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\n \n 2020\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Erratum: Structure of dirithromycin bound to the bacterial ribosome suggests new ways for rational improvement of macrolides (Antimicrobial Agents and Chemotherapy (2019) 63:6 (e02266-18) DOI: 10.1128/AAC.02266-18).\n \n \n \n \n\n\n \n Khabibullina, N.; Tereshchenkov, A.; Komarova, E.; Syroegin, E.; Shiriaev, D.; Paleskava, A.; Kartsev, V.; Bogdanov, A.; Konevega, A.; Dontsova, O.; Sergiev, P.; Osterman, I.; and Polikanov, Y.\n\n\n \n\n\n\n Antimicrobial Agents and Chemotherapy, 64(2). 2020.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Erratum:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Khabibullina2020,\r\nauthor={Khabibullina, N.F. and Tereshchenkov, A.G. and Komarova, E.S. and Syroegin, E.A. and Shiriaev, D.I. and Paleskava, A. and Kartsev, V.G. and Bogdanov, A.A. and Konevega, A.L. and Dontsova, O.A. and Sergiev, P.V. and Osterman, I.A. and Polikanov, Y.S.},\r\ntitle={Erratum: Structure of dirithromycin bound to the bacterial ribosome suggests new ways for rational improvement of macrolides (Antimicrobial Agents and Chemotherapy (2019) 63:6 (e02266-18) DOI: 10.1128/AAC.02266-18)},\r\njournal={Antimicrobial Agents and Chemotherapy},\r\nyear={2020},\r\nvolume={64},\r\nnumber={2},\r\ndoi={10.1128/AAC.02360-19},\r\nart_number={e02360-19},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85078338623&doi=10.1128%2fAAC.02360-19&partnerID=40&md5=ce23dfd091b015ac87e5af4f82945c61},\r\naffiliation={Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States; Department of Chemistry, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Department of Bioengineering and Bioinformatics, A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation; Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russian Federation; Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russian Federation; Interbioscreen, Ltd., Chernogolovka, Russian Federation; NRC Kurchatov Institute, Moscow, Russian Federation; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL, United States; Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, United States},\r\nfunding_details={Russian Foundation for Basic ResearchRussian Foundation for Basic Research},\r\nfunding_details={Russian Science FoundationRussian Science Foundation},\r\nfunding_details={National Institutes of HealthNational Institutes of Health},\r\n}

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\n \n\n \n \n \n \n \n \n How the initiating ribosome copes with ppGpp to translate mRNAs.\n \n \n \n \n\n\n \n Vinogradova, D.; Zegarra, V.; Maksimova, E.; Nakamoto, J.; Kasatsky, P.; Paleskava, A.; Konevega, A.; and MilГіn, P.\n\n\n \n\n\n\n PLoS Biology, 18(1). 2020.\n cited By 2\n\n\n\n
\n\n\n\n \n \n $\"How$ Paper\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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@ARTICLE{Vinogradova2020,\r\nauthor={Vinogradova, D.S. and Zegarra, V. and Maksimova, E. and Nakamoto, J.A. and Kasatsky, P. and Paleskava, A. and Konevega, A.L. and MilГіn, P.},\r\ntitle={How the initiating ribosome copes with ppGpp to translate mRNAs},\r\njournal={PLoS Biology},\r\nyear={2020},\r\nvolume={18},\r\nnumber={1},\r\ndoi={10.1371/journal.pbio.3000593},\r\nart_number={e3000593},\r\nnote={cited By 2},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85078947441&doi=10.1371%2fjournal.pbio.3000593&partnerID=40&md5=f7581aa36b31937583c3363b7c0c26ed},\r\naffiliation={Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC вЂњKurchatov Institute,вЂќ, Gatchina, Russian Federation; NanoTemper Technologies Rus, Saint Petersburg, Russian Federation; Centre for Research and Innovation, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas (UPC), Lima, Peru; Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russian Federation; NRC вЂњKurchatov Institute, Moscow, Russian Federation},\r\nfunding_details={Russian Foundation for Basic ResearchRussian Foundation for Basic Research},\r\nfunding_details={Fondo Nacional de Desarrollo CientГѓВfico y TecnolГѓВіgicoFondo Nacional de Desarrollo CientГѓВfico y TecnolГѓВіgico},\r\nfunding_details={Russian Science FoundationRussian Science Foundation},\r\n}

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\n \n\n \n \n \n \n \n \n Cryo-electron microscopy of extracellular vesicles from cerebrospinal fluid.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n PLoS ONE, 15(1). 2020.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Cryo-electron$ Paper\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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\n \n\n \n \n \n \n \n \n Effect of alpha-lactalbumin and lactoferrin oleic acid complexes on chromatin structural organization.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Biochemical and Biophysical Research Communications, 520(1): 136-139. 2019.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Effect$ Paper\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 4 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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\n \n\n \n \n \n \n \n \n Effect of alpha-lactalbumin and lactoferrin oleic acid complexes on chromatin structural organization.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Biochemical and Biophysical Research Communications, 520(1): 136-139. 2019.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Effect$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 4 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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\n \n\n \n \n \n \n \n \n Structure of dirithromycin bound to the bacterial ribosome suggests new ways for rational improvement of macrolides.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Antimicrobial Agents and Chemotherapy, 63(6). 2019.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Structure$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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\n \n\n \n \n \n \n \n \n Plasma exosomes stimulate breast cancer metastasis through surface interactions and activation of FAK signaling.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Breast Cancer Research and Treatment, 174(1): 129-141. 2019.\n cited By 5\n\n\n\n
\n\n\n\n \n \n $\"Plasma$ Paper\n \n \n\n \n \n doi\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

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\n \n\n \n \n \n \n \n \n Abnormal activity of transcription factors gli in high-grade gliomas.\n \n \n \n \n\n\n \n Volnitskiy, A.; Shtam, T.; Burdakov, V.; Kovalev, R.; Konev, A.; and Filatov, M.\n\n\n \n\n\n\n PLoS ONE, 14(2). 2019.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Abnormal$ Paper\n \n \n\n \n \n doi\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

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@ARTICLE{Volnitskiy2019,\r\nauthor={Volnitskiy, A. and Shtam, T. and Burdakov, V. and Kovalev, R. and Konev, A. and Filatov, M.},\r\ntitle={Abnormal activity of transcription factors gli in high-grade gliomas},\r\njournal={PLoS ONE},\r\nyear={2019},\r\nvolume={14},\r\nnumber={2},\r\ndoi={10.1371/journal.pone.0211980},\r\nart_number={e0211980},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85061246108&doi=10.1371%2fjournal.pone.0211980&partnerID=40&md5=b33be3ba1c58420838f9b1c65e11c6ae},\r\naffiliation={Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute, Gatchina, Russian Federation; N.N. Petrov National Medical Research Center of Oncology, St. Petersburg, Pesochnyj, Leningradskaya, Russian Federation},\r\nabstract={Malignant transformation is associated with loss of cell differentiation, anaplasia. Transcription factors gli, required for embryonic development, may be involved in this process. We studied the activity of transcription factors gli in high-grade gliomas and their role in maintenance of stem cell state and glioma cell survival. 20 glioma cell lines and a sample of a normal adult brain tissue were used in the present study. We found the expression of gli target genes, including GLI1 and FOXM1, in all tested glioma cell lines, but not in the normal tissue. Interestingly, the expression of gli target genes in some glioma cell lines was observed together with a high level of their transcriptional repressor, Gli3R. Knockdown of GLI3 in one of these lines resulted in decrease of gli target gene expression. These data suggest that Gli3R does not prevent the gli target genes transcription, and gli3 acts in glioma cells more as an activator, than a repressor of transcription. We observed that gli regulated the expression of such genes, as SOX2 or OCT4 that maintain stem cell state, and TET1, involving in DNA demethylation. Treatment with GANT61 or siRNA against GLI1, GLI2, or GLI3 could result in complete glioma cell death, while cyclopamine had a weaker and line-specific effect on glioma cell survival. Thus, the gli transcription factors are abnormally active in high-grade gliomas, regulate expression of genes, maintaining the stem cell state, and contribute to glioma cell survival. © 2019 Volnitskiy 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.},\r\ncorrespondence_address1={Volnitskiy, A.; Petersburg Nuclear Physics Institute named by B.P. Konstantinov, National Research Centre "Kurchatov InstituteRussian Federation; email: voln.a@yandex.ru},\r\npublisher={Public Library of Science},\r\nissn={19326203},\r\ncoden={POLNC},\r\npubmed_id={30730955},\r\nlanguage={English},\r\nabbrev_source_title={PLoS ONE},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Isolation of Extracellular Microvesicles from Cell Culture Medium: Comparative Evaluation of Methods.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry, 12(2): 167-175. 2018.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Isolation$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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\n \n\n \n \n \n \n \n \n Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome.\n \n \n \n \n\n\n \n Tereshchenkov, A.; Dobosz-Bartoszek, M.; Osterman, I.; Marks, J.; Sergeeva, V.; Kasatsky, P.; Komarova, E.; Stavrianidi, A.; Rodin, I.; Konevega, A.; Sergiev, P.; Sumbatyan, N.; Mankin, A.; Bogdanov, A.; and Polikanov, Y.\n\n\n \n\n\n\n Journal of Molecular Biology, 430(6): 842-852. 2018.\n cited By 6\n\n\n\n
\n\n\n\n \n \n $\"Binding$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Tereshchenkov2018842,\r\nauthor={Tereshchenkov, A.G. and Dobosz-Bartoszek, M. and Osterman, I.A. and Marks, J. and Sergeeva, V.A. and Kasatsky, P. and Komarova, E.S. and Stavrianidi, A.N. and Rodin, I.A. and Konevega, A.L. and Sergiev, P.V. and Sumbatyan, N.V. and Mankin, A.S. and Bogdanov, A.A. and Polikanov, Y.S.},\r\ntitle={Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome},\r\njournal={Journal of Molecular Biology},\r\nyear={2018},\r\nvolume={430},\r\nnumber={6},\r\npages={842-852},\r\ndoi={10.1016/j.jmb.2018.01.016},\r\nnote={cited By 6},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85042190036&doi=10.1016%2fj.jmb.2018.01.016&partnerID=40&md5=6c8d903882878264824171bd964a4dc7},\r\naffiliation={Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russian Federation; Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL  60607, United States; Skolkovo Institute of Science and Technology, Skolkovo, Moscow region  143025, Russian Federation; Center for Biomolecular Sciences, University of Illinois, Chicago, IL  60607, United States; Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, Gatchina, 188300, Russian Federation; Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russian Federation; Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russian Federation; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL  60607, United States; V. A. Sergeeva, Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115,478, Russian Federation},\r\nabstract={Antibiotic chloramphenicol (CHL) binds with a moderate affinity at the peptidyl transferase center of the bacterial ribosome and inhibits peptide bond formation. As an approach for modifying and potentially improving properties of this inhibitor, we explored ribosome binding and inhibitory activity of a number of amino acid analogs of CHL. The L-histidyl analog binds to the ribosome with the affinity exceeding that of CHL by 10 fold. Several of the newly synthesized analogs were able to inhibit protein synthesis and exhibited the mode of action that was distinct from the action of CHL. However, the inhibitory properties of the semi-synthetic CHL analogs did not correlate with their affinity and in general, the amino acid analogs of CHL were less active inhibitors of translation in comparison with the original antibiotic. The X-ray crystal structures of the Thermus thermophilus 70S ribosome in complex with three semi-synthetic analogs showed that CHL derivatives bind at the peptidyl transferase center, where the aminoacyl moiety of the tested compounds established idiosyncratic interactions with rRNA. Although still fairly inefficient inhibitors of translation, the synthesized compounds represent promising chemical scaffolds that target the peptidyl transferase center of the ribosome and potentially are suitable for further exploration. © 2018 Elsevier Ltd},\r\nauthor_keywords={antibiotic;  peptidyl transferase center;  protein synthesis;  ribosome;  X-ray structure},\r\nfunding_details={Russian Science Foundation14-24-00061-P},\r\nfunding_details={National Institutes of HealthP41 GM103403},\r\nfunding_details={S10 OD021527, S10 RR029205},\r\nfunding_details={Российский Фонд Фундаментальных Исследований (РФФИ)R01 AI125518, 15-34-20139, 16-04-00709},\r\n}

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\n \n\n \n \n \n \n \n \n The ribosomal A-site finger is crucial for binding and activation of the stringent factor RelA.\n \n \n \n \n\n\n \n Kudrin, P.; Dzhygyr, I.; Ishiguro, K.; Beljantseva, J.; Maksimova, E.; Oliveira, S.; Varik, V.; Payoe, R.; Konevega, A.; Tenson, T.; Suzuki, T.; and Hauryliuk, V.\n\n\n \n\n\n\n Nucleic Acids Research, 46(4): 1973-1983. 2018.\n cited By 11\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Kudrin20181973,\r\nauthor={Kudrin, P. and Dzhygyr, I. and Ishiguro, K. and Beljantseva, J. and Maksimova, E. and Oliveira, S.R.A. and Varik, V. and Payoe, R. and Konevega, A.L. and Tenson, T. and Suzuki, T. and Hauryliuk, V.},\r\ntitle={The ribosomal A-site finger is crucial for binding and activation of the stringent factor RelA},\r\njournal={Nucleic Acids Research},\r\nyear={2018},\r\nvolume={46},\r\nnumber={4},\r\npages={1973-1983},\r\ndoi={10.1093/nar/gky023},\r\nnote={cited By 11},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85043232434&doi=10.1093%2fnar%2fgky023&partnerID=40&md5=c0007481c3f4c3c3e742bac01df9a683},\r\naffiliation={University of Tartu, Institute of Technology, Nooruse 1, Tartu, 50411, Estonia; Department of Molecular Biology, Umeå University, Umeå, SE-90187, Sweden; Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, SE-90187, Sweden; Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Petersburg Nuclear Physics Institute, Gatchina, 188300, Russian Federation; Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russian Federation; National Research Centre Kurchatov Institute, Moscow, 123182, Russian Federation},\r\nabstract={During amino acid starvation the Escherichia coli stringent response factor RelA recognizes deacylated tRNA in the ribosomal A-site. This interaction activates RelA-mediated synthesis of alarmone nucleotides pppGpp and ppGpp, collectively referred to as (p)ppGpp. These two alarmones are synthesized by addition of a pyrophosphate moiety to the 3 position of the abundant cellular nucleotide GTP and less abundant nucleotide GDP, respectively. Using untagged native RelA we show that allosteric activation of RelA by pppGpp increases the efficiency of GDP conversion to achieve the maximum rate of (p)ppGpp production. Using a panel of ribosomal RNA mutants, we show that the A-site finger structural element of 23S rRNA helix 38 is crucial for RelA binding to the ribosome and consequent activation, and deletion of the element severely compromises (p)ppGpp accumulation in E. coli upon amino acid starvation. Through binding assays and enzymology, we show that E. coli RelA does not form a stable complex with, and is not activated by, deacylated tRNA off the ribosome. This indicates that in the cell, RelA first binds the empty A-site and then recruits tRNA rather than first binding tRNA and then binding the ribosome. © 2017 The Author(s).},\r\nfunding_details={Eesti TeadusagentuurIUT2-22},\r\nfunding_details={Russian Science Foundation17-14-01416},\r\nfunding_details={Vetenskapsrådet2013-4680},\r\n}

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\n \n\n \n \n \n \n \n \n Isolation of extracellular micro-vesicles from cell culture medium: Comparative evaluation of methods.\n \n \n \n \n\n\n \n Shtam, T.; Samsonov, R.; Volnitskiy, A.; Kamyshinsky, R.; Verlov, N.; Kniazeva, M.; Korobkina, E.; Orehov, A.; Vasiliev, A.; Konevega, A.; and Malek, A.\n\n\n \n\n\n\n Biomeditsinskaya Khimiya, 64(1): 23-30. 2018.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Isolation$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Shtam201823,\r\nauthor={Shtam, T.A. and Samsonov, R.A. and Volnitskiy, A.V. and Kamyshinsky, R.A. and Verlov, N.A. and Kniazeva, M.S. and Korobkina, E.A. and Orehov, A.S. and Vasiliev, A.L. and Konevega, A.L. and Malek, A.V.},\r\ntitle={Isolation of extracellular micro-vesicles from cell culture medium: Comparative evaluation of methods},\r\njournal={Biomeditsinskaya Khimiya},\r\nyear={2018},\r\nvolume={64},\r\nnumber={1},\r\npages={23-30},\r\ndoi={10.18097/PBMC20186401023},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85043459724&doi=10.18097%2fPBMC20186401023&partnerID=40&md5=b472419d6f68dab8bffc8f53af96f345},\r\naffiliation={Petersburg Nuclear Physics Institute of National Research Centre 'Kurchatov Institute', Saint-Petersburg, Gatchina, 188300, Russian Federation; 'Oncosystem' Ltd., Skolkovo, 143026, Russian Federation; N.N.Petrov National Medical Research Center of Oncology, Saint-Petersburg, 197758, Russian Federation; National Research Center 'Kurchatov Institute', Moscow, 123182, Russian Federation; Peter the Great Saint-Petersburg Polytechnic University, St. Petersburg, 195251, Russian Federation},\r\nabstract={Extracellular vesicles (EV) are secreted by cells of multicellular organisms. EV mediate specific mode of intercellular communication by "horizontal" exchange of substances and information. This phenomenon seems to have an essential biological significance and became a subject of intensive research. Biogenesis, structural and functional features of the EV is being commonly studies in in vitro condition. Several methods of EV isolation from cell culture medium are established, however selection of method might influence on obtained results. The choice of the optimal method depends usually from the amount of medium and the aims of the research while is still challenging issue. We performed a comparative analysis of four different methods of EV isolation from cell culture medium: differential ultracentrifugation, ultracentrifugation with a 30% sucrose/D2O "cushion", precipitation with plant proteins and immune-affinity capturing. EV isolated by different approaches were compared in terms of following parameters: size, concentration, morphology of EV, contamination by non-vesicular particles, content of exosomal tetraspanins on the EV surface, content of total proteins, RNA, and several glioma-associated miRNAs. Applied methods included nano-patricle tracking analysis (NTA), dynamic light scattering (DLS), cryo-electron microscopy, flow cytometry and RT-qPCR. On the base of obtained results, we developed practical recommendations that may help researchers to make a best choice of EV isolation method. © 2018 Russian Academy of Medical Sciences. All rights reserved.},\r\nauthor_keywords={Exsosomes;  Extracellular vesicles;  Immunoprecipitation;  Lectines;  Methods of isolation;  Ultracentrifugation},\r\ncorrespondence_address1={Shtam, T.A.; Petersburg Nuclear Physics Institute of National Research Centre 'Kurchatov Institute'Russian Federation; email: tatyana_shtam@mail.ru},\r\npublisher={Russian Academy of Medical Sciences},\r\nissn={23106905},\r\npubmed_id={29460831},\r\nlanguage={Russian},\r\nabbrev_source_title={Biomeditsinskaya Khim.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Exosomal micro-RNA-Potential predictive marker of breast cancer neoadjuvant therapy effect.\n \n \n \n \n\n\n \n Kovalenko, I.; Samsonov, R.; Shtam, T.; Tsyrlina, E.; Kamyshinsky, R.; Semiglazova, T.; Dashyan, G.; Berstein, L.; Semiglazov, V.; and Malek, A.\n\n\n \n\n\n\n Voprosy Onkologii, 64(6): 758-767. 2018.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Exosomal$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Kovalenko2018758,\r\nauthor={Kovalenko, I.M. and Samsonov, R.B. and Shtam, T.A. and Tsyrlina, E.V. and Kamyshinsky, R.A. and Semiglazova, T.Y. and Dashyan, G.A. and Berstein, L.M. and Semiglazov, V.F. and Malek, A.V.},\r\ntitle={Exosomal micro-RNA-Potential predictive marker of breast cancer neoadjuvant therapy effect},\r\njournal={Voprosy Onkologii},\r\nyear={2018},\r\nvolume={64},\r\nnumber={6},\r\npages={758-767},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85063462127&partnerID=40&md5=9845b613691a4a4ac411533063a642b4},\r\naffiliation={N.N.Petrov National Medical Research Center of Oncology, St.Petersburg, Russian Federation; Oncosystem Ltd, Moscow, Russian Federation; Petersburg Nuclear Physics Institute Named by B.RKonstantinov of National Research Center, Kurchatov Institute, Gatchina, Russian Federation; National Research Center Kurchatov Institute, Moscow, Russian Federation},\r\nabstract={Neoadjuvant systemic treatment of patients with breast cancer (BC) may include neoadjuvant chemotherapy (NHT), neoadjuvant hormone therapy (NOT), neoadjuvant targeted therapy. The type of systemic therapy is determined by the level of expression of estrogen/progesterone receptors, HER2, i.e. immimohistochemical characteristic of the disease. In this article, we evaluated the predictive value of the profile of plasma exosomal microRNA, assessing the immediate efficacy of NHT, which included taxanes. Obtained results revealed a correlation between the level of concentration of several miRNA molecules in circulating exosomes and the effect of NHT. Furthermore, the index calculated as the ratio of miR-34a and miR-451 concentrations, allowed to predict the effect of taxanecontaining NHT. The results confirm the assumption on the predictive significance of exosomal miRNA. Further research is needed to confirm the validity of a new method of prediction of the NHT efficacy in breast cancer. © Ruslania 2018. All rights reserved.},\r\nauthor_keywords={Breast cancer;  Exosomes;  MiRNA;  Neoadjuvant chemotherapy;  Predictors of effectiveness},\r\npublisher={Izdatel'stvo Meditsina},\r\nissn={05073758},\r\ncoden={VOONA},\r\nlanguage={Russian},\r\nabbrev_source_title={Vopr. Onkol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2017\n \n \n (6)\n \n \n

