmb.usyd.edu.au},\nissn={09074449},\ncoden={ABCRE},\npubmed_id={12876360},\nlanguage={English},\nabbrev_source_title={Acta Crystallogr. Sect. D Biol. Crystallogr.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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@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

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\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

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@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

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\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

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@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

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\n \n\n \n \n \n \n \n \n The LIM protein FHL3 binds basic Krüppel-like factor/Krüppel-like factor 3 and its co-repressor C-terminal-binding protein 2.\n \n \n \n \n\n\n \n Turner, J.; Nicholas, H.; Bishop, D.; Matthews, J.; and Crossley, M.\n\n\n \n\n\n\n Journal of Biological Chemistry, 278(15): 12786-12795. 2003.\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 \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

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@ARTICLE{Turner200312786,\nauthor={Turner, J. and Nicholas, H. and Bishop, D. and Matthews, J.M. and Crossley, M.},\ntitle={The LIM protein FHL3 binds basic Krüppel-like factor/Krüppel-like factor 3 and its co-repressor C-terminal-binding protein 2},\njournal={Journal of Biological Chemistry},\nyear={2003},\nvolume={278},\nnumber={15},\npages={12786-12795},\ndoi={10.1074/jbc.M300587200},\nnote={cited By 55},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0038645813&doi=10.1074%2fjbc.M300587200&partnerID=40&md5=8fee6abfed7017c0bb769dcbcc4997f0},\nabstract={The ability of DNA-binding transcription factors to recruit specific cofactors is central to the mechanism by which they regulate gene expression. BKLF/KLF3, a member of the Krüppel-like factor family of zinc finger proteins, is a potent transcriptional repressor that recruits a CtBP co-repressor. We show here that BKLF also recruits the four and a half LIM domain protein FHL3. Different but closely linked regions of BKLF mediate contact with CtBP2 and FHL3. We present evidence that CtBP2 also interacts with FHL3 and demonstrate that the three proteins co-elute in gel filtration experiments. CtBP and FHL proteins have been implicated in both nuclear and cytoplasmic functions, but expression of BKLF promotes the nuclear accumulation of both FHL3 and CtBP2. FHL proteins have been shown to act predominantly as co-activators of transcription. However, we find FHL3 can repress transcription. We suggest that LIM proteins like FHL3 are important in assembling specific repression or activation complexes, depending on conditions such as cofactor availability and promoter context.},\nkeywords={Filtration;  Gels;  Genes;  Proteins, Gene expression, Biochemistry, basic kruppel like factor;  binding protein;  c terminal binding protein 2;  DNA binding protein;  kruppel like factor 3;  LIM protein;  messenger RNA;  protein fhl 3;  unclassified drug;  zinc finger protein;  DNA binding protein;  FHL3 protein, human;  glutathione transferase;  homeodomain protein;  hybrid protein;  KLF3 protein, human;  kruppel like factor;  messenger RNA;  phosphoprotein;  recombinant protein;  repressor protein;  signal peptide;  zinc finger protein, animal cell;  article;  complex formation;  embryo;  gel filtration;  mouse;  nonhuman;  priority journal;  promoter region;  protein analysis;  protein binding;  protein domain;  protein interaction;  transcription initiation;  animal;  binding site;  cell strain COS1;  cell strain K 562;  Cercopithecus;  chemistry;  genetic transcription;  genetic transfection;  genetics;  human;  metabolism;  molecular cloning;  Saccharomyces cerevisiae, Animalia, Animals;  Binding Sites;  Cercopithecus aethiops;  Cloning, Molecular;  COS Cells;  DNA-Binding Proteins;  Glutathione Transferase;  Homeodomain Proteins;  Humans;  Intracellular Signaling Peptides and Proteins;  K562 Cells;  Kruppel-Like Transcription Factors;  Phosphoproteins;  Recombinant Fusion Proteins;  Recombinant Proteins;  Repressor Proteins;  RNA, Messenger;  Saccharomyces cerevisiae;  Transcription, Genetic;  Transfection;  Zinc Fingers},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={12556451},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n 2002\n \n \n (5)\n \n \n

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\n \n\n \n \n \n \n \n \n Zinc fingers - Folds for many occasions.\n \n \n \n \n\n\n \n Matthews, J.; and Sunde, M.\n\n\n \n\n\n\n IUBMB Life, 54(6): 351-355. 2002.\n cited By 243\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\n\n\n

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@ARTICLE{Matthews2002351,\nauthor={Matthews, J.M. and Sunde, M.},\ntitle={Zinc fingers - Folds for many occasions},\njournal={IUBMB Life},\nyear={2002},\nvolume={54},\nnumber={6},\npages={351-355},\ndoi={10.1080/15216540216035},\nnote={cited By 243},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0036931270&doi=10.1080%2f15216540216035&partnerID=40&md5=cbe731b974eca3d887225a5fb2bb0f30},\naffiliation={Sch. of Molec. and Microbial Biosci., University of Sydney, Sydney, NSW 2006, Australia},\nabstract={Zinc finger domains (ZnFs) are common, relatively small protein motifs that fold around one or more zinc ions. In addition to their role as a DNA-binding module, ZnFs have recently been shown to mediate protein:protein and protein:lipid interactions. This small zinc-ligating domain, often found in clusters containing fingers with different binding specificities, can facilitate multiple, often independent intermolecular interactions between nucleic acids and proteins. Classical ZnFs, typified by TFIIIA, ligate zinc via pairs of cysteine and histidine residues but there are at least 14 different classes of Zn fingers, which differ in the nature and arrangement of their zinc-binding residues. Some GATA-type ZnFs can bind to both DNA and a variety of other proteins. Thus proteins with multiple GATA-type fingers can play a complex role in regulating transcription through the interplay of these different binding selectivities and affinities. Other ZnFs have more specific functions, such as DNA-binding ZnFs in the nuclear hormone receptor proteins and small-molecule-binding ZnFs in protein kinase C. Some classes of ZnFs appear to act exclusively in protein-only interactions. These include the RING family of ZnFs that are involved in ubiquitination processes and in the assembly of large protein complexes, LIM, TAZ, and PHD domains. We review the similarities and differences in structure and functions of different ZnF classes and highlight the versatility of this fold.},\nauthor_keywords={Domain;  Function;  Interaction;  Structure;  Zinc finger},\nkeywords={cysteine;  DNA;  histidine;  hormone receptor;  nucleic acid;  protein kinase C;  transcription factor;  transcription factor GATA;  transcription factor ring;  unclassified drug;  zinc finger protein, amino acid sequence;  binding affinity;  complex formation;  human;  molecular interaction;  nonhuman;  protein DNA binding;  protein domain;  protein folding;  protein lipid interaction;  protein motif;  protein protein interaction;  protein structure;  Proteus;  review;  transcription regulation;  zinc finger motif, Amino Acid Motifs;  Animals;  Cysteine;  Histidine;  Humans;  Ligands;  Models, Molecular;  Protein Binding;  Protein Folding;  Protein Structure, Secondary;  Protein Structure, Tertiary;  Zinc;  Zinc Fingers},\ncorrespondence_address1={Matthews, J.M.; Sch. of Molec. and Microbial Biosci., , Sydney, NSW 2006, Australia; email: j.matthews@mmb.usyd.edu.au},\nissn={15216543},\ncoden={IULIF},\npubmed_id={12665246},\nlanguage={English},\nabbrev_source_title={IUBMB Life},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

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\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

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@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

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\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

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@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

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\n \n\n \n \n \n \n \n \n Recombinant CLIC1 (NCC27) assembles in lipid bilayers via a pH-dependent two-state process to form chloride ion channels with identical characteristics to those observed in Chinese hamster ovary cells expressing CLIC1.\n \n \n \n \n\n\n \n Warton, K.; Tonini, R.; Douglas Fairlie, W.; Matthews, J.; Valenzuela, S.; Qiu, M.; Wu, W.; Pankhurst, S.; Bauskin, A.; Harrop, S.; Campbell, T.; Curmi, P.; Breit, S.; and Mazzanti, M.\n\n\n \n\n\n\n Journal of Biological Chemistry, 277(29): 26003-26011. 2002.\n cited By 94\n\n\n\n
\n\n\n\n \n \n $\"Recombinant$ 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

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@ARTICLE{Warton200226003,\nauthor={Warton, K. and Tonini, R. and Douglas Fairlie, W. and Matthews, J.M. and Valenzuela, S.M. and Qiu, M.R. and Wu, W.M. and Pankhurst, S. and Bauskin, A.R. and Harrop, S.J. and Campbell, T.J. and Curmi, P.M.G. and Breit, S.N. and Mazzanti, M.},\ntitle={Recombinant CLIC1 (NCC27) assembles in lipid bilayers via a pH-dependent two-state process to form chloride ion channels with identical characteristics to those observed in Chinese hamster ovary cells expressing CLIC1},\njournal={Journal of Biological Chemistry},\nyear={2002},\nvolume={277},\nnumber={29},\npages={26003-26011},\ndoi={10.1074/jbc.M203666200},\nnote={cited By 94},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037135574&doi=10.1074%2fjbc.M203666200&partnerID=40&md5=14c44c36b8e02ab1a95c9297797f3a04},\naffiliation={Centre for Immunology, St Vincent's Hospital, University of New South Wales, Sydney, NSW 2010, Australia; Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Fisiologia Umana e Farmacologia, Università la Sapienza, I-00185 Roma, Italy; Dipartamento di Scienze Internistiche, San Raffaele Alla Pisana, Tosinvest Sanita', I-00163, Italy; Department of Biochemistry, University of Sydney, NSW 2006, Australia; Department of Medicine, University of New South Wales, Sydney, NSW 2052, Australia; Initiative for Biomolecular Structure, School of Physics, University of New South Wales, NSW 2052, Australia; Dipartimento di Biologia Cellulare e Dello Sviluppo, Università la Sapienza, I-00185, Roma, Italy; Dept. of Health Sciences, University of Technology, NSW 2007, Australia; Dipartimento di Biologia Cellulare e dello Sviluppo, Universita' la Sapienza, P.le Aldo Moro 5, I-00185, Roma, Italy},\nabstract={CLIC1 (NCC27) is an unusual, largely intracellular, ion channel that exists in both soluble and membrane-associated forms. The soluble recombinant protein can be expressed in Escherichia coli, a property that has made possible both detailed electrophysiological studies in lipid bilayers and an examination of the mechanism of membrane integration. Soluble E. coli-derived CLIC1 moves from solution into artificial bilayers and forms chloride-selective ion channels with essentially identical conductance, pharmacology, and opening and closing kinetics to those observed in CLIC1-transfected Chinese hamster ovary cells. The process of membrane integration of CLIC1 is pH-dependent. Following addition of protein to the trans solution, small conductance channels with slow kinetics (SCSK) appear in the bilayer. These SCSK modules then appear to undergo a transition to form a high conductance channel with fast kinetics. This has four times the conductance of the SCSK and fast kinetics that characterize the native channel. This suggests that the CLIC1 ion channel is likely to consist of a tetrameric assembly of subunits and indicates that despite its size and unusual properties, it is able to form a completely functional ion channel in the absence of any other ancillary proteins.},\nkeywords={Biological membranes;  Cells;  Escherichia coli;  Lipids;  pH effects;  Pharmacodynamics;  Physiology;  Proteins, Ion channel, Biochemistry, chloride channel;  protein clic1;  recombinant protein;  unclassified drug, animal cell;  article;  CHO cell;  conductance;  Escherichia coli;  kinetics;  lipid bilayer;  nonhuman;  pH;  priority journal;  protein assembly;  protein expression, Animalia;  Cricetinae;  Cricetulus griseus;  Escherichia coli;  Escherichia coli},\ncorrespondence_address1={Mazzanti, M.; Dipto. di Biol. Cellulare e Sviluppo, P.le Aldo Moro 5, I-00185 Roma, Italy; email: michele.mazzanti@uniroma1.it},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={11978800},\nlanguage={English},\nabbrev_source_title={J. Biol. Chem.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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

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@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

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\n \n 2001\n \n \n (3)\n \n \n

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\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

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@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

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\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

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@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

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\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

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@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

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\n \n 2000\n \n \n (3)\n \n \n

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\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

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@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

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\n \n\n \n \n \n \n \n \n The single mutation Phe173 → Ala induces a molten globule-like state in murine interleukin-6.\n \n \n \n \n\n\n \n Matthews, J.; Norton, R.; Hammacher, A.; and Simpson, R.\n\n\n \n\n\n\n Biochemistry, 39(8): 1942-1950. 2000.\n cited By 17\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

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@ARTICLE{Matthews20001942,\nauthor={Matthews, J.M. and Norton, R.S. and Hammacher, A. and Simpson, R.J.},\ntitle={The single mutation Phe173 → Ala induces a molten globule-like state in murine interleukin-6},\njournal={Biochemistry},\nyear={2000},\nvolume={39},\nnumber={8},\npages={1942-1950},\ndoi={10.1021/bi991973i},\nnote={cited By 17},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034728379&doi=10.1021%2fbi991973i&partnerID=40&md5=65fc41abd7a2190e26888292d3c9d3ff},\naffiliation={Joint Protein Structure Laboratory, Walter Eliza Hall Inst. of Med. Res., Royal Melbourne Hospital, P.O. Box 2008, Parkville, Vic. 3050, Australia; Biomolecular Research Institute, 343 Royal Pde, Parkville, Vic. 3052, Australia; Ludwig Institute for Cancer Research, Royal Melbourne Hospital, P.O. Box 2008, Parkville, Vic. 3050, Australia},\nabstract={A series of three aromatic to alanine mutants of recombinant murine interleukin-6 lacking the 22 N-terminal residues (ΔN22mIL-6) were constructed to investigate the role of these residues in the structure and function of mIL-6. While Y78A and Y97A have activities similar to that of ΔN22mIL-6, F173A lacks biological activity. F173A retains high levels of secondary structure, as determined by farUV circular dichroism (CD), but has substantially reduced levels of tertiary structure, as determined by near-UV CD and 1H NMR spectroscopy. F173A also binds the hydrophobic dye 1-anilino- 8-naphthalenesulfonic acid (ANS) over a range of pH values and exhibits noncooperative equilibrium unfolding (as judged by the noncoincidence of monophasic unfolding transitions monitored by far-UV CD and λ(max), with midpoints of unfolding at 2.6 ± 0.1 and 3.5 ± 0.3 M urea, respectively, and the lack of an observable thermal unfolding transition). These are all properties of molten globule states, suggesting that the loss of activity of F173A results from the disruption of the fine structure of the protein, rather than from the loss of a side chain that is important for ligand- receptor interactions. Surprisingly, under some conditions, this loosened conformation is no more susceptible to proteolytic attack than the parent protein. By analogy with human IL-6, Phe173 in ΔN22mIL-6 makes multiple interhelical interactions, the removal of which appear to be sufficient to induce a molten globule-like conformation.},\nkeywords={8 anilino 1 naphthalenesulfonic acid;  alanine;  globular protein;  phenylalanine;  recombinant interleukin 6, amino acid substitution;  animal cell;  article;  circular dichroism;  controlled study;  ligand binding;  mouse;  mutation;  nonhuman;  nuclear magnetic resonance spectroscopy;  priority journal;  protein conformation;  protein degradation;  protein denaturation;  protein secondary structure;  protein structure;  protein tertiary structure;  receptor binding, Alanine;  Animals;  Cell Line;  Circular Dichroism;  Dose-Response Relationship, Drug;  Hydrogen-Ion Concentration;  Interleukin-6;  Magnetic Resonance Spectroscopy;  Mice;  Models, Molecular;  Mutation;  Phenylalanine;  Protein Conformation;  Protein Folding;  Protein Structure, Secondary;  Protein Structure, Tertiary;  Recombinant Proteins;  Temperature;  Time Factors;  Urea, Animalia;  Murinae},\ncorrespondence_address1={Simpson, R.J.; Ludwig Institute for Cancer Research, P.O. Box 2008, Parkville, Vic. 3050, Australia; email: Richard.Simpson@ludwig.edu.au},\nissn={00062960},\ncoden={BICHA},\npubmed_id={10684643},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\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 1998\n \n \n (1)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Physicochemical characterization of an antagonistic human interleukin-6 dimer.\n \n \n \n \n\n\n \n Matthews, J.; Hammacher, A.; Howlett, G.; and Simpson, R.\n\n\n \n\n\n\n Biochemistry, 37(30): 10671-10680. 1998.\n cited By 10\n\n\n\n
\n\n\n\n \n \n $\"Physicochemical$ 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{Matthews199810671,\nauthor={Matthews, J.M. and Hammacher, A. and Howlett, G.J. and Simpson, R.J.},\ntitle={Physicochemical characterization of an antagonistic human interleukin-6 dimer},\njournal={Biochemistry},\nyear={1998},\nvolume={37},\nnumber={30},\npages={10671-10680},\ndoi={10.1021/bi980127p},\nnote={cited By 10},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032575321&doi=10.1021%2fbi980127p&partnerID=40&md5=ae5c5188a5f3234f4f1aaff6b8e9a197},\naffiliation={Joint Protein Structure Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, P.O. 2008, Parkville, Vic. 3050, Australia; Department of Biochemistry, University of Melbourne, Parkville, Vic. 3052, Australia; Ludwig Institute for Cancer Research, Royal Melbourne Hospital, P.O. 2008, Parkville, Vic. 3050, Australia},\nabstract={A noncovalently bound dimeric form of recombinant human IL-6 interleukin-6 (IL-6D) was shown to be an antagonist for IL-6 activity, in a STAT3 tyrosine phosphorylation assay using HepG2 cells, under conditions where it does not dissociate into monomeric IL-6 (IL-6(M)). The fluorescence from Trp157, the single tryptophan residue in the primary sequence of IL-6, is altered in IL-6D, where the wavelength maximum is blue-shifted by 3 nm and the emission intensity is reduced by 30%. These data suggest that Trp157 is close to, but not buried by, the dimer interface. Both IL-6D and IL-6(M) are compact molecules, as determined by sedimentation velocity analysis, and contain essentially identical levels of secondary and tertiary structure, as determined by far- and near-UV CD, respectively. IL-6D and IL-6M show the same susceptibility to limited proteolytic attack, and exhibit identical far- UV CD-monitored urea-denaturation profiles With the midpoint of denaturation occurring at 6.0 ± 0.1 M urea. However, IL-6D was found to dissociate prior to the complete unfolding of the protein, with a midpoint of dissociation of 3 M urea, suggesting that dissociation and dimerization occur when the protein is in a partially unfolded state. Based on these results, we suggest that IL-6D is a metastable domain-swapped dimer, comprising two monomeric units where identical helices from each protein chain are swapped through the loop regions at the 'top' of the protein (i.e., the region of the protein most distal from the N- and C-termini). Such an arrangement would account for the antagonistic activity of IL-6(D). In this model, receptor binding site I, which comprises residues in the A/B loop and the C-terminus of the protein, is free to bind the IL-6 receptor. However, site III, which includes Trp157 and residues in the C/D loop and N-terminal end of helix D, and perhaps site II, which comprises residues in the A and C helices, are no longer able to bind the signal transducing component of the IL-6 receptor complex, gp130.},\nkeywords={interleukin 6;  interleukin 6 receptor, amino acid sequence;  article;  carboxy terminal sequence;  covalent bond;  dimerization;  human;  priority journal;  protein degradation;  protein phosphorylation, Carcinoma, Hepatocellular;  Chemistry, Physical;  Circular Dichroism;  Dimerization;  Escherichia coli;  Fluorescence Polarization;  Humans;  Interleukin-6;  Models, Molecular;  Protein Folding;  Protein Structure, Secondary;  Protein Structure, Tertiary;  Recombinant Proteins;  Signal Transduction;  Temperature;  Tumor Cells, Cultured;  Ultracentrifugation;  Urea},\ncorrespondence_address1={Simpson, R.J.; Ludwig Institute for Cancer Research, P.O. Box 2008, Parkville, Vic. 3050, Australia; email: Richard.Simpson@ludwig.edu.au},\nissn={00062960},\ncoden={BICHA},\npubmed_id={9692957},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n