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\n \n\n \n \n \n \n \n \n Biodiversity, drug discovery, and the future of global health: Introducing the biodiversity to biomedicine consortium, a call to action.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Journal of Global Health, 7(2). 2017.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Biodiversity,$ Paper\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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\n \n\n \n \n \n \n \n \n Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel.\n \n \n \n \n\n\n \n Metelev, M.; Osterman, I.; Ghilarov, D.; Khabibullina, N.; Yakimov, A.; Shabalin, K.; Utkina, I.; Travin, D.; Komarova, E.; Serebryakova, M.; Artamonova, T.; Khodorkovskii, M.; Konevega, A.; Sergiev, P.; Severinov, K.; and Polikanov, Y.\n\n\n \n\n\n\n Nature Chemical Biology, 13(10): 1129-1136. 2017.\n cited By 15\n\n\n\n
\n\n\n\n \n \n $\"Klebsazolicin$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Metelev20171129,\r\nauthor={Metelev, M. and Osterman, I.A. and Ghilarov, D. and Khabibullina, N.F. and Yakimov, A. and Shabalin, K. and Utkina, I. and Travin, D.Y. and Komarova, E.S. and Serebryakova, M. and Artamonova, T. and Khodorkovskii, M. and Konevega, A.L. and Sergiev, P.V. and Severinov, K. and Polikanov, Y.S.},\r\ntitle={Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel},\r\njournal={Nature Chemical Biology},\r\nyear={2017},\r\nvolume={13},\r\nnumber={10},\r\npages={1129-1136},\r\ndoi={10.1038/nchembio.2462},\r\nnote={cited By 15},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85031012229&doi=10.1038%2fnchembio.2462&partnerID=40&md5=c5d5cfc278f69e76c4a9e942481d352e},\r\naffiliation={Research Center of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, Russian Federation; Institute of Antimicrobial Chemotherapy, Smolensk State Medical Academy, Smolensk, Russian Federation; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russian Federation; Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russian Federation; Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States; Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russian Federation; Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation; Waksman Institute for Microbiology Rutgers, State University of New Jersey, Piscataway, NJ, United States; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL, United States},\r\nabstract={Whereas screening of the small-molecule metabolites produced by most cultivatable microorganisms often results in the rediscovery of known compounds, genome-mining programs allow researchers to harness much greater chemical diversity, and result in the discovery of new molecular scaffolds. Here we report the genome-guided identification of a new antibiotic, klebsazolicin (KLB), from Klebsiella pneumoniae that inhibits the growth of sensitive cells by targeting ribosomes. A ribosomally synthesized post-Translationally modified peptide (RiPP), KLB is characterized by the presence of a unique N-Terminal amidine ring that is essential for its activity. Biochemical in vitro studies indicate that KLB inhibits ribosomes by interfering with translation elongation. Structural analysis of the ribosome-KLB complex showed that the compound binds in the peptide exit tunnel overlapping with the binding sites of macrolides or streptogramin-B. KLB adopts a compact conformation and largely obstructs the tunnel. Engineered KLB fragments were observed to retain in vitro activity, and thus have the potential to serve as a starting point for the development of new bioactive compounds.},\r\npublisher={Nature Publishing Group},\r\nissn={15524450},\r\ncoden={NCBAB},\r\npubmed_id={28846667},\r\nlanguage={English},\r\nabbrev_source_title={Nat. Chem. Biol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Exosomes: Some approaches to cancer diagnosis and therapy.\n \n \n \n \n\n\n \n Shtam, T.; Samsonov, R.; Kamyshinsky, R.; Pantina, R.; Verlov, N.; Vasiliev, A.; Konevega, A.; and Malek, A.\n\n\n \n\n\n\n 2017.\n cited By 5; Conference of International Conference on Physics of Cancer: Interdisciplinary Problems and Clinical Applications, PC IPCA 2017 ; Conference Date: 23 May 2017 Through 26 May 2017; Conference Code:133914\n\n\n\n
\n\n\n\n \n \n $\"Exosomes:$ Paper\n \n \n\n \n \n doi\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

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@CONFERENCE{Shtam2017,\r\nauthor={Shtam, T. and Samsonov, R. and Kamyshinsky, R. and Pantina, R. and Verlov, N. and Vasiliev, A. and Konevega, A.L. and Malek, A.V.},\r\ntitle={Exosomes: Some approaches to cancer diagnosis and therapy},\r\njournal={AIP Conference Proceedings},\r\nyear={2017},\r\nvolume={1882},\r\ndoi={10.1063/1.5001645},\r\nart_number={020066},\r\nnote={cited By 5; Conference of International Conference on Physics of Cancer: Interdisciplinary Problems and Clinical Applications, PC IPCA 2017 ; Conference Date: 23 May 2017 Through 26 May 2017;  Conference Code:133914},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85041662414&doi=10.1063%2f1.5001645&partnerID=40&md5=d908b66243d4ade3a27c45bad492f886},\r\naffiliation={Petersburg Nuclear Physics Institute of National Research Centre, Kurchatov Institute, Gatchina, Russian Federation; Petrov Institute of Oncology, Saint-Petersburg, Russian Federation; Ltd. Oncosystem, Skolkovo, Russian Federation; Peter the Great Saint-Petersburg Polytechnic University, St. Petersburg, Russian Federation; National Research Center, Kurchatov Institute, Moscow, Russian Federation},\r\nabstract={Exosomes are membrane-bound, intercellular communication shuttle vesicles that are defined by their endocytic origin and size range of 30-120 nm. Secreted by nearly all mammalian cell types and present in bodily fluids, exosomes confer messages between cells, by transporting functionally relevant proteins, nucleic acids, and lipids. The capability of tumor exosomes to house tumorigenic information and induce cellular responses that promote disease pathogenesis make tumor exosomes an attractive tool in identifying cancer biomarkers and exploiting exosomes for therapy. In this paper, we sum up our previous findings to utilize exosomes as biomarkers for early detection, diagnosis and therapy selection of prostate and thyroid cancer and present our results on exosomes in colon cancer. Some of plasma exosomal miRNAs showed their potential as diagnostic markers for colon cancer. All together, the data suggested the potentials of circulating exosomal miRNAs as liquid biopsy markers for cancer. Here we also present the possibilities of delivering therapeutic molecules by exosomes. Previously, we had demonstrated the potential of exosome-mediated siRNA delivery. Here, we present the possibility of carrying the exogenous p53 protein by exosomes in vitro. © 2017 Author(s).},\r\ncorrespondence_address1={Shtam, T.; Petersburg Nuclear Physics Institute of National Research Centre, Kurchatov InstituteRussian Federation; email: tatyana_shtam@mail.ru},\r\neditor={Gutmanas E.Y., Naimark O.B., Sharkeev Y.P.},\r\nsponsors={Institute of Continuous Media Mechanics of UrB RAS; Institute of Strength Physics and Materials Science of SB RAS; National Research Tomsk Polytechnic University; National Research Tomsk State University; Tomsk Research Institute of Oncology},\r\npublisher={American Institute of Physics Inc.},\r\nissn={0094243X},\r\nisbn={9780735415621},\r\nlanguage={English},\r\nabbrev_source_title={AIP Conf. Proc.},\r\ndocument_type={Conference Paper},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The rare nonsense mutation in p53 triggers alternative splicing to produce a protein capable of inducing apoptosis.\n \n \n \n \n\n\n \n Makarov, E.; Shtam, T.; Kovalev, R.; Pantina, R.; Varfolomeeva, E.; and Filatov, M.\n\n\n \n\n\n\n PLoS ONE, 12(9). 2017.\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

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@ARTICLE{Makarov2017,\r\nauthor={Makarov, E.M. and Shtam, T.A. and Kovalev, R.A. and Pantina, R.A. and Varfolomeeva, E.Y. and Filatov, M.V.},\r\ntitle={The rare nonsense mutation in p53 triggers alternative splicing to produce a protein capable of inducing apoptosis},\r\njournal={PLoS ONE},\r\nyear={2017},\r\nvolume={12},\r\nnumber={9},\r\ndoi={10.1371/journal.pone.0185126},\r\nart_number={e0185126},\r\nnote={cited By 2},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85030163652&doi=10.1371%2fjournal.pone.0185126&partnerID=40&md5=e33272f5dbd1aae05eb33bbe72e9eea2},\r\naffiliation={Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, United Kingdom; National Research Centre Kurchatov Institute B.P. Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; Peter the Great St Petersburg Polytechnic University, St Petersburg, Russian Federation; Petrov Institute of Oncology, St Petersburg, Russian Federation},\r\nabstract={P53 protein is more frequently mutated in human tumours compared with the other proteins. While the majority of the p53 mutations, especially within its DNA-binding domain, lead to the loss of the wild-type function, there are accumulating data demonstrating that the p53 mutants gain tumour promoting activities; the latter triggers a revitalised interest in functional analysis of the p53 mutants. A systematic screening for p53 mutations in surgical materials from patients with glioma revealed a 378C>G mutation that creates a stop codon at the position of amino acid residue 126. The mutation eliminates the recognition site for the restriction endonuclease Sca I that allowed us to carry out RFLP analysis of DNA extracted from the clinical samples and suggests that this mutation is more frequent than is documented in the p53 databases. Both the ECV-304 and EJ cell lines, that probably originate from the bladder carcinoma T24 cell line, were confirmed to contain the homozygous 378C>G mutation but were shown to produce the p53 protein of expected full-length size detected by Western blotting. We provide evidence that the 378C>G mutation generates an alternative 3’ splice site (ss) which is more often used instead of the authentic upstream 3’ ss, driving the production of mRNA encoding the protein with the single amino acid deletion (p53ΔY126). Using endogenous expression, we demonstrated that the p53ΔY126 protein is nearly as active as the wild type protein in inducing the p21/Waf1 expression and apoptosis. © 2017 Makarov 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.},\r\ncorrespondence_address1={Filatov, M.V.; National Research Centre Kurchatov Institute B.P. Konstantinov Petersburg Nuclear Physics InstituteRussian Federation; email: fil53ster@gmail.com},\r\npublisher={Public Library of Science},\r\nissn={19326203},\r\ncoden={POLNC},\r\npubmed_id={28961258},\r\nlanguage={English},\r\nabbrev_source_title={PLoS ONE},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.\n \n \n \n \n\n\n \n Osterman, I.; Khabibullina, N.; Komarova, E.; Kasatsky, P.; Kartsev, V.; Bogdanov, A.; Dontsova, O.; Konevega, A.; Sergiev, P.; and Polikanov, Y.\n\n\n \n\n\n\n Nucleic Acids Research, 45(12): 7507-7514. 2017.\n cited By 11\n\n\n\n
\n\n\n\n \n \n $\"Madumycin$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Osterman20177507,\r\nauthor={Osterman, I.A. and Khabibullina, N.F. and Komarova, E.S. and Kasatsky, P. and Kartsev, V.G. and Bogdanov, A.A. and Dontsova, O.A. and Konevega, A.L. and Sergiev, P.V. and Polikanov, Y.S.},\r\ntitle={Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state},\r\njournal={Nucleic Acids Research},\r\nyear={2017},\r\nvolume={45},\r\nnumber={12},\r\npages={7507-7514},\r\ndoi={10.1093/nar/gkx413},\r\nnote={cited By 11},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85026446380&doi=10.1093%2fnar%2fgkx413&partnerID=40&md5=df4e86fa62a23b849433153492bd3644},\r\naffiliation={Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky, Institute of Physico-Chemical Biology, Moscow, 119992, Russian Federation; Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russian Federation; Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL  60607, United States; Lomonosov Moscow State University, Department of Bioengineering and Bioinformatics, Moscow, 119992, Russian Federation; Petersburg Nuclear Physics Institute, NRC 'Kurchatov Institute', Gatchina, 188300, Russian Federation; Interbioscreen Ltd, Chernogolovka, Moscow Region, 142432, Russian Federation; Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, 195251, Russian Federation; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL  60607, United States},\r\nabstract={The emergence ofmulti-drug resistant bacteria is limiting the effectiveness of commonly used antibiotics, which spurs a renewed interest in revisiting older and poorly studied drugs. Streptogramins A is a class of protein synthesis inhibitors that target the peptidyl transferase center (PTC) on the large subunit of the ribosome. In this work, we have revealed the mode of action of the PTC inhibitor madumycin II, an alanine-containing streptogramin A antibiotic, in the context of a functional 70S ribosome containing tRNA substrates. Madumycin II inhibits the ribosome prior to the first cycle of peptide bond formation. It allows binding of the tRNAs to the ribosomal A and P sites, but prevents correct positioning of their CCA-ends into the PTC thus making peptide bond formation impossible. We also revealed a previously unseen drug-induced rearrangement of nucleotides U2506 and U2585 of the 23S rRNA resulting in the formation of the U2506·G2583 wobble pair that was attributed to a catalytically inactive state of the PTC. The structural and biochemical data reported here expand our knowledge on the fundamental mechanisms by which peptidyl transferase inhibitors modulate the catalytic activity of the ribosome. © The Author(s) 2017.},\r\nfunding_details={Russian Science Foundation15-14-00006},\r\nfunding_details={National Institutes of HealthP41 GM103403},\r\nfunding_details={S10 RR029205},\r\nfunding_details={Российский Фонд Фундаментальных Исследований (РФФИ)16-04-01100},\r\nfunding_details={Argonne National LaboratoryDE-AC02-06CH11357},\r\n}

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\n \n\n \n \n \n \n \n \n Aggregation by lectins as an approach for exosome isolation from biological fluids: Validation for proteomic studies.\n \n \n \n \n\n\n \n Shtam, T.; Burdakov, V.; Landa, S.; Naryzhny, S.; Bairamukov, V.; Malek, A.; Orlov, Y.; and Filatov, M.\n\n\n \n\n\n\n Cell and Tissue Biology, 11(2): 172-179. 2017.\n cited By 4\n\n\n\n
\n\n\n\n \n \n $\"Aggregation$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Shtam2017172,\r\nauthor={Shtam, T.A. and Burdakov, V.S. and Landa, S.B. and Naryzhny, S.N. and Bairamukov, V.Y. and Malek, A.V. and Orlov, Y.N. and Filatov, M.V.},\r\ntitle={Aggregation by lectins as an approach for exosome isolation from biological fluids: Validation for proteomic studies},\r\njournal={Cell and Tissue Biology},\r\nyear={2017},\r\nvolume={11},\r\nnumber={2},\r\npages={172-179},\r\ndoi={10.1134/S1990519X17020043},\r\nnote={cited By 4},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018499633&doi=10.1134%2fS1990519X17020043&partnerID=40&md5=f439cee2262ea4552aa9c299648a59e1},\r\naffiliation={National Research Centre “Kurchatov Institute” B.P. Konstantinov Petersburg Nuclear Physics Institute, Gatchina, 188300, Russian Federation; Peter the Great Polytechnic University, St. Petersburg, 195251, Russian Federation; Petrov Institute of Oncology, Ministry of Healthcare of the Russian Federation, St. Petersburg, 197758, Russian Federation; Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, 119121, Russian Federation},\r\nabstract={Exosomes, a special type of microparticles produced by cells, are currently of considerable interest for researchers. The term “exosomes” denotes extracellular vesicles of less than 120 nm in size derived from intracellular multivesicular bodies. Multiple studies that address the distinctive features of exosome structure and biochemical composition in various pathological states imply the possibility of development of novel diagnostic techniques based on the detection of changes in the pool of proteins and nucleic acids transported by exosomes. However, methods for isolation and investigation of exosomes are rather difficult to develop because of a small size of these vesicles. A novel approach for preparative-scale isolation of exosomes based on the phenomenon of binding and aggregation of these particles in the presence of lectins has been put forward in the present study. The method developed is relatively cost-effective, allows for the isolation of exosomes from various biological fluids, and has been validated for the subsequent analysis of the protein composition of the exosomes in view of the possible clinical applications. The validation showed that the sedimentation of lectin-aggregated exosomes is a suitable approach for the isolation of these microvesicles from the complete conditioned culture medium in a research-laboratory setup. © 2017, Pleiades Publishing, Ltd.},\r\nauthor_keywords={exosomes;  lectins;  methods of exosome isolation},\r\ncorrespondence_address1={Filatov, M.V.; National Research Centre “Kurchatov Institute” B.P. Konstantinov Petersburg Nuclear Physics InstituteRussian Federation; email: fil_53@mail.ru},\r\npublisher={Maik Nauka-Interperiodica Publishing},\r\nissn={1990519X},\r\nlanguage={English},\r\nabbrev_source_title={Cell Tissue Biol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2016\n \n \n (4)\n \n \n

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\n \n\n \n \n \n \n \n \n The pathway to GTPase activation of elongation factor SelB on the ribosome.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Nature, 540(7631): 80-85. 2016.\n cited By 38\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

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\n \n\n \n \n \n \n \n \n New fluorescent macrolide derivatives for studying interactions of antibiotics and their analogs with the ribosomal exit tunnel.\n \n \n \n \n\n\n \n Tereshchenkov, A.; Shishkina, A.; Karpenko, V.; Chertkov, V.; Konevega, A.; Kasatsky, P.; Bogdanov, A.; and Sumbatyan, N.\n\n\n \n\n\n\n Biochemistry (Moscow), 81(10): 1163-1172. 2016.\n cited By 1\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