\n A noncovalently bound dimeric form of recombinant human IL-6 interleukin-6 (IL-6D) was shown to be an antagonist for IL-6 activity, in a STAT3 tyrosine phosphorylation assay using HepG2 cells, under conditions where it does not dissociate into monomeric IL-6 (IL-6(M)). The fluorescence from Trp157, the single tryptophan residue in the primary sequence of IL-6, is altered in IL-6D, where the wavelength maximum is blue-shifted by 3 nm and the emission intensity is reduced by 30%. These data suggest that Trp157 is close to, but not buried by, the dimer interface. Both IL-6D and IL-6(M) are compact molecules, as determined by sedimentation velocity analysis, and contain essentially identical levels of secondary and tertiary structure, as determined by far- and near-UV CD, respectively. IL-6D and IL-6M show the same susceptibility to limited proteolytic attack, and exhibit identical far- UV CD-monitored urea-denaturation profiles With the midpoint of denaturation occurring at 6.0 ± 0.1 M urea. However, IL-6D was found to dissociate prior to the complete unfolding of the protein, with a midpoint of dissociation of 3 M urea, suggesting that dissociation and dimerization occur when the protein is in a partially unfolded state. Based on these results, we suggest that IL-6D is a metastable domain-swapped dimer, comprising two monomeric units where identical helices from each protein chain are swapped through the loop regions at the 'top' of the protein (i.e., the region of the protein most distal from the N- and C-termini). Such an arrangement would account for the antagonistic activity of IL-6(D). In this model, receptor binding site I, which comprises residues in the A/B loop and the C-terminus of the protein, is free to bind the IL-6 receptor. However, site III, which includes Trp157 and residues in the C/D loop and N-terminal end of helix D, and perhaps site II, which comprises residues in the A and C helices, are no longer able to bind the signal transducing component of the IL-6 receptor complex, gp130.\n

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\n \n 1997\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Roles of histidine 31 and tryptophan 34 in the structure, self- association, and folding of murine interleukin-6.\n \n \n \n \n\n\n \n Matthews, J.; Ward, L.; Hammacher, A.; Norton, R.; and Simpson, R.\n\n\n \n\n\n\n Biochemistry, 36(20): 6187-6196. 1997.\n cited By 22\n\n\n\n
\n\n\n\n \n \n $\"Roles$ 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{Matthews19976187,\nauthor={Matthews, J.M. and Ward, L.D. and Hammacher, A. and Norton, R.S. and Simpson, R.J.},\ntitle={Roles of histidine 31 and tryptophan 34 in the structure, self- association, and folding of murine interleukin-6},\njournal={Biochemistry},\nyear={1997},\nvolume={36},\nnumber={20},\npages={6187-6196},\ndoi={10.1021/bi962939w},\nnote={cited By 22},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030991899&doi=10.1021%2fbi962939w&partnerID=40&md5=bc537443aaa4140ae19a929014987445},\naffiliation={Ludwig Institute for Cancer Research, Royal Melbourne Hospital, P.O. 2008, Parkville, Vic. 3050, Australia; Joint Protein Structure Laboratory, Ludwig Institute for Cancer Research, Walter Eliza Hall Inst. of Med. Res., Parkville, Vic. 3050, Australia; AMRAD Operations Pty Ltd., Richmond, Vic. 3121, Australia; Biomolecular Research Institute, Parkville, Vic. 3052, Australia},\nabstract={Interleukin-6 (IL-6) is a multifunctional cytokine which is involved in a broad spectrum of activities such as immune defense, hematopoiesis, and the acute phase response, as well as in the pathogenesis of multiple myeloma. A series of murine IL-6 (mIL-6) mutants, H31A, W34A, and H31A/W34A, were constructed to investigate the roles of His31 and Trp34 in the structure, conformational stability, time-dependent aggregation, folding, and spectral properties of mIL-6. The characteristic pH-dependent quenching of fluorescence of mIL-6 at low pH was shown to be caused by an interaction between Trp34 and protonated His31 at low pH and not associated with Trp157. Denaturant-induced equilibrium unfolding experiments monitored by fluorescence and far-UV CD showed that the increased quantum yield and blue shift of the wavelength of the emission maximum observed for mIL-6 at moderate denaturant concentrations were also associated with Trp34, rather than Trp157. The tendency to form aggregation-prone unfolding intermediates, as judged by poor fits to a two-state unfolding mechanism, low m values (slopes of the unfolding curve in the transition region), and the range of denaturant concentrations over which these intermediates formed, was shown to be higher for H31A than mIL-6 but significantly lower for W34A and H31A/W34A. These differences were most pronounced at pH 7.4 and correlated with the tendencies of the proteins to aggregate at high protein concentrations in the absence of denaturant. As judged by the 1H NMR chemical shifts of the aromatic residues, the global conformations of H31A and W34A were not significantly different from that of mIL-6. Nuclear Overhauser effects (NOE) between the side chains of His31 and Trp34 were consistent with the indole side chain of Trp34 being oriented toward the face of the imidazolium side chain of His31, an arrangement consistent with our estimates of a low interaction energy (0.4-0.6 kcal/mol) between these side chains. A shift in the pK(a) of the His31 side chain in W34A (+0.3 unit) suggested that, in the absence of Trp34, His31 could interact with other residues. Further mutations in this region should yield forms of mIL-6, even less prone to aggregation, which would be more suitable for NMR studies. Mutation of His31 and Trp34 to alanine did not significantly alter the mitogenic activity of the mutants on mouse hybridoma 7TD1 cells, even though the corresponding region of human IL- 6 has been shown to be important for biological activity.},\nkeywords={cytokine;  histidine;  interleukin 6;  mutant protein;  tryptophan, animal cell;  article;  circular dichroism;  hybridoma;  mouse;  nonhuman;  priority journal;  protein expression;  protein folding;  protein purification;  protein structure;  proton nuclear magnetic resonance, Amino Acid Sequence;  Animals;  Biological Assay;  Circular Dichroism;  Guanidine;  Guanidines;  Histidine;  Hydrogen-Ion Concentration;  Interleukin-6;  Magnetic Resonance Spectroscopy;  Mice;  Models, Chemical;  Models, Molecular;  Molecular Sequence Data;  Mutation;  Protein Conformation;  Protein Denaturation;  Protein Folding;  Recombinant Proteins;  Sequence Homology, Amino Acid;  Species Specificity;  Structure-Activity Relationship;  Titrimetry;  Tryptophan, Animalia;  Murinae},\ncorrespondence_address1={Simpson, R.J.; Ludwig Inst. for Cancer Research, P.O. Box 2008, Parkville, Vic. 3050, Australia; email: simpson@licre.ludwig.edu.au},\nissn={00062960},\ncoden={BICHA},\npubmed_id={9166791},\nlanguage={English},\nabbrev_source_title={BIOCHEMISTRY},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n