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@ARTICLE{Tereshchenkov20161163,\r\nauthor={Tereshchenkov, A.G. and Shishkina, A.V. and Karpenko, V.V. and Chertkov, V.A. and Konevega, A.L. and Kasatsky, P.S. and Bogdanov, A.A. and Sumbatyan, N.V.},\r\ntitle={New fluorescent macrolide derivatives for studying interactions of antibiotics and their analogs with the ribosomal exit tunnel},\r\njournal={Biochemistry (Moscow)},\r\nyear={2016},\r\nvolume={81},\r\nnumber={10},\r\npages={1163-1172},\r\ndoi={10.1134/S0006297916100138},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84991669831&doi=10.1134%2fS0006297916100138&partnerID=40&md5=01483b7d6b26f397ecd9fc059902ac13},\r\naffiliation={Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russian Federation; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russian Federation; Molecular and Radiation Biophysics Division, Konstantinov Petersburg Nuclear Physics Institute, National Research Center “Kurchatov Institute”, Gatchina, 188300, Russian Federation; Peter the Great Saint-Petersburg Polytechnic University, St. Petersburg, 195251, Russian Federation},\r\nabstract={Novel fluorescent derivatives of macrolide antibiotics related to tylosin bearing rhodamine, fluorescein, Alexa Fluor 488, BODIPY FL, and nitrobenzoxadiazole (NBD) residues were synthesized. The formation of complexes of these compounds with 70S E. coli ribosomes was studied by measuring the fluorescence polarization depending on the ribosome amount at constant concentration of the fluorescent substance. With the synthesized fluorescent tylosin derivatives, the dissociation constants for ribosome complexes with several known antibiotics and macrolide analogs previously obtained were determined. It was found that the fluorescent tylosin derivatives containing BODIPY FL and NBD groups could be used to screen the binding of novel antibiotics to bacterial ribosomes in the macrolide-binding site. © 2016, Pleiades Publishing, Ltd.},\r\nauthor_keywords={fluorescent derivatives;  fluorescent polarization;  macrolides;  nascent peptide exit tunnel;  tylosin},\r\ncorrespondence_address1={Sumbatyan, N.V.; Faculty of Chemistry, Lomonosov Moscow State UniversityRussian Federation; email: sumbtyan@belozersky.msu.ru},\r\npublisher={Maik Nauka Publishing / Springer SBM},\r\nissn={00062979},\r\ncoden={BIORA},\r\npubmed_id={27908240},\r\nlanguage={English},\r\nabbrev_source_title={Biochemistry Moscow},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Plasma exosomal miR-21 and miR-181a differentiates follicular from papillary thyroid cancer.\n \n \n \n \n\n\n \n Samsonov, R.; Burdakov, V.; Shtam, T.; Radzhabovа, Z.; Vasilyev, D.; Tsyrlina, E.; Titov, S.; Ivanov, M.; Berstein, L.; Filatov, M.; Kolesnikov, N.; Gil-Henn, H.; and Malek, A.\n\n\n \n\n\n\n Tumor Biology, 37(9): 12011-12021. 2016.\n cited By 29\n\n\n\n
\n\n\n\n \n \n $\"Plasma$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Samsonov201612011,\r\nauthor={Samsonov, R. and Burdakov, V. and Shtam, T. and Radzhabovа, Z. and Vasilyev, D. and Tsyrlina, E. and Titov, S. and Ivanov, M. and Berstein, L. and Filatov, M. and Kolesnikov, N. and Gil-Henn, H. and Malek, A.},\r\ntitle={Plasma exosomal miR-21 and miR-181a differentiates follicular from papillary thyroid cancer},\r\njournal={Tumor Biology},\r\nyear={2016},\r\nvolume={37},\r\nnumber={9},\r\npages={12011-12021},\r\ndoi={10.1007/s13277-016-5065-3},\r\nnote={cited By 29},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84966489917&doi=10.1007%2fs13277-016-5065-3&partnerID=40&md5=44202226962197cb45fd5d86662beabe},\r\naffiliation={Oncosystem Ltd, Hoshimina 11/1-207, Saint-Petersburg, 194356, Russian Federation; NN Petrov Institute of Oncology, Leningradskaya 68, Saint-Petersburg, 197758, Russian Federation; FSBI Petersburg Nuclear Physics Institute, Gatchina, Saint-Petersburg  188300, Russian Federation; Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, Saint-Petersburg, 195251, Russian Federation; Institute of Molecular and Cellular Biology SB RAS, Lavrentieva 8/2, Novosibirsk, 630090, Russian Federation; Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold 8, Safed, 13100, Israel},\r\nabstract={Thyroid cancer (TC) is the most common endocrine malignancy and its incidence has increased over the last few decades. As has been revealed by a number of studies, TC tissue’s micro-RNA (miRNA) profile may reflect histological features and the clinical behavior of tumor. However, alteration of the miRNA profile of plasma exosomes associated with TC development has to date not been explored. We isolated exosomes from plasma and assayed their characteristics using laser diffraction particle size analysis, atomic force microscopy, and western blotting. Next, we profiled cancer-associated miRNAs in plasma exosomes obtained from papillary TC patients, before and after surgical removal of the tumor. The diagnostic value of selected miRNAs was evaluated in a large cohort of patients displaying different statuses of thyroid nodule disease. MiRNA assessment was performed by RT-qPCR. In total, 60 patients with different types of thyroid nodal pathology were included in the study. Our results revealed that the development of papillary TC is associated with specific changes in exosomal miRNA profiles; this phenomenon can be used for differential diagnostics. MiRNA-31 was found to be over-represented in the plasma exosomes of patients with papillary TC vs. benign tumors, while miRNA-21 helped to distinguish between benign tumors and follicular TC. MiRNA-21 and MiRNA-181a-5p were found to be expressed reciprocally in the exosomes of patients with papillary and follicular TC, and their comparative assessment may help to distinguish between these types of TC with 100 % sensitivity and 77 % specificity. © 2016, International Society of Oncology and BioMarkers (ISOBM).},\r\nauthor_keywords={Diagnostics;  Exosomes;  MicroRNA;  Thyroid cancer},\r\ncorrespondence_address1={Malek, A.; Oncosystem Ltd, Hoshimina 11/1-207, Russian Federation; email: anastasia@malek.com},\r\npublisher={Springer Netherlands},\r\nissn={10104283},\r\ncoden={TUMBE},\r\npubmed_id={27164936},\r\nlanguage={English},\r\nabbrev_source_title={Tumor Biol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Lectin-induced agglutination method of urinary exosomes isolation followed by mi-RNA analysis: Application for prostate cancer diagnostic.\n \n \n \n \n\n\n \n Samsonov, R.; Shtam, T.; Burdakov, V.; Glotov, A.; Tsyrlina, E.; Berstein, L.; Nosov, A.; Evtushenko, V.; Filatov, M.; and Malek, A.\n\n\n \n\n\n\n Prostate, 76(1): 68-79. 2016.\n cited By 62\n\n\n\n
\n\n\n\n \n \n $\"Lectin-induced$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Samsonov201668,\r\nauthor={Samsonov, R. and Shtam, T. and Burdakov, V. and Glotov, A. and Tsyrlina, E. and Berstein, L. and Nosov, A. and Evtushenko, V. and Filatov, M. and Malek, A.},\r\ntitle={Lectin-induced agglutination method of urinary exosomes isolation followed by mi-RNA analysis: Application for prostate cancer diagnostic},\r\njournal={Prostate},\r\nyear={2016},\r\nvolume={76},\r\nnumber={1},\r\npages={68-79},\r\ndoi={10.1002/pros.23101},\r\nnote={cited By 62},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84955181667&doi=10.1002%2fpros.23101&partnerID=40&md5=10835f69427cb4f1655bac5857581ea3},\r\naffiliation={Laboratory of Oncoendocrinology, N.N. Petrov Institute of Oncology, Pesochny, Saint-Petersburg, Russian Federation; Laboratory of Genetic Engineering, Russian Research Centre for Radiology and Surgical Technologies, St. Petersburg, Russian Federation; Division of Molecular and Radiation Biophysics, SFBI Petersburg Nuclear Physics Institute, Gatchina, Saint-Petersburg, Russian Federation; Department of Genetics and Biotechnology, Saint Petersburg State University, Saint-Petersburg, Russian Federation; Department of Urology, N.N. Petrov Institute of Oncology, Pesochny, Saint-Petersburg, Russian Federation; Laboratory of Cell Migration and Invasion, Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel},\r\nabstract={BACKGROUND Prostate cancer is the most common cancer in men. Prostate-specific antigen has, however, insufficient diagnostic specificity. Novel complementary diagnostic approaches are greatly needed. MiRNAs are small regulatory RNAs which play an important role in tumorogenesis and are being investigated as a cancer biomarker. In addition to their intracellular regulatory functions, miRNAs are secreted into the extracellular space and can be found in various body fluids, including urine. The stability of extracellular miRNAs is defined by association with proteins, lipoprotein particles, and membrane vesicles. Among the known forms of miRNA packaging, tumour-derived exosome-enclosed miRNAs is thought to reflect the vital activity of cancer cells. The assessment of the exosomal fraction of urinary miRNA may present a new and highly specific method for prostate cancer diagnostics; however, this is challenged by the absence of reliable and inexpensive methods for isolation of exosomes. METHODS Prostate cancer (PC) cell lines and urine samples collected from 35 PC patients and 35 healthy donors were used in the study. Lectins, phytohemagglutinin, and concanavalin A were used to induce agglutination of exosomes. The efficiency of isolation process was evaluated by AFM and DLS assays. The protein content of isolated exosomes was analysed by western blotting. Exosomal RNA was assayed by automated electrophoresis and expression level of selected miRNAs was evaluated by RT-qPCR. The diagnostic potency of the urinary exosomal miRNA assessment was estimated by the ROC method. RESULTS The formation of multi-vesicular agglutinates in urine can be induced by incubation with lectin at a final concentration of 2 mg/ml. These agglutinates contain urinary exosomes and may be pelleted by centrifugation with a relatively low G-force. The analysis of PC-related miRNA in urinary exosomes revealed significant up-regulation of miR-574-3p, miR-141-5p, and miR-21-5p associated with PC. CONCLUSIONS Lectin-induced aggregation is a low-cost and easily performed method for isolation of exosomes from urine. Isolated exosomes can be further analysed in terms of miRNA content. The miRNA profile of urinary exosomes reflects development of prostate cancer and may present a promising diagnostic tool. Prostate 76:68-79, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.},\r\nauthor_keywords={diagnostic;  exosomes;  lectin;  miRNA;  prostate cancer},\r\ncorrespondence_address1={Malek, A.; NN Petrov Institute of Oncology, Leningradskaya 68, Russian Federation; email: anastasia@malek.com},\r\npublisher={John Wiley and Sons Inc.},\r\nissn={02704137},\r\ncoden={PRSTD},\r\npubmed_id={26417675},\r\nlanguage={English},\r\nabbrev_source_title={Prostate},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n BACKGROUND Prostate cancer is the most common cancer in men. Prostate-specific antigen has, however, insufficient diagnostic specificity. Novel complementary diagnostic approaches are greatly needed. MiRNAs are small regulatory RNAs which play an important role in tumorogenesis and are being investigated as a cancer biomarker. In addition to their intracellular regulatory functions, miRNAs are secreted into the extracellular space and can be found in various body fluids, including urine. The stability of extracellular miRNAs is defined by association with proteins, lipoprotein particles, and membrane vesicles. Among the known forms of miRNA packaging, tumour-derived exosome-enclosed miRNAs is thought to reflect the vital activity of cancer cells. The assessment of the exosomal fraction of urinary miRNA may present a new and highly specific method for prostate cancer diagnostics; however, this is challenged by the absence of reliable and inexpensive methods for isolation of exosomes. METHODS Prostate cancer (PC) cell lines and urine samples collected from 35 PC patients and 35 healthy donors were used in the study. Lectins, phytohemagglutinin, and concanavalin A were used to induce agglutination of exosomes. The efficiency of isolation process was evaluated by AFM and DLS assays. The protein content of isolated exosomes was analysed by western blotting. Exosomal RNA was assayed by automated electrophoresis and expression level of selected miRNAs was evaluated by RT-qPCR. The diagnostic potency of the urinary exosomal miRNA assessment was estimated by the ROC method. RESULTS The formation of multi-vesicular agglutinates in urine can be induced by incubation with lectin at a final concentration of 2 mg/ml. These agglutinates contain urinary exosomes and may be pelleted by centrifugation with a relatively low G-force. The analysis of PC-related miRNA in urinary exosomes revealed significant up-regulation of miR-574-3p, miR-141-5p, and miR-21-5p associated with PC. CONCLUSIONS Lectin-induced aggregation is a low-cost and easily performed method for isolation of exosomes from urine. Isolated exosomes can be further analysed in terms of miRNA content. The miRNA profile of urinary exosomes reflects development of prostate cancer and may present a promising diagnostic tool. Prostate 76:68-79, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.\n

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\n \n 2015\n \n \n (4)\n \n \n

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\n \n\n \n \n \n \n \n \n Histone deacetylase inhibitors cause TP53-dependent induction of p21/Waf1 in tumor cells with TP53 mutations.\n \n \n \n \n\n\n \n Kovalev, R.; Shtam, T.; Karelov, D.; Burdakov, V.; Volnitskiy, A.; Makarov, E.; and Filatova, M.\n\n\n \n\n\n\n Cell and Tissue Biology, 9(3): 191-197. 2015.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Histone$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Kovalev2015191,\r\nauthor={Kovalev, R.A. and Shtam, T.A. and Karelov, D.V. and Burdakov, V.S. and Volnitskiy, A.V. and Makarov, E.M. and Filatova, M.V.},\r\ntitle={Histone deacetylase inhibitors cause TP53-dependent induction of p21/Waf1 in tumor cells with TP53 mutations},\r\njournal={Cell and Tissue Biology},\r\nyear={2015},\r\nvolume={9},\r\nnumber={3},\r\npages={191-197},\r\ndoi={10.1134/S1990519X15030086},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84934918732&doi=10.1134%2fS1990519X15030086&partnerID=40&md5=0c901448296154db7453d31299ecdd32},\r\naffiliation={Division of Molecular and Radiation Biophysics, National Research Centre “Kurchatov Institute”, Gatchina, Leningrad oblast, 188300, Russian Federation; Department of Biophysics, St. Petersburg State Polytechnical University, St. Petersburg, 194064, Russian Federation; Division of Biosciences, Brunel University, London, United Kingdom},\r\nabstract={The p21/Waf1 protein is one of the main regulators of cell cycle arrest and one of the best-known transcriptional targets of the TP53 protein. Here, we demonstrated that there is activation of expression of the p21/Waf1 gene when the cells were treated with sodium butyrate (NaBu), which is a natural histone deacetylase inhibitor, and investigated whether this phenomenon depends on the presence of a functionally active TP53 protein. For this purpose, we compared the effect of NaBu treatment of human cell lines with different TP53 mutation profiles, including wild-type TP53, single nucleotide substitutions, and the complete absence of the TP53 gene. NaBu activated the TP53 protein via hyperacetylation at the lysine residue K382, without significant changes in the level of protein expression. Western blotting showed that the addition of NaBu triggers a significant increase in the p21/Waf1 protein level in both TP53 wild-type cells and in cells with single nucleotide substitutions in the central DNA-binding core domain (DBD) of the TP53 protein. At the same time, no p21/Waf1 protein induction was observed in cells with complete deletion of the TP53 gene. However, NaBu was not able to induce p21/Waf1 production when the expression of TP53 was transiently knocked down by the p53 siRNA. Overall, our results suggest that NaBu-dependent induction of p21/Waf1 does require the presence of TP53 protein, but, unexpectedly, it can occur regardless of mutational changes in the domain responsible for the TP53 binding to DNA. One possible explanations is that NaBu increases the level of TP53 acetylation and the modified protein is able to establish a new network of protein–protein interactions or trigger conformational changes affecting the TP53-dependent transcriptional machinery even when its DNA binding ability is impaired. © 2015, Pleiades Publishing, Ltd.},\r\nauthor_keywords={HDAC inhibitors;  p21/Waf1/Cip1;  RNA interference;  sodium butyrate;  TP53;  TP53 mutations},\r\ncorrespondence_address1={Filatova, M.V.; Division of Molecular and Radiation Biophysics, National Research Centre “Kurchatov Institute”Russian Federation},\r\npublisher={Maik Nauka-Interperiodica Publishing},\r\nissn={1990519X},\r\nlanguage={English},\r\nabbrev_source_title={Cell Tissue Biol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases.\n \n \n \n \n\n\n \n Byrne, R.; Jenkins, H.; Peters, D.; Whelan, F.; Stowell, J.; Aziz, N.; Kasatsky, P.; Rodnina, M.; Koonin, E.; Konevega, A.; and Antson, A.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 112(19): 6033-6037. 2015.\n cited By 16\n\n\n\n
\n\n\n\n \n \n $\"Major$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Byrne20156033,\r\nauthor={Byrne, R.T. and Jenkins, H.T. and Peters, D.T. and Whelan, F. and Stowell, J. and Aziz, N. and Kasatsky, P. and Rodnina, M.V. and Koonin, E.V. and Konevega, A.L. and Antson, A.A.},\r\ntitle={Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases},\r\njournal={Proceedings of the National Academy of Sciences of the United States of America},\r\nyear={2015},\r\nvolume={112},\r\nnumber={19},\r\npages={6033-6037},\r\ndoi={10.1073/pnas.1500161112},\r\nnote={cited By 16},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84929190405&doi=10.1073%2fpnas.1500161112&partnerID=40&md5=60b746035096d36c59e889828409218c},\r\naffiliation={York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom; Department of Biology, University of York, York, YO10 5DD, United Kingdom; Genome Canada, Ottawa, ON  K2P 1P1, Canada; Molecular and Radiation Biophysics Department, B.P. Konstantinov Petersburg Nucl. Physics Institute of National Research Centre Kurchatov Institute, Gatchina, 188300, Russian Federation; St. Petersburg State Polytechnic University, St. Petersburg, 195251, Russian Federation; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, 37077, Germany; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD  20894, United States},\r\nabstract={The reduction of specific uridines to dihydrouridine is one of the most common modifications in tRNA. Increased levels of the dihydrouridine modification are associated with cancer. Dihydrouridine synthases (Dus) from different subfamilies selectively reduce distinct uridines, located at spatially unique positions of folded tRNA, into dihydrouridine. Because the catalytic center of all Dus enzymes is conserved, it is unclear how the same protein fold can be reprogrammed to ensure that nucleotides exposed at spatially distinct faces of tRNA can be accommodated in the same active site. We show that the Escherichia coli DusC is specific toward U16 of tRNA. Unexpectedly, crystal structures of DusC complexes with tRNAPhe and tRNATrp show that Dus subfamilies that selectively modify U16 or U20 in tRNA adopt identical folds but bind their respective tRNA substrates in an almost reverse orientation that differs by a 160° rotation. The tRNA docking orientation appears to be guided by subfamily-specific clusters of amino acids ("binding signatures") together with differences in the shape of the positively charged tRNA-binding surfaces. tRNA orientations are further constrained by positional differences between the C-terminal "recognition" domains. The exquisite substrate specificity of Dus enzymes is therefore controlled by a relatively simple mechanism involving major reorientation of the whole tRNA molecule. Such reprogramming of the enzymatic specificity appears to be a unique evolutionary solution for altering tRNA recognition by the same protein fold.},\r\nauthor_keywords={Dihydrouridine synthase;  Protein-RNA interaction;  Substrate specificity;  TRNA modification;  X-ray crystallography},\r\n}