\n Interleukin-6 (IL-6) is a multifunctional cytokine which is involved in a broad spectrum of activities such as immune defense, hematopoiesis, and the acute phase response, as well as in the pathogenesis of multiple myeloma. A series of murine IL-6 (mIL-6) mutants, H31A, W34A, and H31A/W34A, were constructed to investigate the roles of His31 and Trp34 in the structure, conformational stability, time-dependent aggregation, folding, and spectral properties of mIL-6. The characteristic pH-dependent quenching of fluorescence of mIL-6 at low pH was shown to be caused by an interaction between Trp34 and protonated His31 at low pH and not associated with Trp157. Denaturant-induced equilibrium unfolding experiments monitored by fluorescence and far-UV CD showed that the increased quantum yield and blue shift of the wavelength of the emission maximum observed for mIL-6 at moderate denaturant concentrations were also associated with Trp34, rather than Trp157. The tendency to form aggregation-prone unfolding intermediates, as judged by poor fits to a two-state unfolding mechanism, low m values (slopes of the unfolding curve in the transition region), and the range of denaturant concentrations over which these intermediates formed, was shown to be higher for H31A than mIL-6 but significantly lower for W34A and H31A/W34A. These differences were most pronounced at pH 7.4 and correlated with the tendencies of the proteins to aggregate at high protein concentrations in the absence of denaturant. As judged by the 1H NMR chemical shifts of the aromatic residues, the global conformations of H31A and W34A were not significantly different from that of mIL-6. Nuclear Overhauser effects (NOE) between the side chains of His31 and Trp34 were consistent with the indole side chain of Trp34 being oriented toward the face of the imidazolium side chain of His31, an arrangement consistent with our estimates of a low interaction energy (0.4-0.6 kcal/mol) between these side chains. A shift in the pK(a) of the His31 side chain in W34A (+0.3 unit) suggested that, in the absence of Trp34, His31 could interact with other residues. Further mutations in this region should yield forms of mIL-6, even less prone to aggregation, which would be more suitable for NMR studies. Mutation of His31 and Trp34 to alanine did not significantly alter the mitogenic activity of the mutants on mouse hybridoma 7TD1 cells, even though the corresponding region of human IL- 6 has been shown to be important for biological activity.\n

\n\n\n

\n \n\n \n \n \n \n \n \n Disruption of the disulfide bonds of recombinant murine interleukin-6 induces formation of a partially unfolded state.\n \n \n \n \n\n\n \n Zhang, J.; Matthews, J.; Ward, L.; and Simpson, R.\n\n\n \n\n\n\n Biochemistry, 36(9): 2380-2389. 1997.\n cited By 17\n\n\n\n
\n\n\n\n \n \n $\"Disruption$ 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{Zhang19972380,\nauthor={Zhang, J.-G. and Matthews, J.M. and Ward, L.D. and Simpson, R.J.},\ntitle={Disruption of the disulfide bonds of recombinant murine interleukin-6 induces formation of a partially unfolded state},\njournal={Biochemistry},\nyear={1997},\nvolume={36},\nnumber={9},\npages={2380-2389},\ndoi={10.1021/bi962164r},\nnote={cited By 17},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0031019982&doi=10.1021%2fbi962164r&partnerID=40&md5=94a611acce56016cddbd13ba2726444c},\naffiliation={Ludwig Institute for Cancer Research, Walter Eliza Hall Inst. of Med. Res., PO Royal Melbourne Hospital, Parkville, Vic. 3050, Australia; Joint Protein Structure Laboratory, Ludwig Institute for Cancer Research, Walter Eliza Hall Inst. of Med. Res., Parkville, Vic. 3050, Australia},\nabstract={A chemical modification approach was used to investigate the role of the two disulfide bonds of recombinant murine interleukin-6 (mIL-6) in terms of biological activity and conformational stability. Disruption of the disulfide bonds of mIL-6 by treatment with iodoacetic acid (IAA-IL-6) or iodoacetamide (IAM-IL-6) reduced the biological activity, in the murine hybridoma growth factor assay, by 500- and 200-fold, respectively. Both alkylated derivatives as well as the fully reduced (but not modified) molecule (DTT-IL-6) retained a high degree of α-helical structure as measured by far-UV CD (37-51%) when compared to the mIL-6 (59%). However, the intensity of the near-UV CD signal of the S-alkylated derivatives was very low relative to that of mIL-6, suggesting a reduction in fixed tertiary interactions. Both IAA-IL-6 and IAM- IL-6 exhibit native-like unfolding properties at pH 4.0, characteristic of a two-state unfolding mechanism, and are destabilized relative to mIL-6, by 0.3 ± 1.6 and 2.4 ± 1.2 kcal/mol, respectively. At pH 7.4, however, both modified proteins display stable unfolding intermediates. These intermediates are stable over a wide range of GdnHCl concentrations (0.5-2 M) and are characterized by increased fluorescence quantum yield and a blue shift of λ(max) from 345 nm, for wild-type recombinant mIL-6, to 335 nm. These properties were identical to those observed for DTT-IL-6 in the absence of denaturant. DTT-IL-6 appears to form a partially unfolded and highly aggregated conformation under all conditions studied, as showed by a high propensity to self-associate (demonstrated using a biosensor employing surface plasmon resonance), and an increased ability to bind the hydrophobic probe 8-anilino-1-naphthalenesulfonic acid. The observed protein concentration dependence of the fluorescence characteristics of these mIL-6 derivatives is consistent with the aggregation of partially folded forms of DTT-IL-6, IAM-IL-6, and IAA-IL-6 during denaturant-induced unfolding. For all forms of the protein studied here, the aggregated intermediates unfold at similar denaturant concentrations (2.1-2.9 M GdnHCl), suggesting that the α- helical structure and nonspecific hydrophobic interprotein interactions are of similar strength in all cases.},\nkeywords={iodoacetamide;  iodoacetic acid;  recombinant interleukin 6, article;  chemical modification;  concentration response;  conformational transition;  denaturation;  disulfide bond;  drug conformation;  drug structure;  immunoregulation;  molecular interaction;  priority journal;  protein folding, Alkylation;  Anilino Naphthalenesulfonates;  Animals;  Chromatography, Gel;  Circular Dichroism;  Cysteine;  Disulfides;  Drug Stability;  Hydrogen-Ion Concentration;  Interleukin-6;  Methylation;  Mice;  Oxidation-Reduction;  Protein Binding;  Protein Conformation;  Protein Denaturation;  Protein Folding;  Recombinant Proteins;  Spectrometry, Fluorescence;  Urea, Murinae},\ncorrespondence_address1={Simpson, R.J.; Ludwig Institute for Cancer Research, , Parkville, Vic. 3050, Australia; email: simpson@licre.ludwig.edu.au},\nissn={00062960},\ncoden={BICHA},\npubmed_id={9054543},\nlanguage={English},\nabbrev_source_title={BIOCHEMISTRY},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n

\n A chemical modification approach was used to investigate the role of the two disulfide bonds of recombinant murine interleukin-6 (mIL-6) in terms of biological activity and conformational stability. Disruption of the disulfide bonds of mIL-6 by treatment with iodoacetic acid (IAA-IL-6) or iodoacetamide (IAM-IL-6) reduced the biological activity, in the murine hybridoma growth factor assay, by 500- and 200-fold, respectively. Both alkylated derivatives as well as the fully reduced (but not modified) molecule (DTT-IL-6) retained a high degree of α-helical structure as measured by far-UV CD (37-51%) when compared to the mIL-6 (59%). However, the intensity of the near-UV CD signal of the S-alkylated derivatives was very low relative to that of mIL-6, suggesting a reduction in fixed tertiary interactions. Both IAA-IL-6 and IAM- IL-6 exhibit native-like unfolding properties at pH 4.0, characteristic of a two-state unfolding mechanism, and are destabilized relative to mIL-6, by 0.3 ± 1.6 and 2.4 ± 1.2 kcal/mol, respectively. At pH 7.4, however, both modified proteins display stable unfolding intermediates. These intermediates are stable over a wide range of GdnHCl concentrations (0.5-2 M) and are characterized by increased fluorescence quantum yield and a blue shift of λ(max) from 345 nm, for wild-type recombinant mIL-6, to 335 nm. These properties were identical to those observed for DTT-IL-6 in the absence of denaturant. DTT-IL-6 appears to form a partially unfolded and highly aggregated conformation under all conditions studied, as showed by a high propensity to self-associate (demonstrated using a biosensor employing surface plasmon resonance), and an increased ability to bind the hydrophobic probe 8-anilino-1-naphthalenesulfonic acid. The observed protein concentration dependence of the fluorescence characteristics of these mIL-6 derivatives is consistent with the aggregation of partially folded forms of DTT-IL-6, IAM-IL-6, and IAA-IL-6 during denaturant-induced unfolding. For all forms of the protein studied here, the aggregated intermediates unfold at similar denaturant concentrations (2.1-2.9 M GdnHCl), suggesting that the α- helical structure and nonspecific hydrophobic interprotein interactions are of similar strength in all cases.\n

\n\n\n

\n \n\n \n \n \n \n \n \n Interleukin-6: Structure-function relationships.\n \n \n \n \n\n\n \n Simpson, R.; Hammacher, A.; Smith, D.; Matthews, J.; and Ward, L.\n\n\n \n\n\n\n Protein Science, 6(5): 929-955. 1997.\n cited By 298\n\n\n\n
\n\n\n\n \n \n $\"Interleukin-6:$ 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{Simpson1997929,\nauthor={Simpson, R.J. and Hammacher, A. and Smith, D.K. and Matthews, J.M. and Ward, L.D.},\ntitle={Interleukin-6: Structure-function relationships},\njournal={Protein Science},\nyear={1997},\nvolume={6},\nnumber={5},\npages={929-955},\ndoi={10.1002/pro.5560060501},\nnote={cited By 298},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030940098&doi=10.1002%2fpro.5560060501&partnerID=40&md5=c746fe5deb4daf4801e0f7780291698a},\naffiliation={Joint Protein Structure Laboratory, Ludwig Institute for Cancer Research, Walter Eliza Hall Inst. of Med. Res., Parkville, Vic. 3050, Australia; Ludwig Institute for Cancer Research, Coop. Res. Ctr. Cell. Growth Factors, Parkville, Vic. 3050, Australia; AMRAD Burnley, Richmond, Vic. 3121, Australia},\nabstract={Interleukin-6 (IL-6) is a multifunctional cytokine that plays a central role in host defense due to its wide range of immune and hematopoietic activities and its potent ability to induce the acute phase response. Overexpression of IL-6 has been implicated in the pathology of a number of diseases including multiple myeloma, rheumatoid arthritis, Castleman's disease, psoriasis, and post-menopausal osteoporosis. Hence, selective antagonists of IL-6 action may offer therapeutic benefits. IL-6 is a member of the family of cytokines that includes interleukin-11, leukemia inhibitory factor, oncostatin M, cardiotrophin-I, and ciliary neurotrophic factor. Like the other members of this family, IL-6 induces growth or differentiation via a receptor system that involves a specific receptor and the use of a shared signaling subunit, gp130. Identification of the regions of IL-6 that are involved in the interactions with the IL-6 receptor and gp130 is an important first step in the rational manipulation of the effects of this cytokine for therapeutic benefit. In this review, we focus on the sites on IL-6 which interact with its low-affinity specific receptor, the IL-6 receptor, and the high-affinity converter gp130. A tentative model for the IL-6 hexameric receptor ligand complex is presented and discussed with respect to the mechanism of action of the other members of the IL-6 family of cytokines.},\nauthor_keywords={cytokine;  gp130;  interleukin-6;  receptor;  structure-function;  ternary complex},\nkeywords={ciliary neurotrophic factor;  interleukin 11;  interleukin 6;  interleukin 6 receptor;  leukemia inhibitory factor;  oncostatin M, angiofollicular lymph node hyperplasia;  binding affinity;  disease association;  ligand binding;  multiple myeloma;  osteoporosis;  priority journal;  protein analysis;  protein tertiary structure;  psoriasis;  receptor affinity;  review;  rheumatoid arthritis;  signal transduction;  structure activity relation},\ncorrespondence_address1={Simpson, R.J.; Ludwig Institute for Cancer Research, PO Box 2008, Melbourne, Vic. 3050, Australia; email: simpson@licre.ludwig.edu.au},\npublisher={Blackwell Publishing Ltd},\nissn={09618368},\ncoden={PRCIE},\npubmed_id={9144766},\nlanguage={English},\nabbrev_source_title={PROTEIN SCI.},\ndocument_type={Review},\nsource={Scopus},\n}\n\n