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\n \n\n \n \n \n \n \n \n Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM.\n \n \n \n \n\n\n \n Fischer, N.; Neumann, P.; Konevega, A.; Bock, L.; Ficner, R.; Rodnina, M.; and Stark, H.\n\n\n \n\n\n\n Nature, 520(7548): 567-570. 2015.\n cited By 194\n\n\n\n
\n\n\n\n \n \n $\"Structure$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Fischer2015567,\r\nauthor={Fischer, N. and Neumann, P. and Konevega, A.L. and Bock, L.V. and Ficner, R. and Rodnina, M.V. and Stark, H.},\r\ntitle={Structure of the E. coli ribosome-EF-Tu complex at &lt;3 Å resolution by Cs-corrected cryo-EM},\r\njournal={Nature},\r\nyear={2015},\r\nvolume={520},\r\nnumber={7548},\r\npages={567-570},\r\ndoi={10.1038/nature14275},\r\nnote={cited By 194},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84928560614&doi=10.1038%2fnature14275&partnerID=40&md5=fa92f09423e603e57b94c7a59be68197},\r\naffiliation={3D Electron Cryomicroscopy Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany; Abteilung Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August Universität Göttingen, Justus-von Liebig Weg 11, Göttingen, 37077, Germany; Molecular and Radiation Biophysics Department, B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Centre 'Kurchatov Institute', Gatchina, 188300, Russian Federation; St. Petersburg Polytechnic University, Polytechnicheskaya, 29, St Petersburg, 195251, Russian Federation; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany; Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany; Department of 3D Electron Cryomicroscopy, Institute of Microbiology and Genetics, Georg-August Universität, Göttingen, 37077, Germany},\r\nabstract={Single particle electron cryomicroscopy (cryo-EM) has recently made significant progress in high-resolution structure determination of macromolecular complexes due to improvements in electron microscopic instrumentation and computational image analysis. However, cryo-EM structures can be highly non-uniform in local resolution and all structures available to date have been limited to resolutions above 3 Å. Here we present the cryo-EM structure of the 70S ribosome from Escherichia coli in complex with elongation factor Tu, aminoacyl-tRNA and the antibiotic kirromycin at 2.65-2.9 Å resolution using spherical aberration (Cs)-corrected cryo-EM. Overall, the cryo-EM reconstruction at 2.9 Å resolution is comparable to the best-resolved X-ray structure of the E. coli 70S ribosome (2.8 Å), but provides more detailed information (2.65 Å) at the functionally important ribosomal core. The cryo-EM map elucidates for the first time the structure of all 35 rRNA modifications in the bacterial ribosome, explaining their roles in fine-tuning ribosome structure and function and modulating the action of antibiotics. We also obtained atomic models for flexible parts of the ribosome such as ribosomal proteins L9 and L31. The refined cryo-EM-based model presents the currently most complete high-resolution structure of the E. coli ribosome, which demonstrates the power of cryo-EM in structure determination of large and dynamic macromolecular complexes. ©2015 Macmillan Publishers Limited. All rights reserved.},\r\nfunding_details={Deutsche ForschungsgemeinschaftFOR 1805},\r\ncorrespondence_address1={Fischer, N.; 3D Electron Cryomicroscopy Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, Germany; email: niels.fischer@mpibpc.mpg.de},\r\npublisher={Nature Publishing Group},\r\nissn={00280836},\r\ncoden={NATUA},\r\npubmed_id={25707802},\r\nlanguage={English},\r\nabbrev_source_title={Nature},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Histone deacetylase inhibitors cause the TP53-dependent induction of p21/Waf1 in tumor cells carrying mutations in TP53.\n \n \n \n \n\n\n \n Kovalev, R.; Shtam, T.; Karelov, D.; Burdakov, V.; Volnitskiy, A.; Makarov, E.; and Filatov, M.\n\n\n \n\n\n\n Tsitologiia, 57(3): 204-211. 2015.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Histone$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Kovalev2015204,\r\nauthor={Kovalev, R.A. and Shtam, T.A. and Karelov, D.V. and Burdakov, V.S. and Volnitskiy, A.V. and Makarov, E.M. and Filatov, M.V.},\r\ntitle={Histone deacetylase inhibitors cause the TP53-dependent induction of p21/Waf1 in tumor cells carrying mutations in TP53},\r\njournal={Tsitologiia},\r\nyear={2015},\r\nvolume={57},\r\nnumber={3},\r\npages={204-211},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930790634&partnerID=40&md5=bd66a7bb8e7e0ed78b3edf4820c210f3},\r\nabstract={p21/Waf1 protein is one of the main cell cycle arrest regulators and one of the most well-known transcriptional targets of TP53 protein. Here, we demonstrated the activation of expression of the p21/Waf1 gene when the cells were treated to sodium butyrate (NaBu)--one of the natural inhibitors of deacetylase, and investigated whether this phenomenon depends on the presence of functionally active TP53 protein. We compared the effect of the NaBu treatment on the human cell line with different TP53 mutation profile, including: wild-type TP53, single nucleotide substitutions, and the complete absence of TP53 gene. NaBu activated the TP53 protein via hyper acetylation at lysine residue K382, without significant changes in the level of protein expression. Western blotting demonstrated that the addition of NaBu triggers a significant increase in the p21/Waf1 protein level in both the TP53 wild-type cells and in the cells with single nucleotide substitutions in the domain responsible for the binding of TP53 protein to DNA. At the same time, no the p21/Waf1 protein induction was observed in the cells with complete deletion of the TP53 gene. However, NaBu was not able to induce the p2 1/Waf1 production when the expression of TP53 was transiently knocked down by the p53 siRNA. Overall, our results suggest that the NaBu-dependent induction of p21/Waf1 does require the presence of TP53 protein but unexpectedly it can occur regardless of mutational changes in the domain responsible for the TP53 binding to DNA. One of the hypothetical explanations is that NaBu increases the level of TP53 acetylation, and the modified protein is able to establish a new network of protein-protein interactions or trigger some conformational changes affecting the TP53-dependent transcriptional machinery even when its DNA binding ability is impaired.},\r\nissn={00413771},\r\npubmed_id={26021170},\r\nlanguage={Russian},\r\nabbrev_source_title={Tsitologiia},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide.\n \n \n \n \n\n\n \n Samatova, E.; Konevega, A.; Wills, N.; Atkins, J.; and Rodnina, M.\n\n\n \n\n\n\n Nature Communications, 5. 2014.\n cited By 19\n\n\n\n
\n\n\n\n \n \n $\"High-efficiency$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Samatova2014,\r\nauthor={Samatova, E. and Konevega, A.L. and Wills, N.M. and Atkins, J.F. and Rodnina, M.V.},\r\ntitle={High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide},\r\njournal={Nature Communications},\r\nyear={2014},\r\nvolume={5},\r\ndoi={10.1038/ncomms5459},\r\nart_number={4459},\r\nnote={cited By 19},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84904638535&doi=10.1038%2fncomms5459&partnerID=40&md5=da07ba675f153e7cc397c47d33669802},\r\naffiliation={Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; Molecular and Radiation Biophysics Department, B.P. Konstantinov Petersburg Nuclear Physics Institute, 188300 Gatchina, Russian Federation; St. Petersburg State Polytechnical University, Polytechnicheskaya 29, 195251 St. Petersburg, Russian Federation; Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, United States; School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland},\r\nabstract={The gene product 60 (gp60) of bacteriophage T4 is synthesized as a single polypeptide chain from a discontinuous reading frame as a result of bypassing of a non-coding mRNA region of 50 nucleotides by the ribosome. To identify the minimum set of signals required for bypassing, we recapitulated efficient translational bypassing in an in vitro reconstituted translation system from Escherichia coli. We find that the signals, which promote efficient and accurate bypassing, are specified by the gene 60 mRNA sequence. Systematic analysis of the mRNA suggests unexpected contributions of sequences upstream and downstream of the non-coding gap region as well as of the nascent peptide. During bypassing, ribosomes glide forward on the mRNA track in a processive way. Gliding may have a role not only for gp60 synthesis, but also during regular mRNA translation for reading frame selection during initiation or tRNA translocation during elongation. © 2014 Macmillan Publishers Limited.},\r\nfunding_details={Российский Фонд Фундаментальных Исследований (РФФИ)13-04-40212-H},\r\n}

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\n \n\n \n \n \n \n \n \n GTP hydrolysis by EF-G synchronizes tRNA movement on small and large ribosomal subunits.\n \n \n \n \n\n\n \n Holtkamp, W.; Cunha, C.; Peske, F.; Konevega, A.; Wintermeyer, W.; and Rodnina, M.\n\n\n \n\n\n\n EMBO Journal, 33(9): 1073-1085. 2014.\n cited By 41\n\n\n\n
\n\n\n\n \n \n $\"GTP$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Holtkamp20141073,\r\nauthor={Holtkamp, W. and Cunha, C.E. and Peske, F. and Konevega, A.L. and Wintermeyer, W. and Rodnina, M.V.},\r\ntitle={GTP hydrolysis by EF-G synchronizes tRNA movement on small and large ribosomal subunits},\r\njournal={EMBO Journal},\r\nyear={2014},\r\nvolume={33},\r\nnumber={9},\r\npages={1073-1085},\r\ndoi={10.1002/embj.201387465},\r\nnote={cited By 41},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84899892794&doi=10.1002%2fembj.201387465&partnerID=40&md5=ca2711c3751f3360616d7e7058d47d9e},\r\naffiliation={Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Department of Molecular and Radiation Biophysics, B.P. Konstantinov St. Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; Department of Biophysics, St. Petersburg State Polytechnical University, St.Petersburg, Russian Federation},\r\nabstract={Elongation factor G (EF-G) promotes the movement of two tRNAs and the mRNA through the ribosome in each cycle of peptide elongation. During translocation, the tRNAs transiently occupy intermediate positions on both small (30S) and large (50S) ribosomal subunits. How EF-G and GTP hydrolysis control these movements is still unclear. We used fluorescence labels that specifically monitor movements on either 30S or 50S subunits in combination with EF-G mutants and translocation-specific antibiotics to investigate timing and energetics of translocation. We show that EF-G-GTP facilitates synchronous movements of peptidyl-tRNA on the two subunits into an early post-translocation state, which resembles a chimeric state identified by structural studies. EF-G binding without GTP hydrolysis promotes only partial tRNA movement on the 50S subunit. However, rapid 30S translocation and the concomitant completion of 50S translocation require GTP hydrolysis and a functional domain 4 of EF-G. Our results reveal two distinct modes for utilizing the energy of EF-G binding and GTP hydrolysis and suggest that coupling of GTP hydrolysis to translocation is mediated through rearrangements of the 30S subunit. Synopsis A new dual-color labeling approach yields dynamic insight on synchronous tRNA movement on both ribosomal subunits and shows that GTP hydrolysis by the translocation factor EF-G drives rearrangement of the 30S subunit. Rapid translocation promoted by EF-G-GTP proceeds synchronously on both ribosomal subunits. Synchronization of translocation is mediated through the 30S subunit. Rapid 30S translocation requires GTP hydrolysis and movement of domain 4 of EF-G. 50S translocation entails a transient intermediate distinct from the hybrid state. A new dual-color labeling approach yields dynamic insight on synchronous tRNA movement on both ribosomal subunits and shows that GTP hydrolysis by the translocation factor EF-G drives rearrangement of the 30S subunit. © 2014 The Authors.},\r\nauthor_keywords={molecular machines;  movement;  protein synthesis;  ribosome;  translation},\r\nfunding_details={Russian Foundation for Basic Research13 04 40212},\r\ncorrespondence_address1={Rodnina, M.V.; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; email: rodnina@mpibpc.mpg.de},\r\npublisher={Nature Publishing Group},\r\nissn={02614189},\r\ncoden={EMJOD},\r\npubmed_id={24614227},\r\nlanguage={English},\r\nabbrev_source_title={EMBO J.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n Elongation factor G (EF-G) promotes the movement of two tRNAs and the mRNA through the ribosome in each cycle of peptide elongation. During translocation, the tRNAs transiently occupy intermediate positions on both small (30S) and large (50S) ribosomal subunits. How EF-G and GTP hydrolysis control these movements is still unclear. We used fluorescence labels that specifically monitor movements on either 30S or 50S subunits in combination with EF-G mutants and translocation-specific antibiotics to investigate timing and energetics of translocation. We show that EF-G-GTP facilitates synchronous movements of peptidyl-tRNA on the two subunits into an early post-translocation state, which resembles a chimeric state identified by structural studies. EF-G binding without GTP hydrolysis promotes only partial tRNA movement on the 50S subunit. However, rapid 30S translocation and the concomitant completion of 50S translocation require GTP hydrolysis and a functional domain 4 of EF-G. Our results reveal two distinct modes for utilizing the energy of EF-G binding and GTP hydrolysis and suggest that coupling of GTP hydrolysis to translocation is mediated through rearrangements of the 30S subunit. Synopsis A new dual-color labeling approach yields dynamic insight on synchronous tRNA movement on both ribosomal subunits and shows that GTP hydrolysis by the translocation factor EF-G drives rearrangement of the 30S subunit. Rapid translocation promoted by EF-G-GTP proceeds synchronously on both ribosomal subunits. Synchronization of translocation is mediated through the 30S subunit. Rapid 30S translocation requires GTP hydrolysis and movement of domain 4 of EF-G. 50S translocation entails a transient intermediate distinct from the hybrid state. A new dual-color labeling approach yields dynamic insight on synchronous tRNA movement on both ribosomal subunits and shows that GTP hydrolysis by the translocation factor EF-G drives rearrangement of the 30S subunit. © 2014 The Authors.\n

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\n \n\n \n \n \n \n \n \n Aberrant expression of the sox2 gene in malignant gliomas.\n \n \n \n \n\n\n \n Volnitskiy, A.; Semenova, E.; Shtam, T.; Kovalev, R.; and Filatov, M.\n\n\n \n\n\n\n Cell and Tissue Biology, 8(5): 368-373. 2014.\n cited By 3\n\n\n\n
\n\n\n\n \n \n $\"Aberrant$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Volnitskiy2014368,\r\nauthor={Volnitskiy, A.V. and Semenova, E.V. and Shtam, T.A. and Kovalev, R.A. and Filatov, M.V.},\r\ntitle={Aberrant expression of the sox2 gene in malignant gliomas},\r\njournal={Cell and Tissue Biology},\r\nyear={2014},\r\nvolume={8},\r\nnumber={5},\r\npages={368-373},\r\ndoi={10.1134/S1990519X14050101},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84918775524&doi=10.1134%2fS1990519X14050101&partnerID=40&md5=761056e34f65f3402cadffe380c42b4e},\r\naffiliation={Konstantinov St. Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; St. Petersburg State Polytechnic University, St. Petersburg, Russian Federation},\r\nabstract={Both genetic and epigenetic changes underlie the mechanisms of tumor initiation and progression. In this study, we analyzed sox2 gene expression and its epigenetic changes in primary cultures of malignant gliomas. The sox2 expression was detected in most (74%) gliomas, but not in morphologically normal brain tissue. These facts point to relationships between the sox2 transcription activity and the process of glioma malignant transformation. It was demonstrated that association of different areas of the sox2 gene with important epigenetic markers—posttranslational modifications of H3 histone H3K4ac and H3K9met3—did not correlate with sox2 expression. However, it suggests stochastic regulation of sox2 gene expression in malignant gliomas. © 2014, Pleiades Publishing, Ltd.},\r\nauthor_keywords={aberrant gene expression;  gliomas;  posttranslational H3 histone modifications;  Sox2},\r\ncorrespondence_address1={Filatov, M.V.; Konstantinov St. Petersburg Nuclear Physics InstituteRussian Federation},\r\npublisher={Maik Nauka-Interperiodica Publishing},\r\nissn={1990519X},\r\nlanguage={English},\r\nabbrev_source_title={Cell Tissue Biol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Amicoumacin A Inhibits Translation by Stabilizing mRNA Interaction with the Ribosome.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Molecular Cell, 56(4): 531-540. 2014.\n cited By 43\n\n\n\n
\n\n\n\n \n \n $\"Amicoumacin$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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\n \n 2013\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Exosomes are natural carriers of exogenous siRNA to human cells in vitro.\n \n \n \n \n\n\n \n Shtam, T.; Kovalev, R.; Varfolomeeva, E.; Makarov, E.; Kil, Y.; and Filatov, M.\n\n\n \n\n\n\n Cell Communication and Signaling, 11(1). 2013.\n cited By 160\n\n\n\n
\n\n\n\n \n \n $\"Exosomes$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Shtam2013,\r\nauthor={Shtam, T.A. and Kovalev, R.A. and Varfolomeeva, E.Y. and Makarov, E.M. and Kil, Y.V. and Filatov, M.V.},\r\ntitle={Exosomes are natural carriers of exogenous siRNA to human cells in vitro},\r\njournal={Cell Communication and Signaling},\r\nyear={2013},\r\nvolume={11},\r\nnumber={1},\r\ndoi={10.1186/1478-811X-11-88},\r\nart_number={88},\r\nnote={cited By 160},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84887703287&doi=10.1186%2f1478-811X-11-88&partnerID=40&md5=da53d624b8be3bfd1494f309cb115de5},\r\naffiliation={Division of Molecular and Radiation Biophysics, SFBI Petersburg Nuclear Physics Institute, Gatchina 188300, Russian Federation; School of Health Sciences and Social Care, Brunel University, Uxbridge UB8 3PH, United Kingdom; Department of Biophysics, St. Petersburg State Polytechnical University, St.-Petersburg 195251, Russian Federation},\r\nabstract={Background: Exosomes are nano-sized vesicles of endocytic origin that are involved in cell-to-cell communication including shuttle RNA, mainly mRNA and microRNA. As exosomes naturally carry RNA between cells, these particles might be useful in gene cancer therapy to deliver therapeutic short interfering RNA (siRNA) to the target cells. Despite the promise of RNA interference (RNAi) for use in therapy, several technical obstacles must be overcome. Exogenous siRNA is prone to degradation, has a limited ability to cross cell membranes and may induce an immune response. Naturally occurring RNA carriers, such as exosomes, might provide an untapped source of effective delivery strategies. Results: This study demonstrates that exosomes can deliver siRNA to recipient cells in vitro. The different strategies were used to introduce siRNAs into human exosomes of various origins. The delivery of fluorescently labeled siRNA via exosomes to cells was confirmed using confocal microscopy and flow cytometry. Two different siRNAs against RAD51 and RAD52 were used to transfect into the exosomes for therapeutic delivery into target cells. The exosome-delivered siRNAs were effective at causing post-transcriptional gene silencing in recipient cells. Moreover, the exosome-delivered siRNA against RAD51 was functional and caused the massive reproductive cell death of recipient cancer cells. Conclusions: The results strongly suggest that exosomes effectively delivered the siRNA into the target cells. The therapeutic potential of exosome-mediated siRNA delivery was demonstrated in vitro by the strong knockdown of RAD51, a prospective therapeutic target for cancer cells. The results give an additional evidence of the ability to use human exosomes as vectors in cancer therapy, including RNAi-based gene therapy. © 2013 Shtam et al.; licensee BioMed Central Ltd.},\r\nauthor_keywords={Cancer therapy;  Drug delivery system;  Exosomes;  RAD51;  RNA interference (RNAi)},\r\ncorrespondence_address1={Filatov, M.V.; Division of Molecular and Radiation Biophysics, SFBI Petersburg Nuclear Physics Institute, Gatchina 188300, Russian Federation; email: filatov@omrb.pnpi.spb.ru},\r\nissn={1478811X},\r\npubmed_id={24245560},\r\nlanguage={English},\r\nabbrev_source_title={Cell Commun. Signal.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n A kinetic safety gate controlling the delivery of unnatural amino acids to the ribosome.\n \n \n \n \n\n\n \n Mittelstaet, J.; Konevega, A.; and Rodnina, M.\n\n\n \n\n\n\n Journal of the American Chemical Society, 135(45): 17031-17038. 2013.\n cited By 35\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

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@ARTICLE{Mittelstaet201317031,\r\nauthor={Mittelstaet, J. and Konevega, A.L. and Rodnina, M.V.},\r\ntitle={A kinetic safety gate controlling the delivery of unnatural amino acids to the ribosome},\r\njournal={Journal of the American Chemical Society},\r\nyear={2013},\r\nvolume={135},\r\nnumber={45},\r\npages={17031-17038},\r\ndoi={10.1021/ja407511q},\r\nnote={cited By 35},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84887780795&doi=10.1021%2fja407511q&partnerID=40&md5=d6741088f1a8a8b1e9284fb11e679e6c},\r\naffiliation={Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; Molecular and Radiation Biophysics Department, B. P. Konstantinov Petersburg Nuclear Physics Institute, 188300 Gatchina, Russian Federation},\r\nabstract={Improving the yield of unnatural amino acid incorporation is an important challenge in producing novel designer proteins with unique chemical properties. Here we examine the mechanisms that restrict the incorporation of the fluorescent unnatural amino acid εNH2-Bodipy576/589-lysine (BOP-Lys) into a model protein. While the delivery of BOP-Lys-tRNALys to the ribosome is limited by its poor binding to elongation factor Tu (EF-Tu), the yield of incorporation into peptide is additionally controlled at the step of BOP-Lys-tRNA release from EF-Tu into the ribosome. The unnatural amino acid appears to disrupt the interactions that balance the strength of tRNA binding to EF-Tu-GTP with the velocity of tRNA dissociation from EF-Tu-GDP on the ribosome, which ensure uniform incorporation of standard amino acids. Circumventing this potential quality control checkpoint that specifically prevents incorporation of unnatural amino acids into proteins may provide a new strategy to increase yields of unnatural polymers. © 2013 American Chemical Society.},\r\nfunding_details={Deutsche ForschungsgemeinschaftFOR 1805},\r\ncorrespondence_address1={Rodnina, M.V.; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; email: rodnina@mpibpc.mpg.de},\r\nissn={00027863},\r\ncoden={JACSA},\r\npubmed_id={24079513},\r\nlanguage={English},\r\nabbrev_source_title={J. Am. Chem. Soc.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n TRNA tKUUU, tQUUG, and tEUUC wobble position modifications fine-tune protein translation by promoting ribosome A-site binding.\n \n \n \n \n\n\n \n Rezgui, V.; Tyagi, K.; Ranjan, N.; Konevega, A.; Mittelstaet, J.; Rodnina, M.; Peter, M.; and Pedrioli, P.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 110(30): 12289-12294. 2013.\n cited By 74\n\n\n\n
\n\n\n\n \n \n $\"TRNA$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Rezgui201312289,\r\nauthor={Rezgui, V.A.N. and Tyagi, K. and Ranjan, N. and Konevega, A.L. and Mittelstaet, J. and Rodnina, M.V. and Peter, M. and Pedrioli, P.G.A.},\r\ntitle={TRNA tKUUU, tQUUG, and tEUUC wobble position modifications fine-tune protein translation by promoting ribosome A-site binding},\r\njournal={Proceedings of the National Academy of Sciences of the United States of America},\r\nyear={2013},\r\nvolume={110},\r\nnumber={30},\r\npages={12289-12294},\r\ndoi={10.1073/pnas.1300781110},\r\nnote={cited By 74},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84880672169&doi=10.1073%2fpnas.1300781110&partnerID=40&md5=e385d09cd50bf42ca6cd62f1eca83eaa},\r\naffiliation={Department of Biology, Institute of Biochemistry, Eidgenössiche Technische Hochschule Zürich, 8093 Zurich, Switzerland; Scottish Institute for Cell Signalling, College of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany; Molecular and Radiation Biophysics Department, B. P. Konstantinov Petersburg Nuclear Physics Institute, 188300 Gatchina, Russian Federation},\r\nabstract={tRNA modifications are crucial to ensure translation efficiency and fidelity. In eukaryotes, the URM1 and ELP pathways increase cellular resistance to various stress conditions, such as nutrient starvation and oxidative agents, by promoting thiolation and methoxycarbonylmethylation, respectively, of the wobble uridine of cytoplasmic tRNAUUU Lys (tKUUU), tRNAUUG Gln (tQUUG), and tRNAUUC Glu (tEUUC). Although in vitro experiments have implicated these tRNA modifications in modulating wobbling capacity and translation efficiency, their exact in vivo biological roles remain largely unexplored. Using a combination of quantitative proteomics and codon- specific translation reporters, we find that translation of a specific gene subset enriched for AAA, CAA, and GAA codons is impaired in the absence of URM1- and ELP-dependent tRNA modifications. Moreover, in vitro experiments using native tRNAs demonstrate that both modifications enhance binding of tK UUU to the ribosomal A-site. Taken together, our data suggest that tRNA thiolation and methoxycarbonylmethylation regulate translation of genes with specific codon content.},\r\nauthor_keywords={SILAC;  Systems biology;  Translation regulation},\r\ncorrespondence_address1={Pedrioli, P.G.A.; Department of Biology, Institute of Biochemistry, Eidgenössiche Technische Hochschule Zürich, 8093 Zurich, Switzerland; email: p.g.a.pedrioli@dundee.ac.uk},\r\nissn={00278424},\r\ncoden={PNASA},\r\npubmed_id={23836657},\r\nlanguage={English},\r\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2012\n \n \n (4)\n \n \n

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\n \n\n \n \n \n \n \n \n In vitro potential of histone deacetylase inhibitors for anticancer therapy.\n \n \n \n \n\n\n \n Kovalev, R.; Shtam, T.; Ibatullin, F.; Bondarev, G.; and Filatov, M.\n\n\n \n\n\n\n Voprosy Onkologii, 58(6): 800-807. 2012.\n cited By 2\n\n\n\n
\n\n\n\n \n \n $\"In$ Paper\n \n \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

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@ARTICLE{Kovalev2012800,\r\nauthor={Kovalev, R.A. and Shtam, T.A. and Ibatullin, F.M. and Bondarev, G.N. and Filatov, M.V.},\r\ntitle={In vitro potential of histone deacetylase inhibitors for anticancer therapy},\r\njournal={Voprosy Onkologii},\r\nyear={2012},\r\nvolume={58},\r\nnumber={6},\r\npages={800-807},\r\nnote={cited By 2},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84875510733&partnerID=40&md5=330a4b66718da144b754fc8a404b3fd9},\r\naffiliation={Nuclear Physics Institute, Saint-Petersburg, Russian Federation},\r\nabstract={Research during the past decade has shown that epigenetic events have a key role in carcinogenesis and tumour progression. Histone deacetylase inhibitors (HDACi) comprise structurally diverse compounds that are a group of targeted epigenetic anticancer agents. Here we explored the in vitro efficacy of HDACi such as sodium butyrate (BuNa), valproic acid (VaNa) and several novel HDAC inhibitors for the treatment of cancer. Both BuNa and VaNa inhibited cancer cell proliferation in a time - and dose-dependent fashion. In the present study we demonstrated the significant effect of two novel HDACi, Adipo or BuNHOH, able to induce apoptosis of cancer cells, but not of normal line. Since HDAC inhibitors have been proposed as radio - or chemosensitizers in cancer therapy, we have studied the radiosensitizing effect of sodium butyrate on cancer cells. The combination of BuNa and radiation significantly inhibited tumor cell growth. Besides, combining Cisplatin or Gemzar with HDAC inhibitors results in synergistic antiproliferative activity that could be therapeutically exploited. These results suggest that HDACi acts as an antitumor agent and that combining HDAC inhibitors with radio or - chemotherapeutic strategy may provide a novel chemotherapeutic treatment of cancers insensitive to traditional antitumor agents.},\r\ncorrespondence_address1={Kovalev, R.A.; Nuclear Physics Institute, Saint-Petersburg, Russian Federation},\r\nissn={05073758},\r\ncoden={VOONA},\r\npubmed_id={23600307},\r\nlanguage={Russian},\r\nabbrev_source_title={Vopr. Onkol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Isolation and proteomic analysis of exosomes secreted by human cancer cells in vitro.\n \n \n \n \n\n\n \n Shtam, T.; Naiyzhny, S.; Landa, S.; Burdackov, V.; Artamonova, T.; and Filatov, M.\n\n\n \n\n\n\n Tsitologiya, 54(5): 430-438. 2012.\n cited By 2\n\n\n\n
\n\n\n\n \n \n $\"Isolation$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Shtam2012430,\r\nauthor={Shtam, T.A. and Naiyzhny, S.N. and Landa, S.B. and Burdackov, V.S. and Artamonova, T.O. and Filatov, M.V.},\r\ntitle={Isolation and proteomic analysis of exosomes secreted by human cancer cells in vitro},\r\njournal={Tsitologiya},\r\nyear={2012},\r\nvolume={54},\r\nnumber={5},\r\npages={430-438},\r\nnote={cited By 2},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84864549288&partnerID=40&md5=66c4733440532eaa83659d67c8673764},\r\naffiliation={B. P. Konstantinov St. Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; St. Petersburg State Polytechnic University, Russian Federation},\r\nabstract={Exosomes are 20-100 nm membrane vesicles of endocytic origin secreted by most cell types in vitro and in vivo. Since exosomes contain both RNA (mRNA and microRNA) and proteins, which can be transferred to another cell, and be functional in that new environment, these vesicles may be involved in the communication between cells. The secretion of exosomes by tumor cells and their implication in the transport and propagation of infectious cargo suggest their participation in pathological situations. Our purpose here is to describe methods for the production, purification, and proteomic characterization of exosomes derived from human cancer cells in vitro. Based on exosomes' unique lipidic composition, we have developed the new approach to increase production of exosomes by cells in vitro. Secondly, we have developed quality control by laser correlation spectroscopy for exosomal assays based on the amount of MHC class I and CD63 molecules on their surface. At last, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry was used after 2D electrophoresis for the proteomic analysis of exosomes derived from cancer cell lines. This study describes the protein composition of brain tumor cell-derived exosomes in more detail.},\r\nauthor_keywords={Exosomes;  Laser correlation spectroscopy;  Proteomic analysis},\r\ncorrespondence_address1={Filatov, M.V.; B. P. Konstantinov St. Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; email: fil53@mail.ru},\r\nissn={00413771},\r\ncoden={TSITA},\r\npubmed_id={22827041},\r\nlanguage={Russian},\r\nabbrev_source_title={Tsitologiya},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Thermodynamics of the GTP-GDP-operated conformational switch of selenocysteine-specific translation factor SelB.\n \n \n \n \n\n\n \n Paleskava, A.; Konevega, A.; and Rodnina, M.\n\n\n \n\n\n\n Journal of Biological Chemistry, 287(33): 27906-27912. 2012.\n cited By 18\n\n\n\n
\n\n\n\n \n \n $\"Thermodynamics$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Paleskava201227906,\r\nauthor={Paleskava, A. and Konevega, A.L. and Rodnina, M.V.},\r\ntitle={Thermodynamics of the GTP-GDP-operated conformational switch of selenocysteine-specific translation factor SelB},\r\njournal={Journal of Biological Chemistry},\r\nyear={2012},\r\nvolume={287},\r\nnumber={33},\r\npages={27906-27912},\r\ndoi={10.1074/jbc.M112.366120},\r\nnote={cited By 18},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84865020706&doi=10.1074%2fjbc.M112.366120&partnerID=40&md5=6ee40a6472e482ee393ec313677a3f5b},\r\naffiliation={Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany},\r\nabstract={SelB is a specialized translation factor that binds GTP and GDP and delivers selenocysteyl-tRNA (Sec-tRNA Sec) to the ribosome. By analogy to elongation factor Tu (EF-Tu), SelB is expected to control the delivery and release of Sec-tRNA Sec to the ribosome by the structural switch between GTP- and GDP-bound conformations. However, crystal structures of SelB suggested a similar domain arrangement in the apo form and GDP- and GTP-bound forms of the factor, raising the question of how SelB can fulfill its delivery function. Here, we studied the thermodynamics of guanine nucleotide binding to SelB by isothermal titration calorimetry in the temperature range between 10 and 25°C using GTP, GDP, and two nonhydrolyzable GTP analogs, guanosine 5′-O-(γ-thio)triphosphate (GTPγS) and guanosine 5′-(β,γ-imido)-triphosphate (GDPNP). The binding of SelB to either guanine nucleotide is characterized by a large heat capacity change (-621, -467, -235, and -275 cal × mol -1 × K -1, with GTP, GTPγS, GDPNP, and GDP, respectively), associated with compensatory changes in binding entropy and enthalpy. Changes in heat capacity indicate a large decrease of the solvent-accessible surface area in SelB, amounting to 43 or 32 amino acids buried upon binding of GTP or GTPγS, respectively, and 15-19 amino acids upon binding GDP or GDPNP. The similarity of the GTP and GDP forms in the crystal structures can be attributed to the use of GDPNP, which appears to induce a structure of SelB that is more similar to the GDP than to the GTP-bound form. © 2012 by The American Society for Biochemistry and Molecular Biology, Inc.},\r\ncorrespondence_address1={Rodnina, M.V.; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; email: rodnina@mpibpc.mpg.de},\r\nissn={00219258},\r\ncoden={JBCHA},\r\npubmed_id={22740700},\r\nlanguage={English},\r\nabbrev_source_title={J. Biol. Chem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Purification and in vitro analysis of exosomes secreted by malignantly transformed human cells.\n \n \n \n \n\n\n \n Shtam, T.; Naryzhny, S.; Landa, S.; Burdakov, V.; Artamonova, T.; and Filatov, M.\n\n\n \n\n\n\n Cell and Tissue Biology, 6(4): 317-325. 2012.\n cited By 6\n\n\n\n
\n\n\n\n \n \n $\"Purification$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Shtam2012317,\r\nauthor={Shtam, T.A. and Naryzhny, S.N. and Landa, S.B. and Burdakov, V.S. and Artamonova, T.O. and Filatov, M.V.},\r\ntitle={Purification and in vitro analysis of exosomes secreted by malignantly transformed human cells},\r\njournal={Cell and Tissue Biology},\r\nyear={2012},\r\nvolume={6},\r\nnumber={4},\r\npages={317-325},\r\ndoi={10.1134/S1990519X12040116},\r\nnote={cited By 6},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84865567518&doi=10.1134%2fS1990519X12040116&partnerID=40&md5=621ea006f96d0bd38461fec3a60fde94},\r\naffiliation={Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; St. Petersburg State Polytechnic University, St. Petersburg, Russian Federation},\r\nabstract={Exosomes are natural nanoparticles secreted by different cells and capable of carrying protein markers and genetic information, thus participating in cellular communication. There is good reason to think that quantitative and qualitative characterization of these microparticles produced by different tissues in normal and pathological states can give valuable diagnostic and prognostic information and be a biomarker of different diseases, including oncological ones. Elaboration of the purification of exosomes and their proteome analysis was the aim of the present work. An original approach to enhancing exosome production in cultured transformed human cells was developed. The data obtained allowed us to detect exosomes in cultural conditioned samples and control the quality of produced exosomes at all stages of their purification. Electrophoretic analysis of proteins obtained from exosomes of different origins shows differences in protein profiles. Proteins from exosomes of glioblastoma cell lines were separated by two-dimensional electrophoresis. Protein profiles were further analyzed by densitometry and mass spectrometry, which allowed more than 30 proteins, including specific tumor markers, to be identified. © 2012 Pleiades Publishing, Ltd.},\r\nauthor_keywords={exosomes;  laser correlation spectroscopy;  proteome analysis},\r\ncorrespondence_address1={Filatov, M. V.; Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; email: fil_53@mail.ru},\r\nissn={1990519X},\r\nlanguage={English},\r\nabbrev_source_title={Cell Tissue Biol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\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 The structure of helix 89 of 23S rRNA is important for peptidyl transferase function of Escherichia coli ribosome.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n FEBS Letters, 585(19): 3073-3078. 2011.\n cited By 15\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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\n \n\n \n \n \n \n \n \n Distortion of tRNA upon near-cognate codon recognition on the ribosome.\n \n \n \n \n\n\n \n Mittelstaet, J.; Konevega, A.; and Rodnina, M.\n\n\n \n\n\n\n Journal of Biological Chemistry, 286(10): 8158-8164. 2011.\n cited By 15\n\n\n\n
\n\n\n\n \n \n $\"Distortion$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Mittelstaet20118158,\r\nauthor={Mittelstaet, J. and Konevega, A.L. and Rodnina, M.V.},\r\ntitle={Distortion of tRNA upon near-cognate codon recognition on the ribosome},\r\njournal={Journal of Biological Chemistry},\r\nyear={2011},\r\nvolume={286},\r\nnumber={10},\r\npages={8158-8164},\r\ndoi={10.1074/jbc.M110.210021},\r\nnote={cited By 15},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79953159145&doi=10.1074%2fjbc.M110.210021&partnerID=40&md5=91fad014db99141147fb6b778267b6dc},\r\naffiliation={Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany},\r\nabstract={The accurate decoding of the genetic information by the ribosome relies on the communication between the decoding center of the ribosome, where the tRNA anticodon interacts with the codon, and the GTPase center of EF-Tu, where GTP hydrolysis takes place. In the A/T state of decoding, the tRNA undergoes a large conformational change that results in a more open, distorted tRNA structure. Here we use a real-time transient fluorescence quenching approach to monitor the timing and the extent of the tRNA distortion upon reading cognate or near-cognate codons. The tRNA is distorted upon codon recognition and remains in that conformation until the tRNA is released from EF-Tu, although the extent of distortion gradually changes upon transition from the pre- to the post-hydrolysis steps of decoding. The timing and extent of the rearrangement is similar on cognate and near-cognate codons, suggesting that the tRNA distortion alone does not provide a specific switch for the preferential activation of GTP hydrolysis on the cognate codon. Thus, although the tRNA plays an active role in signal transmission between the decoding and GTPase centers, other regulators of signaling must be involved. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.},\r\ncorrespondence_address1={Rodnina, M. V.; Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; email: rodnina@mpibpc.mpg.de},\r\nissn={00219258},\r\ncoden={JBCHA},\r\npubmed_id={21212264},\r\nlanguage={English},\r\nabbrev_source_title={J. Biol. Chem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Evolutionary optimization of speed and accuracy of decoding on the ribosome.\n \n \n \n \n\n\n \n Wohlgemuth, I.; Pohl, C.; Mittelstaet, J.; Konevega, A.; and Rodnina, M.\n\n\n \n\n\n\n Philosophical Transactions of the Royal Society B: Biological Sciences, 366(1580): 2979-2986. 2011.\n cited By 74\n\n\n\n
\n\n\n\n \n \n $\"Evolutionary$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Wohlgemuth20112979,\r\nauthor={Wohlgemuth, I. and Pohl, C. and Mittelstaet, J. and Konevega, A.L. and Rodnina, M.V.},\r\ntitle={Evolutionary optimization of speed and accuracy of decoding on the ribosome},\r\njournal={Philosophical Transactions of the Royal Society B: Biological Sciences},\r\nyear={2011},\r\nvolume={366},\r\nnumber={1580},\r\npages={2979-2986},\r\ndoi={10.1098/rstb.2011.0138},\r\nnote={cited By 74},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-80052945496&doi=10.1098%2frstb.2011.0138&partnerID=40&md5=1b5aa708a66185564c73bc994488d086},\r\naffiliation={Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany},\r\nabstract={Speed and accuracy of protein synthesis are fundamental parameters for the fitness of living cells, the quality control of translation, and the evolution of ribosomes. The ribosome developed complex mechanisms that allow for a uniform recognition and selection of any cognate aminoacyl-tRNA (aa-tRNA) and discrimination against any near-cognate aa-tRNA, regardless of the nature or position of the mismatch. This review describes the principles of the selection-kinetic partitioning and induced fit-and discusses the relationship between speed and accuracy of decoding, with a focus on bacterial translation. The translational machinery apparently has evolved towards high speed of translation at the cost of fidelity. © 2011 The Royal Society.},\r\nauthor_keywords={Error frequency;  mRNA decoding;  Protein synthesis;  Ribosome;  Translation fidelity;  tRNA},\r\ncorrespondence_address1={Rodnina M.V., M. V.; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany; email: rodnina@mpibpc.mpg.de},\r\npublisher={Royal Society},\r\nissn={09628436},\r\ncoden={PTRBA},\r\nlanguage={English},\r\nabbrev_source_title={Philos. Trans. R. Soc. B Biol. Sci.},\r\ndocument_type={Review},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2010\n \n \n (5)\n \n \n