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

\n

\n \n 1996\n \n \n (2)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n The association of unfolding intermediates during the equilibrium unfolding of recombinant murine interleukin-6.\n \n \n \n \n\n\n \n Matthews, J.; Ward, L.; Zhang, J.; and Simpson, R.\n\n\n \n\n\n\n Techniques in Protein Chemistry, 7(C): 449-457. 1996.\n cited By 2\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\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Matthews1996449,\nauthor={Matthews, J.M. and Ward, L.D. and Zhang, J.-G. and Simpson, R.J.},\ntitle={The association of unfolding intermediates during the equilibrium unfolding of recombinant murine interleukin-6},\njournal={Techniques in Protein Chemistry},\nyear={1996},\nvolume={7},\nnumber={C},\npages={449-457},\ndoi={10.1016/S1080-8914(96)80049-4},\nnote={cited By 2},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0343390996&doi=10.1016%2fS1080-8914%2896%2980049-4&partnerID=40&md5=adb029a66aeb82567a4101944d5e4fcb},\naffiliation={Joint Protein Structure Laboratory, Ludwig Institute for Cancer Research, Parkville, Vic. 3050, Australia; For Medical Research, Walter and Eliza Hall, Parkville, Vic. 3050, Australia},\ncorrespondence_address1={Matthews, J.M.; Joint Protein Structure Laboratory, , Parkville, Vic. 3050, Australia},\nissn={10808914},\nlanguage={English},\nabbrev_source_title={Tech. Protein 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 Influence of interleukin-6 (IL-6) dimerization on formation of the high affinity hexameric IL-6·receptor complex.\n \n \n \n \n\n\n \n Ward, L.; Hammacher, A.; Howlett, G.; Matthews, J.; Fabri, L.; Moritz, R.; Nice, E.; Weinstock, J.; and Simpson, R.\n\n\n \n\n\n\n Journal of Biological Chemistry, 271(33): 20138-20144. 1996.\n cited By 47\n\n\n\n
\n\n\n\n \n \n $\"Influence$ 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{Ward199620138,\nauthor={Ward, L.D. and Hammacher, A. and Howlett, G.J. and Matthews, J.M. and Fabri, L. and Moritz, R.L. and Nice, E.C. and Weinstock, J. and Simpson, R.J.},\ntitle={Influence of interleukin-6 (IL-6) dimerization on formation of the high affinity hexameric IL-6·receptor complex},\njournal={Journal of Biological Chemistry},\nyear={1996},\nvolume={271},\nnumber={33},\npages={20138-20144},\ndoi={10.1074/jbc.271.33.20138},\nnote={cited By 47},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029786666&doi=10.1074%2fjbc.271.33.20138&partnerID=40&md5=350809a25b796d05d261f7e889ab2346},\naffiliation={Joint Protein Structure Laboratory, Ludwig Institute for Cancer Research, Walter Eliza Hall Inst. of Med. Res., Parkville, Vic. 3050, Australia; Department of Biochemistry, University of Melbourne, Parkville, Vic. 3050, Australia; Ludwig Institute for Cancer Research, Parkville, Vic. 3050, Australia; AMRAD Burnley, 576 Swan St., Richmond, Vic. 3121, Australia; Joint Protein Structure Laboratory, Ludwig Inst. for Cancer Research, Royal Melbourne Hospital, P. O. Box 2008, Victoria 3050, Australia},\nabstract={The high affinity interleukin-6 (IL-6) signaling complex consists of IL- 6 and two membrane-associated receptor components: a low affinity but specific IL-6 receptor and the affinity converter/signal transducing protein gp130. Monomeric (IL-6(M)) and dimeric (IL-6(D)) forms of Escherichia coli-derived human IL-6 and the extracellular ('soluble') portions of the IL-6 receptor (sIL- 6R) and gp130 have been purified in order to investigate the effect of IL-6 dimerization on binding to the receptor complex. Although IL-6(D) has a higher binding affinity for immobilized sIL-6R, as determined by biosensor analysis employing surface plasmon resonance detection, IL-6(M) is more potent than IL- 6(D) in a STAT3 phosphorylation assay. The difference in potency is significantly less pronounced when measured in the murine 7TD1 hybridoma growth factor assay and the human hepatoma HepG2 bioassay due to time-dependent dissociation at 37°C of IL-6 dimers into active monomers. The increased binding affinity of IL-6(D) appears to be due to its ability to cross-link two sIL-6R molecules on the biosensor surface. Studies of the IL-6 ternary complex formation demonstrated that the reduced biological potency of IL-6(D) resulted from a decreased ability of the IL-6(D)-(sIL-6R)2 complex to couple with the soluble portion of gp130. These data imply that IL-6-induced dimerization of sIL-6R is not the driving force in promoting formation of the hexameric (IL- 6 · IL-6R · gp130)2 complex. A model is presented whereby the trimeric complex of IL-6R, gp130, and IL-6(M) forms before the functional hexamer. Due to its increased affinity for the IL-6R but its decreased ability to couple with gp130, we suggest that a stable IL-6 dimer may be an efficient IL-6 antagonist.},\nkeywords={interleukin 6;  interleukin 6 receptor, article;  complex formation;  dimerization;  molecular interaction;  priority journal;  protein cross linking;  protein protein interaction;  receptor binding, Escherichia coli;  Murinae},\ncorrespondence_address1={Simpson, R.J.; Joint Protein Structure Laboratory, P.O. Box 2008, Melbourne, Vic. 3050, Australia},\npublisher={American Society for Biochemistry and Molecular Biology Inc.},\nissn={00219258},\ncoden={JBCHA},\npubmed_id={8702737},\nlanguage={English},\nabbrev_source_title={J. BIOL. CHEM.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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

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\n \n 1995\n \n \n (2)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Equilibrium Denaturation of Recombinant Murine Interleukin-6: Effect of pH, Denaturants, and Salt on Formation of Folding Intermediates.\n \n \n \n \n\n\n \n Ward, L.; Matthews, J.; Zhang, J.; and Simpson, R.\n\n\n \n\n\n\n Biochemistry, 34(37): 11652-11659. 1995.\n cited By 19\n\n\n\n
\n\n\n\n \n \n $\"Equilibrium$ 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{Ward199511652,\nauthor={Ward, L.D. and Matthews, J.M. and Zhang, J.-G. and Simpson, R.J.},\ntitle={Equilibrium Denaturation of Recombinant Murine Interleukin-6: Effect of pH, Denaturants, and Salt on Formation of Folding Intermediates},\njournal={Biochemistry},\nyear={1995},\nvolume={34},\nnumber={37},\npages={11652-11659},\ndoi={10.1021/bi00037a002},\nnote={cited By 19},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029148380&doi=10.1021%2fbi00037a002&partnerID=40&md5=c1f77be59a33eb6287f9bd1780655ab6},\naffiliation={Joint Protein Structure Laboratory, Ludwig Institute for Cancer Research, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia},\nabstract={The equilibrium denaturation of an Escherichia coli-derived recombinant murine interleukin-6 (mIL-6) was studied using fluorescence and circular dichroism spectroscopy. The urea-induced unfolding of mIL-6 at pH 4.0 can be described by a two-state unfolding mechanism based on the superimposibility of the CD and fluorescence unfolding transitions. Assuming a two-state mechanism and a linear dependence of the free energy of unfolding on denaturant concentration, a value of 6.9-9.0 kcal/mol was calculated for the free energy of unfolding in the absence of denaturant [∆GU(H2O)]. However, when GuHCl was used as a denaturant at pH 4.0, a biphasic unfolding transition was observed. This unfolding transition has a distinct midpoint occurring at 2.5 M GuHCl, which is indicative of the formation of stable folding intermediates. Similar intermediate folded species were also observed at pH 7.4 when either urea or GuHCl were used as denaturants. The intermediate folded states of mIL-6 exhibited a tendency to aggregate, as judged by the concentration dependence of their fluorescence characteristics. The fluorescence emission maximum of mIL-6 at pH 7.4 in the presence of 1.5 M GuHCl, for example, was blue-shifted from 343 nm at a protein concentration of 50 µg/mL to 336 nm at 500 µg/mL. Intermediate formation at pH 4.0, using 10 mM sodium acetate buffer and urea as the denaturant, was facilitated by the addition of 0.4 and 0.8 M salt, where the salt was either NaCl or GuHCl. These data, together with the pHdependent fluorescence characteristics, suggest that ionic effects and the charged state of mIL-6-particularly in the region of Trp36-play an important role in the formation of folding intermediates and aggregation. © 1995, American Chemical Society. All rights reserved.},\nkeywords={interleukin 6, article;  conformational transition;  escherichia coli;  nonhuman;  ph;  priority journal;  protein conformation;  protein denaturation;  protein folding, Amino Acid Sequence;  Animal;  Circular Dichroism;  Drug Stability;  Guanidine;  Guanidines;  Hydrogen-Ion Concentration;  In Vitro;  Interleukin-6;  Mice;  Molecular Sequence Data;  Protein Denaturation;  Protein Folding;  Recombinant Proteins;  Sodium Chloride;  Spectrometry, Fluorescence;  Support, Non-U.S. Gov't, Escherichia coli;  Murinae},\ncorrespondence_address1={Simpson, R.J.; Ludwig Institute for Cancer Research, PO 2008, Parkville, Victoria 3050, Australia},\nissn={00062960},\npubmed_id={7547897},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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