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\n \n\n \n \n \n \n \n \n Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.\n \n \n \n \n\n\n \n Fischer, N.; Konevega, A.; Wintermeyer, W.; Rodnina, M.; and Stark, H.\n\n\n \n\n\n\n Nature, 466(7304): 329-333. 2010.\n cited By 246\n\n\n\n
\n\n\n\n \n \n $\"Ribosome$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Fischer2010329,\r\nauthor={Fischer, N. and Konevega, A.L. and Wintermeyer, W. and Rodnina, M.V. and Stark, H.},\r\ntitle={Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy},\r\njournal={Nature},\r\nyear={2010},\r\nvolume={466},\r\nnumber={7304},\r\npages={329-333},\r\ndoi={10.1038/nature09206},\r\nnote={cited By 246},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77954650144&doi=10.1038%2fnature09206&partnerID=40&md5=c0ad9546cd677e0c2e6e082e266c6b68},\r\naffiliation={3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Petersburg Nuclear Physics Institute, 188300 Gatchina, Russian Federation},\r\nabstract={The translocation step of protein synthesis entails large-scale rearrangements of the ribosome-transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during translocation by time-resolved single-particle electron cryomicroscopy (cryo-EM). Unbiased computational sorting of cryo-EM images yielded 50 distinct three-dimensional reconstructions, showing the tRNAs in classical, hybrid and various novel intermediate states that provide trajectories and kinetic information about tRNA movement through the ribosome. The structures indicate how tRNA movement is coupled with global and local conformational changes of the ribosome, in particular of the head and body of the small ribosomal subunit, and show that dynamic interactions between tRNAs and ribosomal residues confine the path of the tRNAs through the ribosome. The temperature dependence of ribosome dynamics reveals a surprisingly flat energy landscape of conformational variations at physiological temperature. The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement. © 2010 Macmillan Publishers Limited. All rights reserved.},\r\nfunding_details={Sixth Framework Programme3DRepertoire},\r\n}

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\n \n\n \n \n \n \n \n \n The ribosome-bound initiation factor 2 recruits initiator tRNA to the 30S initiation complex.\n \n \n \n \n\n\n \n Milon, P.; Carotti, M.; Konevega, A.; Wintermeyer, W.; Rodnina, M.; and Gualerzi, C.\n\n\n \n\n\n\n EMBO Reports, 11(4): 312-316. 2010.\n cited By 49\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

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@ARTICLE{Milon2010312,\r\nauthor={Milon, P. and Carotti, M. and Konevega, A.L. and Wintermeyer, W. and Rodnina, M.V. and Gualerzi, C.O.},\r\ntitle={The ribosome-bound initiation factor 2 recruits initiator tRNA to the 30S initiation complex},\r\njournal={EMBO Reports},\r\nyear={2010},\r\nvolume={11},\r\nnumber={4},\r\npages={312-316},\r\ndoi={10.1038/embor.2010.12},\r\nnote={cited By 49},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77950371305&doi=10.1038%2fembor.2010.12&partnerID=40&md5=67d3a8aa9c343d5481c28f705c5c06db},\r\naffiliation={Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany; Laboratory of Genetics, Department of Biology MCA, University of Camerino, Gentille III da Varano, Camerino 62032, Italy; Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Gatchina 188300, Russian Federation},\r\nabstract={Bacterial translation initiation factor 2 (IF2) is a GTPase that promotes the binding of the initiator fMet-tRNA fMet to the 30S ribosomal subunit. It is often assumed that IF2 delivers fMet-tRNA fMet to the ribosome in a ternary complex, IF2GTPfMet-tRNA fMet. By using rapid kinetic techniques, we show here that binding of IF2GTP to the 30S ribosomal subunit precedes and is independent of fMet-tRNA fMet binding. The ternary complex formed in solution by IF2GTP and fMet-tRNA is unstable and dissociates before IF2GTP and, subsequently, fMet-tRNA fMet bind to the 30S subunit. Ribosome-bound IF2 might accelerate the recruitment of fMet-tRNA fMet to the 30S initiation complex by providing anchoring interactions or inducing a favourable ribosome conformation. The mechanism of action of IF2 seems to be different from that of tRNA carriers such as EF-Tu, SelB and eukaryotic initiation factor 2 (eIF2), instead resembling that of eIF5B, the eukaryotic subunit association factor. © 2010 European molecular biology organization.},\r\nauthor_keywords={FRET;  GTPase;  Rapid filtration;  Stopped-flow fluorescence},\r\ncorrespondence_address1={Rodnina, M. V.; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany; email: rodnina@mpibpc.de},\r\nissn={1469221X},\r\ncoden={ERMEA},\r\npubmed_id={20224578},\r\nlanguage={English},\r\nabbrev_source_title={EMBO Rep.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The crystal structure of unmodified tRNAPhe from Escherichia coli.\n \n \n \n \n\n\n \n Byrne, R.; Konevega, A.; Rodnina, M.; and Antson, A.\n\n\n \n\n\n\n Nucleic Acids Research, 38(12): 4154-4162. 2010.\n cited By 47\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Byrne20104154,\r\nauthor={Byrne, R.T. and Konevega, A.L. and Rodnina, M.V. and Antson, A.A.},\r\ntitle={The crystal structure of unmodified tRNAPhe from Escherichia coli},\r\njournal={Nucleic Acids Research},\r\nyear={2010},\r\nvolume={38},\r\nnumber={12},\r\npages={4154-4162},\r\ndoi={10.1093/nar/gkq133},\r\nart_number={gkq133},\r\nnote={cited By 47},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77953652658&doi=10.1093%2fnar%2fgkq133&partnerID=40&md5=0c785762270a3a35a8306dd08db66441},\r\naffiliation={York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, North Yorkshire, YO10 5YW, United Kingdom; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077, Göttingen, Germany; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, 188300 Gatchina, Russian Federation},\r\nabstract={Post-transcriptional nucleoside modifications finetune the biophysical and biochemical properties of transfer RNA (tRNA) so that it is optimized for participation in cellular processes. Here we report the crystal structure of unmodified tRNAPhe from Escherichia coli at a resolution of 3Å. We show that in the absence of modifications the overall fold of the tRNA is essentially the same as that of mature tRNA. However, there are a number of significant structural differences, such as rearrangements in a triplet base pair and a widened angle between the acceptor and anticodon stems. Contrary to previous observations, the anticodon adopts the same conformation as seen in mature tRNA. © The Author(s) 2010. Published by Oxford University Press.},\r\n}

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\n \n\n \n \n \n \n \n \n Thermodynamic and kinetic framework of selenocysteyl-tRNASec recognition by elongation factor SelB.\n \n \n \n \n\n\n \n Paleskava, A.; Konevega, A.; and Rodnina, M.\n\n\n \n\n\n\n Journal of Biological Chemistry, 285(5): 3014-3020. 2010.\n cited By 30\n\n\n\n
\n\n\n\n \n \n $\"Thermodynamic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Paleskava20103014,\r\nauthor={Paleskava, A. and Konevega, A.L. and Rodnina, M.V.},\r\ntitle={Thermodynamic and kinetic framework of selenocysteyl-tRNASec recognition by elongation factor SelB},\r\njournal={Journal of Biological Chemistry},\r\nyear={2010},\r\nvolume={285},\r\nnumber={5},\r\npages={3014-3020},\r\ndoi={10.1074/jbc.M109.081380},\r\nnote={cited By 30},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77449117999&doi=10.1074%2fjbc.M109.081380&partnerID=40&md5=9b2186a405bce9e36519386eb8157336},\r\naffiliation={Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany},\r\nabstract={SelB is a specialized translation elongation factor that delivers selenocysteyl-tRNASec (Sec-tRNASec) to the ribosome. Here we show that Sec-tRNASec binds to SelB·GTP with an extraordinary high affinity (Kd = 0.2 pM). The tight binding is driven enthalpically and involves the net formation of four ion pairs, three of which may involve the Sec residue. The dissociation of tRNA from the ternary complex SelB·GTP·Sec-tRNASec is very slow (0.3 h -1), and GTP hydrolysis accelerates the release of Sec-tRNA Sec by more than a million-fold (to 240 s-1). The affinities of Sec-tRNASec to SelB in the GDP or apoforms, or Ser-tRNASec and tRNASec to SelB in any form, are similar (Kd = 0.5 μM). Thermodynamic coupling in binding of Sec-tRNA Sec and GTP to SelB ensures at the same time the specificity of Sec- versus Ser-tRNASec selection and rapid release of Sec-tRNA Sec from SelB after GTP cleavage on the ribosome. SelB provides an example for the evolution of a highly specialized protein-RNA complex toward recognition of unique set of identity elements. The mode of tRNA recognition by SelB is reminiscent of another specialized factor, eIF2, rather than of EF-Tu, the common delivery factor for all other aminoacyl-tRNAs, in line with a common evolutionary ancestry of SelB and eIF2. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.},\r\ncorrespondence_address1={Rodnina, M. V.; Department of Physical Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; email: rodnina@mpibpc.mpg.de},\r\nissn={00219258},\r\ncoden={JBCHA},\r\npubmed_id={19940162},\r\nlanguage={English},\r\nabbrev_source_title={J. Biol. Chem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Mutations at the accommodation gate of the ribosome impair RF2-dependent translation termination.\n \n \n \n \n\n\n \n Burakovsky, D.; Sergiev, P.; Steblyanko, M.; Kubarenko, A.; Konevega, A.; Bogdanov, A.; Rodnina, M.; and Dontsova, O.\n\n\n \n\n\n\n RNA, 16(9): 1848-1853. 2010.\n cited By 14\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

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@ARTICLE{Burakovsky20101848,\r\nauthor={Burakovsky, D.E. and Sergiev, P.V. and Steblyanko, M.A. and Kubarenko, A.V. and Konevega, A.L. and Bogdanov, A.A. and Rodnina, M.V. and Dontsova, O.A.},\r\ntitle={Mutations at the accommodation gate of the ribosome impair RF2-dependent translation termination},\r\njournal={RNA},\r\nyear={2010},\r\nvolume={16},\r\nnumber={9},\r\npages={1848-1853},\r\ndoi={10.1261/rna.2185710},\r\nnote={cited By 14},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77956026059&doi=10.1261%2frna.2185710&partnerID=40&md5=49e2557942611d1ca829e52a86e2ba03},\r\naffiliation={Department of Chemistry, Moscow State University, Moscow, 119899, Russian Federation; A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119899, Russian Federation; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany; Petersburg Nuclear Physics Institute, 188300 Gatchina, Russian Federation; Kimmel Cancer Center, Thomas Jefferson University, BLSB, 706, 233 South 10th Street, Philadelphia, PA 19107, United States; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany},\r\nabstract={During protein synthesis, aminoacyl-tRNA (aa-tRNA) and release factors 1 and 2 (RF1 and RF2) have to bind at the catalytic center of the ribosome on the 50S subunit where they take part in peptide bond formation or peptidyl-tRNA hydrolysis, respectively. Computer simulations of aa-tRNA movement into the catalytic site (accommodation) suggested that three nucleotides of 23S rRNA, U2492, C2556, and C2573, form a "gate" at which aa-tRNA movement into the A site is retarded. Here we examined the role of nucleotides C2573 of 23S rRNA, a part of the putative accommodation gate, and of the neighboring A2572 for aa-tRNA binding followed by peptide bond formation and for the RF2-dependent peptide release. Mutations at the two positions did not affect aa-tRNA accommodation, peptide bond formation, or the fidelity of aa-tRNA selection, but impaired RF2-catalyzed peptide release. The data suggest that the ribosome is a robust machine that allows rapid aa-tRNA accommodation despite the defects at the accommodation gate. In comparison, peptide release by RF2 appears more sensitive to these mutations, due to slower accommodation of the factor or effects on RF2 positioning in the A site. Copyright © 2010 RNA Society.},\r\nauthor_keywords={Accommodation;  Decoding;  Release factor;  Ribosome;  Translation},\r\ncorrespondence_address1={Rodnina, M. V.; Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; email: rodnina@mpibpc.mpg.de},\r\npublisher={Cold Spring Harbor Laboratory Press},\r\nissn={13558382},\r\ncoden={RNARF},\r\npubmed_id={20668033},\r\nlanguage={English},\r\nabbrev_source_title={RNA},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2008\n \n \n (4)\n \n \n

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\n \n\n \n \n \n \n \n \n Human rad51 recombinase: The role in the cell cycle checkpoint and cellular survival.\n \n \n \n \n\n\n \n Shtam, T.; Varfolomeeva, E.; Semenova, E.; and Filatov, M.\n\n\n \n\n\n\n Tsitologiya, 50(11): 958-963. 2008.\n cited By 4\n\n\n\n
\n\n\n\n \n \n $\"Human$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Shtam2008958,\r\nauthor={Shtam, T.A. and Varfolomeeva, E.Y. and Semenova, E.V. and Filatov, M.V.},\r\ntitle={Human rad51 recombinase: The role in the cell cycle checkpoint and cellular survival},\r\njournal={Tsitologiya},\r\nyear={2008},\r\nvolume={50},\r\nnumber={11},\r\npages={958-963},\r\nnote={cited By 4},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-59449089348&partnerID=40&md5=5313418d75141a24ef0926ff2a58d2ff},\r\naffiliation={Petersburg B. P. Konstantinov Nuclear Physics Institute RAS, Gatchina, Russian Federation},\r\nabstract={The RAD 51 protein, an eukaryotic homologue of Escherichia coli Rec A, plays a central role in both mitotic and meiotic homologous recombination. Here, we demonstrate that short-term silencing of Rad5l gene by specific small interfering (si) RNA induces cell death of the most part of investigated cancer cell lines and normal fibroblasts. Disruption of the Rad51 gene in these cells results in S or(and) G 2 cell cycle arrest leading to apoptosis. But some human cancer cell lines demonstrate abolishment of premitotic checkpoint and are not sensitive to siRNA silencing of RAD51 recombinase. Recent experiments show that normal functioning of the recombination repair system is essential for maintenance of genome stability, proliferation of vertebrate cells and, finally, for prevention of dramatic cell death.},\r\nauthor_keywords={Cell cycle;  DNA reparation;  Homologous recombination;  Rad51},\r\ncorrespondence_address1={Shtam, T. A.; Petersburg B. P. Konstantinov Nuclear Physics Institute RAS, Gatchina, Russian Federation},\r\nissn={00413771},\r\ncoden={TSITA},\r\npubmed_id={19140342},\r\nlanguage={Russian},\r\nabbrev_source_title={Tsitologiya},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Role of human RAD51 recombinase in the cycle checkpoint and survival of a cell.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Cell and Tissue Biology, 2(5): 463-467. 2008.\n cited By 3\n\n\n\n
\n\n\n\n \n \n $\"Role$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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\n \n\n \n \n \n \n \n \n Perturbation of the tRNA tertiary core differentially affects specific steps of the elongation cycle.\n \n \n \n \n\n\n \n Pan, D.; Zhang, C.; Kirillov, S.; Hou, Y.; and Cooperman, B.\n\n\n \n\n\n\n Journal of Biological Chemistry, 283(26): 18431-18440. 2008.\n cited By 17\n\n\n\n
\n\n\n\n \n \n $\"Perturbation$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Pan200818431,\r\nauthor={Pan, D. and Zhang, C.-M. and Kirillov, S. and Hou, Y.-M. and Cooperman, B.S.},\r\ntitle={Perturbation of the tRNA tertiary core differentially affects specific steps of the elongation cycle},\r\njournal={Journal of Biological Chemistry},\r\nyear={2008},\r\nvolume={283},\r\nnumber={26},\r\npages={18431-18440},\r\ndoi={10.1074/jbc.M801560200},\r\nnote={cited By 17},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-49649091161&doi=10.1074%2fjbc.M801560200&partnerID=40&md5=4023e95c1f6c0b47454dbc0a01510cca},\r\naffiliation={Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States; Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, United States; Vector BioLabs, Inc., 3701 Market St., Philadelphia, PA 19104, United States; Petersburg Nuclear Physics Institute RAS, 188300 Gatchina, Russian Federation},\r\nabstract={The tRNA tertiary core region is important for both tRNA stability and activity in the translation elongation cycle. Here we report the effects of mutating each of two highly conserved base pairs in the tertiary core of Phe-tRNAPhe, 18-55 and 19-56, on rate and equilibrium constants for specific steps of this cycle, beginning with formation of aminoacyl- tRNA·EF-Tu·GTP ternary complexs and culminating with translocation of A-site- bound peptidyl-tRNA into the P-site. We find that codon-dependent binding of aminoacyl-tRNA to the A/T-site and proofreading of near-cognate tRNA are sensitive to perturbation of either base pair; formation of the ternary complex and accommodation from the A/T to the A-site are sensitive to 18-55 perturbation only, and translocation of peptidyl-tRNA from the A- to P-site is insensitive to perturbation of either. These results underline the importance of the core region in promoting the efficiency and accuracy of translation, and they likely reflect different requirements for structural integrity of the core during specific steps of the elongation cycle. © 2008 by The American Society for Biochemistry and Molecular Biology, Inc.},\r\ncorrespondence_address1={Cooperman, B. S.; Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States; email: cooprman@pobox.upenn.edu},\r\nissn={00219258},\r\ncoden={JBCHA},\r\npubmed_id={18448426},\r\nlanguage={English},\r\nabbrev_source_title={J. Biol. Chem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Kinetic Checkpoint at a Late Step in Translation Initiation.\n \n \n \n \n\n\n \n Milon, P.; Konevega, A.; Gualerzi, C.; and Rodnina, M.\n\n\n \n\n\n\n Molecular Cell, 30(6): 712-720. 2008.\n cited By 85\n\n\n\n
\n\n\n\n \n \n $\"Kinetic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Milon2008712,\r\nauthor={Milon, P. and Konevega, A.L. and Gualerzi, C.O. and Rodnina, M.V.},\r\ntitle={Kinetic Checkpoint at a Late Step in Translation Initiation},\r\njournal={Molecular Cell},\r\nyear={2008},\r\nvolume={30},\r\nnumber={6},\r\npages={712-720},\r\ndoi={10.1016/j.molcel.2008.04.014},\r\nnote={cited By 85},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-44949260971&doi=10.1016%2fj.molcel.2008.04.014&partnerID=40&md5=6a584b2d76a11943cbfa3aa725884913},\r\naffiliation={Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino, Italy; Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany; Max Planck Institute of Biophysical Chemistry, 37077 Göttingen, Germany; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, 188300 Gatchina, Russian Federation},\r\nabstract={The translation initiation efficiency of a given mRNA is determined by its translation initiation region (TIR). mRNAs are selected into 30S initiation complexes according to the strengths of the secondary structure of the TIR, the pairing of the Shine-Dalgarno sequence with 16S rRNA, and the interaction between initiator tRNA and the start codon. Here, we show that the conversion of the 30S initiation complex into the translating 70S ribosome constitutes another important mRNA control checkpoint. Kinetic analysis reveals that 50S subunit joining and dissociation of IF3 are strongly influenced by the nature of the codon used for initiation and the structural elements of the TIR. Coupling between the TIR and the rate of 70S initiation complex formation involves IF3- and IF1-induced rearrangements of the 30S subunit, providing a mechanism by which the ribosome senses the TIR and determines the efficiency of translational initiation of a particular mRNA. © 2008 Elsevier Inc. All rights reserved.},\r\nauthor_keywords={RNA},\r\n}

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\n \n 2007\n \n \n (8)\n \n \n

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\n \n\n \n \n \n \n \n \n Response to tamoxifen in estrogen receptor-positive cell line MCF-7 is independent of p53 expression.\n \n \n \n \n\n\n \n Shtam, T.; Pantina, R.; Varfolomeyeva, Y.; and Filatov, M.\n\n\n \n\n\n\n Voprosy Onkologii, 53(2): 194-199. 2007.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Response$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Shtam2007194,\r\nauthor={Shtam, T.A. and Pantina, R.A. and Varfolomeyeva, Ye.Yu. and Filatov, M.V.},\r\ntitle={Response to tamoxifen in estrogen receptor-positive cell line MCF-7 is independent of p53 expression},\r\njournal={Voprosy Onkologii},\r\nyear={2007},\r\nvolume={53},\r\nnumber={2},\r\npages={194-199},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34547598534&partnerID=40&md5=dd7854f4ddd307cb94f5c9ebb3362452},\r\naffiliation={B.P.Konstantinov Institute of Nuclear Physics, Russian Academy of Sciences, St.Petersburg, Russian Federation},\r\nabstract={The study was concerned with identification of predictive value of p53 expression on sensitivity to tamoxifen in breast cancer management. Estrogen receptor-positive cell line MCF-7 was used to establish p53 expression influence on the rate of cell proliferation after tamoxifen. The investigation demonstrated the absence of that effect when p53 was silenced.},\r\ncorrespondence_address1={Shtam, T. A.; B.P.Konstantinov Institute of Nuclear Physics, Russian Academy of Sciences, St.Petersburg, Russian Federation},\r\nissn={05073758},\r\ncoden={VOONA},\r\nlanguage={Russian},\r\nabbrev_source_title={Vopr. Onkol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n A Quantitative Kinetic Scheme for 70 S Translation Initiation Complex Formation.\n \n \n \n \n\n\n \n Grigoriadou, C.; Marzi, S.; Kirillov, S.; Gualerzi, C.; and Cooperman, B.\n\n\n \n\n\n\n Journal of Molecular Biology, 373(3): 562-572. 2007.\n cited By 60\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

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@ARTICLE{Grigoriadou2007562,\r\nauthor={Grigoriadou, C. and Marzi, S. and Kirillov, S. and Gualerzi, C.O. and Cooperman, B.S.},\r\ntitle={A Quantitative Kinetic Scheme for 70 S Translation Initiation Complex Formation},\r\njournal={Journal of Molecular Biology},\r\nyear={2007},\r\nvolume={373},\r\nnumber={3},\r\npages={562-572},\r\ndoi={10.1016/j.jmb.2007.07.032},\r\nnote={cited By 60},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34748843156&doi=10.1016%2fj.jmb.2007.07.032&partnerID=40&md5=05aead5dcc0d393071404c775068a179},\r\naffiliation={Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States; Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino, MC, Italy; Petersburg Nuclear Physics Institute RAS, 188300 Gatchina, Russian Federation},\r\nabstract={Association of the 30 S initiation complex (30SIC) and the 50 S ribosomal subunit, leading to formation of the 70 S initiation complex (70SIC), is a critical step of the translation initiation pathway. The 70SIC contains initiator tRNA, fMet-tRNA fMet , bound in the P (peptidyl)-site in response to the AUG start codon. We have formulated a quantitative kinetic scheme for the formation of an active 70SIC from 30SIC and 50 S subunits on the basis of parallel rapid kinetics measurements of GTP hydrolysis, Pi release, light-scattering, and changes in fluorescence intensities of fluorophore-labeled IF2 and fMet-tRNA f Met . According to this scheme, an initially formed labile 70 S complex, which promotes rapid IF2-dependent GTP hydrolysis, either dissociates reversibly into 30 S and 50 S subunits or is converted to a more stable form, leading to 70SIC formation. The latter process takes place with intervening conformational changes of ribosome-bound IF2 and fMet-tRNA fMet , which are monitored by spectral changes of fluorescent derivatives of IF2 and fMet-tRNA fMet . The availability of such a scheme provides a useful framework for precisely elucidating the mechanisms by which substituting the non-hydrolyzable analog GDPCP for GTP or adding thiostrepton inhibit formation of a productive 70SIC. GDPCP does not affect stable 70 S formation, but perturbs fMet-tRNA fMet positioning in the P-site. In contrast, thiostrepton severely retards stable 70 S formation, but allows normal binding of fMet-tRNA fMet (prf20) to the P-site. © 2007 Elsevier Ltd. All rights reserved.},\r\nauthor_keywords={fMet-tRNA fMet;  IF2;  kinetic scheme;  thiostrepton;  translation initiation complex},\r\nfunding_details={National Institutes of HealthGM071014},\r\n}

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\n \n\n \n \n \n \n \n \n Towards understanding selenocysteine incorporation into bacterial proteins.\n \n \n \n \n\n\n \n Fischer, N.; Paleskava, A.; Gromadski, K.; Konevega, A.; Wahl, M.; Stark, H.; and Rodnina, M.\n\n\n \n\n\n\n Biological Chemistry, 388(10): 1061-1067. 2007.\n cited By 12\n\n\n\n
\n\n\n\n \n \n $\"Towards$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Fischer20071061,\r\nauthor={Fischer, N. and Paleskava, A. and Gromadski, K.B. and Konevega, A.L. and Wahl, M.C. and Stark, H. and Rodnina, M.V.},\r\ntitle={Towards understanding selenocysteine incorporation into bacterial proteins},\r\njournal={Biological Chemistry},\r\nyear={2007},\r\nvolume={388},\r\nnumber={10},\r\npages={1061-1067},\r\ndoi={10.1515/BC.2007.108},\r\nnote={cited By 12},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-35348893826&doi=10.1515%2fBC.2007.108&partnerID=40&md5=ec0ea08d7c33f8f461af621f8e5e6e2c},\r\naffiliation={3D Electron Cryomicroscopy Group, Max-Planck-Institute for Biophysical Chemistry, D-37077 Göttingen, Germany; Institute of Physical Biochemistry, University of Witten/Herdecke, D-58448 Witten, Germany; X-Ray Crystallography Group, Max-Planck-Institute for Biophysical Chemistry, D-37077 Göttingen, Germany},\r\nabstract={In bacteria, UGA stop codons can be recoded to direct the incorporation of selenocysteine into proteins on the ribosome. Recoding requires a selenocysteine incorporation sequence (SECIS) downstream of the UGA codon, a specialized translation factor SelB, and the non-canonical Sec-tRNASec, which is formed from Ser-tRNASec by selenocysteine synthase, SelA, using selenophosphate as selenium donor. Here we describe a rapid-kinetics approach to study the mechanism of selenocysteine insertion into proteins on the ribosome. Labeling of SelB, Sec-tRNASec and other components of the translational machinery allows direct observation of the formation or dissociation of complexes by monitoring changes in the fluorescence of single dyes or fluorescence resonance energy transfer between two fluorophores. Furthermore, the structure of SelA was studied by electron cryomicroscopy (cryo-EM). We report that intact SelA from the thermophilic bacterium Moorella thermoacetica (mthSelA) can be vitrified for cryo-EM using a controlled-environment vitrification system. Two-dimensional image analysis of vitrified mthSelA images shows that SelA can adopt the wide range of orientations required for high-resolution structure determination by cryo-EM. The results indicate that mthSelA forms a homodecamer that has a ring-like structure with five bilobed wings, similar to the structure of the E. coli complex determined previously. © 2007 by Walter de Gruyter.},\r\nauthor_keywords={Electron cryomicroscopy;  Fluorescence;  Protein synthesis;  Recoding;  Ribosome;  Selenocysteine},\r\n}

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\n \n\n \n \n \n \n \n \n Single-molecule structural dynamics of EF-G-ribosome interaction during translocation.\n \n \n \n \n\n\n \n Wang, Y.; Qin, H.; Kudaravalli, R.; Kirillov, S.; Dempsey, G.; Pan, D.; Cooperman, B.; and Goldman, Y.\n\n\n \n\n\n\n Biochemistry, 46(38): 10767-10775. 2007.\n cited By 49\n\n\n\n
\n\n\n\n \n \n $\"Single-molecule$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Wang200710767,\r\nauthor={Wang, Y. and Qin, H. and Kudaravalli, R.D. and Kirillov, S.V. and Dempsey, G.T. and Pan, D. and Cooperman, B.S. and Goldman, Y.E.},\r\ntitle={Single-molecule structural dynamics of EF-G-ribosome interaction during translocation},\r\njournal={Biochemistry},\r\nyear={2007},\r\nvolume={46},\r\nnumber={38},\r\npages={10767-10775},\r\ndoi={10.1021/bi700657d},\r\nnote={cited By 49},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34648813439&doi=10.1021%2fbi700657d&partnerID=40&md5=6cd038b5a069ff59431c4869f690d09a},\r\naffiliation={Pennsylvania Muscle Institute, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6083, United States; Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States; Petersburg Nuclear Physics Institute, Russian Academy of Science, 188300 Gatchina, Russian Federation},\r\nabstract={EF-G catalyzes translocation of mRNA and tRNAs within the ribosome during protein synthesis. Detection of structural states in the reaction sequence that are not highly populated can be facilitated by studying the process one molecule at a time. Here we present single-molecule studies of translocation showing that, for ribosomes engaged in poly(Phe) synthesis, fluorescence resonance energy transfer (FRET) between the G′ domain of EF-G and the N-terminal domain of ribosomal protein L11 occurs within two rapidly interconverting states, having FRET efficiencies of 0.3 and 0.6. The antibiotic fusidic acid increases the population of the 0.6 state, indicating that it traps the ribosome-EF-G complex in a preexisting conformation formed during translation. Only the 0.3 state is observed when poly(Phe) synthesis is prevented by omission of EF-Tu, or in studies on vacant ribosomes. These results suggest that the 0.6 state results from the conformational lability of unlocked ribosomes formed during translocation. An idling state, possibly pertinent to regulation of protein synthesis, is detected in some ribosomes in the poly(Phe) system. © 2007 American Chemical Society.},\r\ncorrespondence_address1={Cooperman, B.S.; Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States; email: cooprman@pobox.upenn.edu},\r\nissn={00062960},\r\ncoden={BICHA},\r\npubmed_id={17727272},\r\nlanguage={English},\r\nabbrev_source_title={Biochemistry},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Fluorescent labeling of tRNAs for dynamics experiments.\n \n \n \n \n\n\n \n Betteridge, T.; Liu, H.; Gamper, H.; Kirillov, S.; Cooperman, B.; and Hou, Y.\n\n\n \n\n\n\n RNA, 13(9): 1594-1601. 2007.\n cited By 19\n\n\n\n
\n\n\n\n \n \n $\"Fluorescent$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Betteridge20071594,\r\nauthor={Betteridge, T. and Liu, H. and Gamper, H. and Kirillov, S. and Cooperman, B.S. and Hou, Y.-M.},\r\ntitle={Fluorescent labeling of tRNAs for dynamics experiments},\r\njournal={RNA},\r\nyear={2007},\r\nvolume={13},\r\nnumber={9},\r\npages={1594-1601},\r\ndoi={10.1261/rna.475407},\r\nnote={cited By 19},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34548341807&doi=10.1261%2frna.475407&partnerID=40&md5=c80be1682b5e6c4118e92002f0bc6961},\r\naffiliation={Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, United States; Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States; Petersburg Nuclear Physics Institute, RAS, 188300 Gatchina, Russian Federation; Thomas Jefferson University, Department of Biochemistry and Molecular Biology, 233 South 10th Street, Philadelphia, PA 19107, United States},\r\nabstract={Transfer RNAs (tRNAs) are substrates for complex enzymes, such as aminoacyl-tRNA synthetases and ribosomes, and play an essential role in translation of genetic information into protein sequences. Here we describe a general method for labeling tRNAs with fluorescent dyes, so that the activities and dynamics of the labeled tRNAs can be directly monitored by fluorescence during the ribosomal decoding process. This method makes use of the previously reported fluorescent labeling of natural tRNAs at dihydrouridine (D) positions, but extends the previous method to synthetic tRNAs by preparing tRNA transcripts and introducing D residues into transcripts with the yeast enzyme Dus1p dihydrouridine synthase. Using the unmodified transcript of Escherichia coli tRNA Pro as an example, which has U17 and U17a in the D loop, we show that Dus1p catalyzes conversion of one of these Us (mostly U17a) to D, and that the modified tRNA can be labeled with the fluorophores proflavin and rhodamine 110, with overall labeling yields comparable to those obtained with the native yeast tRNA Phe . Further, the transcript of yeast tRNA Phe , modified by Dus1p and labeled with proflavin, translocates on the ribosome at a rate similar to that of the proflavin-labeled native yeast tRNA Phe . These results demonstrate that synthetic tRNA transcripts, which may be designed to contain mutations not found in nature, can be labeled and studied. Such labeled tRNAs should have broad utility in research that involves studies of tRNA maturation, aminoacylation, and tRNA-ribosome interactions. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 RNA Society.},\r\nauthor_keywords={Dihydrouridine;  Dihydrouridine synthase;  Dus1p;  Fluorescent tRNA;  Rhodamine 110},\r\ncorrespondence_address1={Cooperman, B.S.; Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States; email: cooprman@pobox.upenn.edu},\r\nissn={13558382},\r\ncoden={RNARF},\r\npubmed_id={17652134},\r\nlanguage={English},\r\nabbrev_source_title={RNA},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.\n \n \n \n \n\n\n \n Konevega, A.; Fischer, N.; Semenkov, Y.; Stark, H.; Wintermeyer, W.; and Rodnina, M.\n\n\n \n\n\n\n Nature Structural and Molecular Biology, 14(4): 318-324. 2007.\n cited By 72\n\n\n\n
\n\n\n\n \n \n $\"Spontaneous$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Konevega2007318,\r\nauthor={Konevega, A.L. and Fischer, N. and Semenkov, Y.P. and Stark, H. and Wintermeyer, W. and Rodnina, M.V.},\r\ntitle={Spontaneous reverse movement of mRNA-bound tRNA through the ribosome},\r\njournal={Nature Structural and Molecular Biology},\r\nyear={2007},\r\nvolume={14},\r\nnumber={4},\r\npages={318-324},\r\ndoi={10.1038/nsmb1221},\r\nnote={cited By 72},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-34247231999&doi=10.1038%2fnsmb1221&partnerID=40&md5=76fcd2b328f40c9bfc6927499577e695},\r\naffiliation={Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany; 3D Electron Cryomicroscopy Group, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, 188300 Gatchina, Russian Federation; Institute of Molecular Biology, University of Witten/Herdecke, 58448 Witten, Germany},\r\nabstract={During the translocation step of protein synthesis, a complex of two transfer RNAs bound to messenger RNA (tRNA-mRNA) moves through the ribosome. The reaction is promoted by an elongation factor, called EF-G in bacteria, which, powered by GTP hydrolysis, induces an open, unlocked conformation of the ribosome that allows for spontaneous tRNA-mRNA movement. Here we show that, in the absence of EF-G, there is spontaneous backward movement, or retrotranslocation, of two tRNAs bound to mRNA. Retrotranslocation is driven by the gain in affinity when a cognate E-site tRNA moves into the P site, which compensates the affinity loss accompanying the movement of peptidyl-tRNA from the P to the A site. These results lend support to the diffusion model of tRNA movement during translocation. In the cell, tRNA movement is biased in the forward direction by EF-G, which acts as a Brownian ratchet and prevents backward movement. © 2007 Nature Publishing Group.},\r\n}

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\n \n\n \n \n \n \n \n \n Kinetically Competent Intermediates in the Translocation Step of Protein Synthesis.\n \n \n \n \n\n\n \n Pan, D.; Kirillov, S.; and Cooperman, B.\n\n\n \n\n\n\n Molecular Cell, 25(4): 519-529. 2007.\n cited By 146\n\n\n\n
\n\n\n\n \n \n $\"Kinetically$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Pan2007519,\r\nauthor={Pan, D. and Kirillov, S.V. and Cooperman, B.S.},\r\ntitle={Kinetically Competent Intermediates in the Translocation Step of Protein Synthesis},\r\njournal={Molecular Cell},\r\nyear={2007},\r\nvolume={25},\r\nnumber={4},\r\npages={519-529},\r\ndoi={10.1016/j.molcel.2007.01.014},\r\nnote={cited By 146},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33847024820&doi=10.1016%2fj.molcel.2007.01.014&partnerID=40&md5=c849509fb4cc0bdd5ffb0d2e3f401637},\r\naffiliation={Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States; Petersburg Nuclear Physics Institute RAS, 188300 Gatchina, Russian Federation},\r\nabstract={Translocation requires large-scale movements of ribosome-bound tRNAs. Using tRNAs that are proflavin labeled and single-turnover rapid kinetics assays, we identify one or possibly two kinetically competent intermediates in translocation. EF-G.GTP binding to the pretranslocation (PRE) complex and GTP hydrolysis are rapidly followed by formation of the securely identified intermediate complex (INT), which is more slowly converted to the posttranslocation (POST) complex. Peptidyl tRNA within the INT complex occupies a hybrid site, which has a puromycin reactivity intermediate between those of the PRE and POST complexes. Thiostrepton and viomycin inhibit INT formation, whereas spectinomycin selectively inhibits INT disappearance. The effects of other translocation modulators suggest that EF-G-dependent GTP hydrolysis is more important for INT complex formation than for INT complex conversion to POST complex and that subtle changes in tRNA structure influence coupling of tRNA movement to EF-G.GTP-induced conformational changes. © 2007 Elsevier Inc. All rights reserved.},\r\nauthor_keywords={RNA},\r\nfunding_details={GM071014},\r\n}

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\n \n\n \n \n \n \n \n \n Transient Kinetics, Fluorescence, and FRET in Studies of Initiation of Translation in Bacteria.\n \n \n \n \n\n\n \n Milon, P.; Konevega, A.; Peske, F.; Fabbretti, A.; Gualerzi, C.; and Rodnina, M.\n\n\n \n\n\n\n Methods in Enzymology, 430: 1-30. 2007.\n cited By 61\n\n\n\n
\n\n\n\n \n \n $\"Transient$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Milon20071,\r\nauthor={Milon, P. and Konevega, A.L. and Peske, F. and Fabbretti, A. and Gualerzi, C.O. and Rodnina, M.V.},\r\ntitle={Transient Kinetics, Fluorescence, and FRET in Studies of Initiation of Translation in Bacteria},\r\njournal={Methods in Enzymology},\r\nyear={2007},\r\nvolume={430},\r\npages={1-30},\r\ndoi={10.1016/S0076-6879(07)30001-3},\r\nnote={cited By 61},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-35348895336&doi=10.1016%2fS0076-6879%2807%2930001-3&partnerID=40&md5=074280ac6b248b38dc8cb8fb9c8a3579},\r\naffiliation={Laboratory of Genetics, Department of Biology MCA, University of Camerino, Camerino, Italy; Institute of Physical Biochemistry, University of Witten/Herdecke, Witten, Germany; Petersburg Nuclear Physics Institute, Russian Academy of Science, Gatchina, Russian Federation; Institute of Molecular Biology, University of Witten/Herdecke, Witten, Germany},\r\nabstract={Initiation of mRNA translation in prokaryotes requires the small ribosomal subunit (30S), initiator fMet-tRNAfMet, three initiation factors, IF1, IF2, and IF3, and the large ribosomal subunit (50S). During initiation, the 30S subunit, in a complex with IF3, binds mRNA, IF1, IF2·GTP, and fMet-tRNAfMet to form a 30S initiation complex which then recruits the 50S subunit to yield a 70S initiation complex, while the initiation factors are released. Here we describe a transient kinetic approach to study the timing of elemental steps of 30S initiation complex formation, 50S subunit joining, and the dissociation of the initiation factors from the 70S initiation complex. Labeling of ribosomal subunits, fMet-tRNAfMet, mRNA, and initiation factors with fluorescent reporter groups allows for the direct observation of the formation or dissociation of complexes by monitoring changes in the fluorescence of single dyes or fluorescence resonance energy transfer (FRET) between two fluorophores. Subunit joining was monitored by light scattering or by FRET between dyes attached to the ribosomal subunits. The kinetics of chemical steps, that is, GTP hydrolysis by IF2 and peptide bond formation following the binding of aminoacyl-tRNA to the 70S initiation complex, were measured by the quench-flow technique. The methods described here are based on results obtained with initiation components from Escherichia coli but can be adopted for mechanistic studies of initiation in other prokaryotic or eukaryotic systems. © 2007 Elsevier Inc. All rights reserved.},\r\n}