\n\n\n

\n \n\n \n \n \n \n \n \n Exploring the Energy Surface of Protein Folding by Structure-Reactivity Relationships and Engineered Proteins: Observation of Ftammond Behavior for the Gross Structure of the Transition State and Anti-Hammond Behavior for Structural Elements for Unfolding/Folding of Bamase.\n \n \n \n \n\n\n \n Matthews, J.; and Fersht, A.\n\n\n \n\n\n\n Biochemistry, 34(20): 6805-6814. 1995.\n cited By 125\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 \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{Matthews19956805,\nauthor={Matthews, J.M. and Fersht, A.R.},\ntitle={Exploring the Energy Surface of Protein Folding by Structure-Reactivity Relationships and Engineered Proteins: Observation of Ftammond Behavior for the Gross Structure of the Transition State and Anti-Hammond Behavior for Structural Elements for Unfolding/Folding of Bamase},\njournal={Biochemistry},\nyear={1995},\nvolume={34},\nnumber={20},\npages={6805-6814},\ndoi={10.1021/bi00020a027},\nnote={cited By 125},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029041315&doi=10.1021%2fbi00020a027&partnerID=40&md5=75ca73d12825c1a02d81101b017f2470},\naffiliation={MRC Unit for Protein Function and Design, Cambridge Centre for Protein Engineering, University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, U.K., United Kingdom},\nabstract={The structure of α-helix1 (residues 6-18) in the transition state for the unfolding of bamase has been previously characterized by comparing the kinetics and thermodynamics of folding of wild-type protein with those of mutants whose side chains have been cut back, in the main, to that of alanine. The structure of the transition state has now been explored further by comparing the kinetics and thermodynamics of folding of glycine mutants with those of the alanine mutants at solvent-exposed positions in the α-helices of bamase. Such “Ala→Gly scanning” provides a general procedure for examining the structure of solventexposed regions in the transition state. A gradual change of structure of the transition state was detected as helix1 becomes increasingly destabilized on mutation. The extent of change of stmcture of helix1 in the transition state for the mutant proteins was probed by a further round of Ala→Gly scanning of those mutants. Destabilization of the helix1 was found to cause the overall transition state for unfolding to become closer in stmcture to that of the folded protein. This is analogous to the conventional Hammond effect in physical-organic chemistry whereby the transition state moves parallel to the reaction coordinate with change in stmcture. But, paradoxically, the stmcture of helix1 itself becomes less folded in the transition state as helix1 becomes destabilized. This is analogous, however, to the rarer anti-Hammond effect in which there is movement perpendicular to the reaction coordinate. These observations are rationalized by plotting correlation diagrams of degree of formation of individual elements of stmcture against the degree of formation of overall stmcture in the transition state. There is a relatively smooth movement of the degree of compactness in the transition state against changes in activation energy on mutation that suggests a smooth movement of the transition state along the energy surface on mutation rather than a switch between two different parallel pathways. The results are consistent with the transition state having closely spaced energy levels. Helix1, which appears to be an initiation point and forms early in the folding of wild-type protein, may be radically destabilized to the extent that it forms late in the folding of mutants. The order of events in folding may thus not be cmcial. © 1995, American Chemical Society. All rights reserved.},\nkeywords={alanine;  glycine;  ribonuclease, amino acid substitution;  article;  conformational transition;  enzyme stability;  mutation;  nonhuman;  priority journal;  protein folding;  structure activity relation;  thermodynamics, Alanine;  Base Sequence;  Glycine;  Hydrogen Bonding;  Kinetics;  Molecular Sequence Data;  Mutagenesis;  Protein Denaturation;  Protein Engineering;  Protein Folding;  Protein Structure, Secondary;  Ribonucleases;  Structure-Activity Relationship;  Support, Non-U.S. Gov't;  Thermodynamics},\ncorrespondence_address1={Matthews, J.M.; Joint Protein Structure Laboratory, , Victoria 3050, Australia},\nissn={00062960},\npubmed_id={7756312},\nlanguage={English},\nabbrev_source_title={Biochemistry},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

\n

\n\n\n

\n The structure of α-helix1 (residues 6-18) in the transition state for the unfolding of bamase has been previously characterized by comparing the kinetics and thermodynamics of folding of wild-type protein with those of mutants whose side chains have been cut back, in the main, to that of alanine. The structure of the transition state has now been explored further by comparing the kinetics and thermodynamics of folding of glycine mutants with those of the alanine mutants at solvent-exposed positions in the α-helices of bamase. Such “Ala→Gly scanning” provides a general procedure for examining the structure of solventexposed regions in the transition state. A gradual change of structure of the transition state was detected as helix1 becomes increasingly destabilized on mutation. The extent of change of stmcture of helix1 in the transition state for the mutant proteins was probed by a further round of Ala→Gly scanning of those mutants. Destabilization of the helix1 was found to cause the overall transition state for unfolding to become closer in stmcture to that of the folded protein. This is analogous to the conventional Hammond effect in physical-organic chemistry whereby the transition state moves parallel to the reaction coordinate with change in stmcture. But, paradoxically, the stmcture of helix1 itself becomes less folded in the transition state as helix1 becomes destabilized. This is analogous, however, to the rarer anti-Hammond effect in which there is movement perpendicular to the reaction coordinate. These observations are rationalized by plotting correlation diagrams of degree of formation of individual elements of stmcture against the degree of formation of overall stmcture in the transition state. There is a relatively smooth movement of the degree of compactness in the transition state against changes in activation energy on mutation that suggests a smooth movement of the transition state along the energy surface on mutation rather than a switch between two different parallel pathways. The results are consistent with the transition state having closely spaced energy levels. Helix1, which appears to be an initiation point and forms early in the folding of wild-type protein, may be radically destabilized to the extent that it forms late in the folding of mutants. The order of events in folding may thus not be cmcial. © 1995, American Chemical Society. All rights reserved.\n

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\n \n 1994\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n Single versus parallel pathways of protein folding and fractional formation of structure in the transition state.\n \n \n \n \n\n\n \n Fersht, A.; Itzhaki, L.; Elmasry, N.; Matthews, J.; and Otzen, D.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 91(22): 10426-10429. 1994.\n cited By 169\n\n\n\n
\n\n\n\n \n \n $\"Single$ 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

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@ARTICLE{Fersht199410426,\nauthor={Fersht, A.R. and Itzhaki, L.S. and Elmasry, N.F. and Matthews, J.M. and Otzen, D.E.},\ntitle={Single versus parallel pathways of protein folding and fractional formation of structure in the transition state},\njournal={Proceedings of the National Academy of Sciences of the United States of America},\nyear={1994},\nvolume={91},\nnumber={22},\npages={10426-10429},\ndoi={10.1073/pnas.91.22.10426},\nnote={cited By 169},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0028037217&doi=10.1073%2fpnas.91.22.10426&partnerID=40&md5=30cf24d57681d64e4821e72e03f96a26},\naffiliation={Cambridge Ctr. for Protein Eng., Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom},\nabstract={Protein engineering and kinetic experiments indicate that some regions of proteins have partially formed structure in the transition state for protein folding. A crucial question is whether there is a genuine single transition state that has interactions that are weakened in those regions or there are parallel pathways involving many transition states, some with the interactions fully formed and others with the structural elements fully unfolded. We describe a kinetic test to distinguish between these possibilities. The kinetics rule out those mechanisms that involve a mixture of fully formed or fully unfolded structures for regions of the barley chymotrypsin inhibitor 2 and barnase, and so those regions are genuinely only partially folded in the transition state. The implications for modeling of protein folding pathways are discussed.},\nauthor_keywords={barnase;  chymotrypsin inhibitor 2;  linear free-energy relationships},\nkeywords={chymotrypsin inhibitor, article;  barley;  enzyme kinetics;  genetic engineering;  priority journal;  protein conformation;  protein folding;  protein structure, Amino Acid Sequence;  Chymotrypsin;  Comparative Study;  Kinetics;  Mathematics;  Models, Structural;  Molecular Sequence Data;  Mutagenesis, Site-Directed;  Plant Proteins;  Protein Folding;  Protein Structure, Secondary;  Recombinant Proteins;  Ribonucleases;  Support, Non-U.S. Gov't;  Thermodynamics, Hordeum vulgare subsp. vulgare},\ncorrespondence_address1={Fersht, A.R.; Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, United Kingdom},\nissn={00278424},\ncoden={PNASA},\npubmed_id={7937968},\nlanguage={English},\nabbrev_source_title={PROC. NATL. ACAD. SCI. U. S. A.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n Extrapolation to water of kinetic and equilibrium data for the unfolding of barnase in urea solutions.\n \n \n \n \n\n\n \n Matouschek, A.; Matthews, J.; Johnson, C.; and Fersht, A.\n\n\n \n\n\n\n Protein Engineering, Design and Selection, 7(9): 1089-1095. 1994.\n cited By 95\n\n\n\n
\n\n\n\n \n \n $\"Extrapolation$ 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

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@ARTICLE{Matouschek19941089,\nauthor={Matouschek, A. and Matthews, J.M. and Johnson, C.M. and Fersht, A.R.},\ntitle={Extrapolation to water of kinetic and equilibrium data for the unfolding of barnase in urea solutions},\njournal={Protein Engineering, Design and Selection},\nyear={1994},\nvolume={7},\nnumber={9},\npages={1089-1095},\ndoi={10.1093/protein/7.9.1089},\nnote={cited By 95},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0028168139&doi=10.1093%2fprotein%2f7.9.1089&partnerID=40&md5=a2b2085234cafbe60d580e8251ad73fd},\naffiliation={MRC Unit for Protein Function and Design, Cambridge Centre for Protein Engineering, University Chemical Laboratory, Lensfield Road, United Kingdom; Cambridge CB2 1EW and MRC Centre, Hills Road, Cambridge CB2 2QH, United Kingdom},\nabstract={Assumptions about the dependence of protein unfolding on the concentration of urea have been examined by an extensive survey of the equilibrium unfolding of barnase and many of its mutants measured by urea denaturation and differential scanning calorimetry. The free energy of equilibrium unfolding and the activation energy for the kinetics of unfolding of proteins are generally assumed to change linearly with [urea]. A slight downward curvature is detected, however, in plots of highly precise measurements of logjtu versus [urea] (where ku is the observed rate constant for the unfolding of barnase). The data fit the equation logkku = logkuH2O* + mku*.[urea] - 0.014[urea]2, where mku* is a variable which depends on the mutation. The constant 0.014 was measured directly on four destabilized mutants and wildtype, and was also determined from a global analysis of data from &gt;60 mutants of barnase. Any equivalent deviations from linearity in the equilibrium unfolding are small and in the same region, as determined from measurements on 166 mutants. The free energy of unfolding of barnase, ΔGU-F, appears significantly larger by 1.6 kcal mol-1 when measured by calorimetry than when determined by urea denaturation. However, the changes in ΔGU-F on mutation, ΔΔGU-F, determined by calorimetry and by urea denaturation are identical. We show analytically how, hi general, the curvature in plots of activation or equilibrium energies against [denaturant] should not affect the changes of these values on mutation provided measurements are made over the same concentration ranges of denaturant and the curvature is independent of mutation. © 1994 Oxford University Press.},\nauthor_keywords={Calorimetry;  Protein folding;  Protein stability;  Urea},\nkeywords={mutant protein;  ribonuclease;  urea, article;  concentration response;  differential scanning calorimetry;  energy transfer;  enzyme denaturation;  enzyme structure;  equilibrium constant;  gene mutation;  kinetics;  priority journal;  protein folding;  protein stability;  structure activity relation;  thermodynamics, Bacillus;  In Vitro;  Kinetics;  Models, Chemical;  Mutagenesis, Site-Directed;  Protein Denaturation;  Protein Engineering;  Protein Folding;  Ribonucleases;  Solutions;  Thermodynamics;  Urea;  Water},\ncorrespondence_address1={Fersht, A.R.; MRC Unit for Protein Function and Design, Lensfield Road, United Kingdom},\nissn={17410126},\ncoden={PEDSB},\npubmed_id={7831279},\nlanguage={English},\nabbrev_source_title={Protein Eng. Des. Sel.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n α-Helix stability in proteins. II. Factors that influence stability at an internal position.\n \n \n \n \n\n\n \n Horovitz, A.; Matthews, J.; and Fersht, A.\n\n\n \n\n\n\n Journal of Molecular Biology, 227(2): 560-568. 1992.\n cited By 229\n\n\n\n
\n\n\n\n \n \n $\"α-Helix$ 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

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@ARTICLE{Horovitz1992560,\nauthor={Horovitz, A. and Matthews, J.M. and Fersht, A.R.},\ntitle={α-Helix stability in proteins. II. Factors that influence stability at an internal position},\njournal={Journal of Molecular Biology},\nyear={1992},\nvolume={227},\nnumber={2},\npages={560-568},\ndoi={10.1016/0022-2836(92)90907-2},\nnote={cited By 229},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0026674251&doi=10.1016%2f0022-2836%2892%2990907-2&partnerID=40&md5=085699b34d6dcbe5576199a6445212e0},\naffiliation={MRC Unit for Protein Function, Design Cambridge Centre for Protein Engineering, Department of Chemistry University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom},\nabstract={The solvent-exposed residue Ala32 in the second α-helix of barnase was replaced by all other naturally occurring amino acids and the concomitant effects on the protein stability were determined. The results are assumed to reflect both the distinct conformational preferences of the different amino acids and also possible intrahelical interactions. The conformational preferences may be fully rationalized by invoking only a few physical principles. The results agree well with recently experimentally determined ran-korder of helix-forming tendencies determined on a model peptide. There is very weak correlation between the results and the experimental host-guest values. There is a weak correlation between our results and the statistical helix propensities and a slightly better correlation with the positional-dependent statistical parameters of J. S. Richardson, and D. C. Richardson. © 1992.},\nauthor_keywords={barnase;  protein folding;  protein stability;  α-helix},\nkeywords={alanine;  amino acid;  ribonuclease, amino acid substitution;  article;  chemical structure;  priority journal;  protein conformation;  protein folding;  protein secondary structure;  protein stability;  statistical analysis, Amino Acid Sequence;  Amino Acids;  Base Sequence;  DNA;  Electrochemistry;  Enzyme Stability;  Hydrogen Bonding;  Molecular Sequence Data;  Mutagenesis;  Protein Conformation;  Protein Denaturation;  Ribonucleases;  Solvents;  Thermodynamics},\ncorrespondence_address1={Horovitz, A.; MRC Unit for Protein Function, Design Cambridge Centre for Protein Engineering, Department of Chemistry University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom},\nissn={00222836},\ncoden={JMOBA},\npubmed_id={1404369},\nlanguage={English},\nabbrev_source_title={J. Mol. Biol.},\ndocument_type={Article},\nsource={Scopus},\n}\n\n

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\n \n\n \n \n \n \n \n \n The pathway of arginine catabolism in Giardia intestinalis.\n \n \n \n \n\n\n \n Schofield, P.; Edwards, M.; Matthews, J.; and Wilson, J.\n\n\n \n\n\n\n Molecular and Biochemical Parasitology, 51(1): 29-36. 1992.\n cited By 73\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

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@ARTICLE{Schofield199229,\nauthor={Schofield, P.J. and Edwards, M.R. and Matthews, J. and Wilson, J.R.},\ntitle={The pathway of arginine catabolism in Giardia intestinalis},\njournal={Molecular and Biochemical Parasitology},\nyear={1992},\nvolume={51},\nnumber={1},\npages={29-36},\ndoi={10.1016/0166-6851(92)90197-R},\nnote={cited By 73},\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0026518513&doi=10.1016%2f0166-6851%2892%2990197-R&partnerID=40&md5=797ed3c7525719801cba4d8261135c18},\naffiliation={School of Biochemistry, University of New South Wales, Kensington, NSW, Australia},\nabstract={In Giardia intestinalis, arginine is catabolised by the arginine dihydrolase pathway. The enzymes of the pathway (arginine deiminase, ornithine transcarbamoylase and carbamate kinase) were investigated and their basic kinetic parameters determined. The specific activity of arginine deiminase was 270 ± 23 nmol min-1 (mg protein)-1; ornithine transcarbamoylase, in the direction of citrulline utilisation 170 ± 22 nmol min-1 (mg protein)-1, and in the direction of ornithine utilisation 2100 ± 100 nmol min-1 (mg protein)-1; and carbamate kinase 2100 ± 400 nmol min-1 (mg protein)-1. The activities of these enzymes are between 10 and 250 fold greater than those reported for the enzymes in Trichomonas vaginalis, the only other parasite in which the arginine dihydrolase pathway has been reported. The flux through the pathway in G. intestinalis, as determined by the liberation of 14CO2 from 1 mM [14C-guanidino]arginine was 30 nmol min-1 (mg protein)-1. This flux was not affected by valinomycin (0.1 μM), nigericin (3 μM), azide (5 mM) or cyanide (1 mM). The flux was only marginally affected by glucose up to 10 mM concentration. Conversely, the flux through glucose metabolism, as determined by the release of 14CO2 from 1 mM [1-14C]glucose was only 2 nmol min-1 (mg protein)-1, and was unaffected by arginine concentrations up to 10 mM. These observations suggest that there is no direct metabolic interface between arginine and glucose catabolism. The potential energy yield of ATP from the arginine flux is 7-8-fold greater than that from glucose, providing evidence for the prime importance of arginine in the energy economy of G. intestinalis. It is suggested that the flux through the arginine dihydrolase pathway is the major source of energy production, particularly in anaerobic conditions. © 1992.},\nauthor_keywords={Arginine deiminase;  Arginine dihydrolase pathway;  Arginine metabolism;  Carbamate kinase;  Giardia intestinalis;  Ornithine transcarbamoylase},\nkeywords={arginine;  arginine deiminase;  carbamate kinase;  ornithine;  ornithine carbamoyltransferase, animal cell;  article;  controlled study;  enzyme activity;  giardia lamblia;  metabolism;  nonhuman;  priority journal, Animal;  Arginine;  Biological Transport;  Giardia lamblia;  Hydrolases;  Ornithine Carbamoyltransferase;  Phosphotransferases;  Support, Non-U.S. Gov't, Animalia;  Giardia intestinalis;  Trichomonas vaginalis},\ncorrespondence_address1={Schofield, P.J.; School of Biochemistry, University of New South Wales, Kensington, NSW, Australia},\nissn={01666851},\ncoden={MBIPD},\npubmed_id={1314332},\nlanguage={English},\nabbrev_source_title={Mol. Biochem. Parasitol.},\ndocument_type={Article},\nsource={Scopus},\n}\n

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