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\n \n 2006\n \n \n (4)\n \n \n

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\n \n\n \n \n \n \n \n \n Single-step purification of specific tRNAs by hydrophobic tagging.\n \n \n \n \n\n\n \n Kothe, U.; Paleskava, A.; Konevega, A.; and Rodnina, M.\n\n\n \n\n\n\n Analytical Biochemistry, 356(1): 148-150. 2006.\n cited By 12\n\n\n\n
\n\n\n\n \n \n $\"Single-step$ Paper\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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@ARTICLE{Kothe2006148,\r\nauthor={Kothe, U. and Paleskava, A. and Konevega, A.L. and Rodnina, M.V.},\r\ntitle={Single-step purification of specific tRNAs by hydrophobic tagging},\r\njournal={Analytical Biochemistry},\r\nyear={2006},\r\nvolume={356},\r\nnumber={1},\r\npages={148-150},\r\ndoi={10.1016/j.ab.2006.04.038},\r\nnote={cited By 12},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33747180809&doi=10.1016%2fj.ab.2006.04.038&partnerID=40&md5=5f4d43d3bf73c0a7f3e78ab575075fa7},\r\naffiliation={Institute of Physical Biochemistry, University of Witten/Herdecke, D-58448 Witten, Germany},\r\n}

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\n \n\n \n \n \n \n \n \n The effect of modification of tRNA nucleotide-37 on the tRNA interaction with the P- and A-site of the 70S ribosome Escherichia coli.\n \n \n \n \n\n\n \n Konevega, A.; Soboleva, N.; Makhno, V.; Peshekhonov, A.; and Katunin, V.\n\n\n \n\n\n\n Molekuliarnaia biologiia., 40(4): 669-683. 2006.\n cited By 6\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Konevega2006669,\r\nauthor={Konevega, A.L. and Soboleva, N.G. and Makhno, V.I. and Peshekhonov, A.V. and Katunin, V.I.},\r\ntitle={The effect of modification of tRNA nucleotide-37 on the tRNA interaction with the P- and A-site of the 70S ribosome Escherichia coli},\r\njournal={Molekuliarnaia biologiia.},\r\nyear={2006},\r\nvolume={40},\r\nnumber={4},\r\npages={669-683},\r\nnote={cited By 6},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33749066025&partnerID=40&md5=7eb6533d775986f49cbe70542290ec2d},\r\nabstract={A modified nucleotide on the 3'-side of the anticodon loop of tRNA is one of the most important structure element regulating codon-anticodone interaction on the ribosome owing to the stacking interaction with the stack of codon-anticodon bases. The presence and identity (pyrimidine, purine or modified purine) of this nucleotide has an essential influence on the energy of the stacking interaction on A- and P-sites of the ribosome. There is a significant influence of the 37-modification by itself on the P-site, whereas there is no such one on the A-site of the ribosome. Comparison of binding enthalpies of tRNA interactions on the P- or A-site of the ribosome with the binding enthalpies of the complex of two tRNAs with the complementary anticodones suggests that the ribosome by itself significantly endows in the thermodynamics of codon-anticodon complex formation. It happens by additional ribosomal interactions with the molecule of tRNA or indirectly by the stabilization of codon-anticodon conformation. In addition to the stacking, tRNA binding in the A and P sites is futher stabilized by the interactions involving some magnesium ions. The number of them involved in those interactions strongly depends on the nucleotide identity in the 37-position of tRNA anticodon loop.},\r\ncorrespondence_address1={Konevega, A.L.},\r\nissn={00268984},\r\npubmed_id={16913226},\r\nlanguage={Russian},\r\nabbrev_source_title={Mol. Biol. (Mosk.)},\r\ndocument_type={Review},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Effect of modification of tRNA nucleotide 37 on the tRNA interaction with the A and P sites of the Escherichia coli 70S ribosome.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Molecular Biology, 40(4): 597-610. 2006.\n cited By 2\n\n\n\n
\n\n\n\n \n \n $\"Effect$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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\n \n\n \n \n \n \n \n \n Rapid ribosomal translocation depends on the conserved 18-55 base pair in P-site transfer RNA.\n \n \n \n \n\n\n \n Pan, D.; Kirillov, S.; Zhang, C.; Hou, Y.; and Cooperman, B.\n\n\n \n\n\n\n Nature Structural and Molecular Biology, 13(4): 354-359. 2006.\n cited By 38\n\n\n\n
\n\n\n\n \n \n $\"Rapid$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Pan2006354,\r\nauthor={Pan, D. and Kirillov, S. and Zhang, C.-M. and Hou, Y.-M. and Cooperman, B.S.},\r\ntitle={Rapid ribosomal translocation depends on the conserved 18-55 base pair in P-site transfer RNA},\r\njournal={Nature Structural and Molecular Biology},\r\nyear={2006},\r\nvolume={13},\r\nnumber={4},\r\npages={354-359},\r\ndoi={10.1038/nsmb1074},\r\nnote={cited By 38},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33745044746&doi=10.1038%2fnsmb1074&partnerID=40&md5=44d2957da3baa1f98417ed8d4997f51f},\r\naffiliation={Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, United States; Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, Philadelphia, PA 19107, United States; Petersburg Nuclear Physics Institute RAS, 188300 Gatchina, Russian Federation},\r\nabstract={The L shape of tRNA is stabilized by the 'tertiary core' region, which contains base-pairing interactions between the D and T loops. Distortions of the L shape accompany tRNA movement across the ribosomal surface. Here, using single-turnover rapid kinetics assays, we determine the effects of mutations within the tertiary core of P site-bound tRNA fMet on three measures of the rate of translocation, the part of the elongation cycle involving the most extensive tRNA movement. Mutations in the strictly conserved G18·U55 base pair result in as much as an 80-fold decrease in the rate of translocation, demonstrating the importance of the 18-55 interaction for rapid translocation. This implicates the core region as a locus for functionally important dynamic interactions with the ribosome and leads to the proposal that translocation of ribosome-bound tRNAs may be sequential rather than concerted. © 2006 Nature Publishing Group.},\r\nfunding_details={GM56662, GM071014},\r\n}

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\n \n 2005\n \n \n (1)\n \n \n

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\n \n\n \n \n \n \n \n \n Conformation of 4.5S RNA in the signal recognition particle and on the 30S ribosomal subunit.\n \n \n \n \n\n\n \n Gu, S.; Jöckel, J.; Beinker, P.; Warnecke, J.; Semenkov, Y.; Rodnina, M.; and Wintermeyer, W.\n\n\n \n\n\n\n RNA, 11(9): 1374-1384. 2005.\n cited By 20\n\n\n\n
\n\n\n\n \n \n $\"Conformation$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Gu20051374,\r\nauthor={Gu, S.-Q. and Jöckel, J. and Beinker, P. and Warnecke, J. and Semenkov, Y.P. and Rodnina, M.V. and Wintermeyer, W.},\r\ntitle={Conformation of 4.5S RNA in the signal recognition particle and on the 30S ribosomal subunit},\r\njournal={RNA},\r\nyear={2005},\r\nvolume={11},\r\nnumber={9},\r\npages={1374-1384},\r\ndoi={10.1261/rna.7219805},\r\nnote={cited By 20},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-22444448158&doi=10.1261%2frna.7219805&partnerID=40&md5=0d07f5d32f93d15afd45c83d2d438bdd},\r\naffiliation={Institute of Molecular Biology, University of Witten/Herdecke, 58448 Witten, Germany; Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany; Petersburg Nuclear Physics Institute, 188355, Gatchina, Russian Federation; Department of Molecular Structural Biology MBB, Karolinska Institute, S-17177 Stockholm, Sweden; Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany; Institute of Molecular Biology, University of Witten/Herdecke, Stockumer Str. 10, 58448 Witten, Germany},\r\nabstract={The signal recognition particle (SRP) from Escherichia coli consists of 4.5S RNA and protein Ffh. It is essential for targeting ribosomes that are translating integral membrane proteins to the translocation pore in the plasma membrane. Independently of Ffh, 4.5S RNA also interacts with elongation factor G (EF-G) and the 30S ribosomal subunit. Here we use a cross-linking approach to probe the conformation of 4.5S RNA in SRP and in the complex with the 30S ribosomal subunit and to map the binding site. The UV-activatable cross-linker p-azidophenacyl bromide (AzP) was attached to positions 1, 21, and 54 of wildtype or modified 4.5S RNA. In SRP, cross-links to Ffh were formed from AzP in all three positions in 4.5S RNA, indicating a strongly bent conformation in which the 5′ end (position 1) and the tetraloop region (including position 54) of the molecule are close to one another and to Ffh. In ribosomal complexes of 4.5S RNA, AzP in both positions 1 and 54 formed cross-links to the 30S ribosomal subunit, independently of the presence of Ffh. The major cross-linking target on the ribosome was protein S7; minor cross-links were formed to S2, S18, and S21. There were no cross-links from 4.5S RNA to the 50S subunit, where the primary binding site of SRP is located close to the peptide exit. The functional role of 4.5S RNA binding to the 30S subunit is unclear, as the RNA had no effect on translation or tRNA translocation on the ribosome. Copyright © 2005 RNA Society.},\r\nauthor_keywords={4.5S RNA;  Cross-linking;  Ribosomal proteins;  Signal recognition particle},\r\ncorrespondence_address1={Wintermeyer, W.; Institute of Molecular Biology, University of Witten/Herdecke, Stockumer Str. 10, 58448 Witten, Germany; email: winterme@uni-wh.de},\r\nissn={13558382},\r\ncoden={RNARF},\r\npubmed_id={16043501},\r\nlanguage={English},\r\nabbrev_source_title={RNA},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n General changes of progression of hereditary nonpolyposis colorectal cancer.\n \n \n \n \n\n\n \n Shtam, T.; Vostrukhina, O.; Gulyaev, A.; Pozharisskij, K.; and Lantsov, V.\n\n\n \n\n\n\n Doklady Akademii Nauk, 395(1): 126-131. 2004.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"General$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Shtam2004126,\r\nauthor={Shtam, T.A. and Vostrukhina, O.A. and Gulyaev, A.V. and Pozharisskij, K.M. and Lantsov, V.A.},\r\ntitle={General changes of progression of hereditary nonpolyposis colorectal cancer},\r\njournal={Doklady Akademii Nauk},\r\nyear={2004},\r\nvolume={395},\r\nnumber={1},\r\npages={126-131},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-8644283771&partnerID=40&md5=c9a985e57637b1209b06c1acb79c9333},\r\naffiliation={Peterburgskij Inst. Yadernoj Fiziki, RAN, Sankt-Peterburg, Russian Federation},\r\nabstract={Retrospective analysis of genetic changes in cells of a patient with inheritable nonpolypoid large intestine cancer has been carried out. Neoplastic progression appeared to be a result of damages in a system of non-paired DNA bases correction. New inheritable mutation in hMLH1 gene has been described. This mutation induced 3 consecutive stages of disease: 1) appearance of mutations, aggravating the damage of DNA reparation system; 2) accumulation of mutations and metastasizing of transformed cell; 3) independent development of new clones and appearance of a large number of tumors.},\r\ncorrespondence_address1={Shtam, T.A.; Peterburgskij Inst. Yadernoj Fiziki, RAN, Sankt-Peterburg, Russian Federation},\r\nissn={08695652},\r\ncoden={DAKNE},\r\nlanguage={Russian},\r\nabbrev_source_title={Dokl Akad Nauk},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Genetic lesions during progression of hereditary non-polypous colorectal cancer.\n \n \n \n \n\n\n \n Shtam, T.; Vostryukhina, O.; Gulyaev, A.; Pozharissky, K.; and Lantsov, V.\n\n\n \n\n\n\n Doklady Biochemistry and Biophysics, 395(1-6): 69-74. 2004.\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\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Shtam200469,\r\nauthor={Shtam, T.A. and Vostryukhina, O.A. and Gulyaev, A.V. and Pozharissky, K.M. and Lantsov, V.A.},\r\ntitle={Genetic lesions during progression of hereditary non-polypous colorectal cancer},\r\njournal={Doklady Biochemistry and Biophysics},\r\nyear={2004},\r\nvolume={395},\r\nnumber={1-6},\r\npages={69-74},\r\ndoi={10.1023/B:DOBI.0000025549.84403.b5},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-3342900114&doi=10.1023%2fB%3aDOBI.0000025549.84403.b5&partnerID=40&md5=a01dee224a88cbef18f4840021390ced},\r\naffiliation={Konstantinov St. Petersburg Inst. N., Russian Academy of Sciences, Gatchina, Leningrad Oblast, 188300, Russian Federation; Petrov Res. Institute for Oncology, Min. of Pub. Hlth. of Russ. Fed., St. Petersburg, 189646, Russian Federation},\r\n}

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\n \n\n \n \n \n \n \n \n Purine bases at position 37 of tRNA stabilize codon-anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions.\n \n \n \n \n\n\n \n Konevega, A.; Soboleva, N.; Makhno, V.; Semenkov, Y.; Wintermeyer, W.; Rodnina, M.; and Katunin, V.\n\n\n \n\n\n\n RNA, 10(1): 90-101. 2004.\n cited By 73\n\n\n\n
\n\n\n\n \n \n $\"Purine$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Konevega200490,\r\nauthor={Konevega, A.L. and Soboleva, N.G. and Makhno, V.I. and Semenkov, Y.P. and Wintermeyer, W. and Rodnina, M.V. and Katunin, V.I.},\r\ntitle={Purine bases at position 37 of tRNA stabilize codon-anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions},\r\njournal={RNA},\r\nyear={2004},\r\nvolume={10},\r\nnumber={1},\r\npages={90-101},\r\ndoi={10.1261/rna.5142404},\r\nnote={cited By 73},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0347623198&doi=10.1261%2frna.5142404&partnerID=40&md5=c0ac9c400bbb3e2d3a57147153225962},\r\naffiliation={Petersburg Nuclear Physics Institute, Russian Academy of Sciences, 188300 Gatchina, Russian Federation; Institute of Molecular Biology, University of Witten/Herdecke, 58448 Witten, Germany; Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany},\r\nabstract={The anticodon loop of tRNA contains a number of conserved or semiconserved nucleotides. In most tRNAs, a highly modified purine is found at position 37 immediately 3′ to the anticodon. Here, we examined the role of the base at position 37 for tRNAPhe binding to the A site of Escherichia coli ribosomes. Affinities and rate constants of A-site binding of native yeast peptidyl-tRNAPhe with hypermodified G (wybutine), or of unmodified peptidyl-tRNAPhe transcripts with G, A, C, or U, at position 37 were measured. The data indicate that purines stabilize binding due to stronger stacking and additional interactions with the ribosome mediated by Mg 2+ ions. Paromomycin, an antibiotic that binds to 16S rRNA in the decoding center, greatly stabilized tRNAs in the A site and abolished the Mg2+ -dependence of binding. Comparison of binding enthalpies and entropies suggests that hypermodification of the base at position 37 does not affect stacking in the codon-anticodon complex, but rather decreases the entropic penalty for A-site binding. Substitution of purines with pyrimidines at position 37 increases the rates of tRNA binding to and dissociation from the A site. The data suggest that initial binding of tRNA to the A site is followed by a rate-limiting rearrangement of the anticodon loop or the ribosome decoding center that is favored by purines at position 37 and involves stronger stacking, additional Mg2+ binding, and interactions with 16S rRNA.},\r\nauthor_keywords={Ribosome decoding;  Translation;  TRNA conformational change;  TRNA modifications;  TRNA selection},\r\ncorrespondence_address1={Katunin, V.I.; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, 188300 Gatchina, Russian Federation; email: katunin@omrb.pnpi.spb.ru},\r\nissn={13558382},\r\ncoden={RNARF},\r\npubmed_id={14681588},\r\nlanguage={English},\r\nabbrev_source_title={RNA},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 2003\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n The effect of modification of nucleotide-37 on the interaction of aminoacyl-tRNA with the a site of the 70S ribosome.\n \n \n \n \n\n\n \n Soboleva, N.; Makhno, V.; Konevega, A.; Semenkov, Y.; and Katunin, V.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 37(1): 121-127. 2003.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Soboleva2003121,\r\nauthor={Soboleva, N.G. and Makhno, V.I. and Konevega, A.L. and Semenkov, Yu.P. and Katunin, V.I.},\r\ntitle={The effect of modification of nucleotide-37 on the interaction of aminoacyl-tRNA with the a site of the 70S ribosome},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={2003},\r\nvolume={37},\r\nnumber={1},\r\npages={121-127},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037667672&partnerID=40&md5=5c8ad0bf4218457eab4cbe1a75ed3345},\r\naffiliation={Konstantinov Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina, Leningrad oblast, 188300, Russian Federation},\r\nabstract={To estimate the effect of modified nucleotide-37, the interaction of two yeast aminoacyl-tRNAs (Phe-tRNA K +Y Phe and Phe-tRNA K -Y Phe ) with the A site of complex [70S · poly(U) · deacylated tRNA Phe in the P site] was assayed at 0-20°C. As comparisons with native Phe-tRNA K +Y Phe showed, removal of the Y base decreased the association constant of Phe-tRNA K -Y Phe and the complex by an order of magnitude at any temperature, and increased the enthalpy of their interaction by 23 kJ/mol. When the Y base was present in the anticodon loop of deacylated tRNA Phe bound to the P site of the 70S ribosome, twice higher affinity for the A site was observed for Phe-tRNA K -Y Phe but not for Phe-tRNA K +Y Phe . Thus, the modified nucleotide 3′ of the Phe-tRNA Phe anticodon stabilized the codon-anticodon interaction both in the A and in the P sites of the 70S ribosome.},\r\ncorrespondence_address1={Soboleva, N.G.; Konstantinov Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina, Leningrad oblast, 188300, Russian Federation},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={12624954},\r\nlanguage={Russian},\r\nabbrev_source_title={Mol. Biol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The Effect of Modification of Nucleotide-37 on the Interaction of Aminoacyl-tRNA with the a Site of the 70S Ribosome.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Molecular Biology, 37(1): 110-115. 2003.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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\n \n 2002\n \n \n (1)\n \n \n

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\n \n\n \n \n \n \n \n \n Transit of tRNA through the Escherichia coli ribosome: Cross-linking of the 3′ end of tRNA to ribosomal proteins at the P and E sites.\n \n \n \n \n\n\n \n Kirillov, S.; Wower, J.; Hixson, S.; and Zimmermann, R.\n\n\n \n\n\n\n FEBS Letters, 514(1): 60-66. 2002.\n cited By 15\n\n\n\n
\n\n\n\n \n \n $\"Transit$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Kirillov200260,\r\nauthor={Kirillov, S.V. and Wower, J. and Hixson, S.S. and Zimmermann, R.A.},\r\ntitle={Transit of tRNA through the Escherichia coli ribosome: Cross-linking of the 3′ end of tRNA to ribosomal proteins at the P and E sites},\r\njournal={FEBS Letters},\r\nyear={2002},\r\nvolume={514},\r\nnumber={1},\r\npages={60-66},\r\ndoi={10.1016/S0014-5793(02)02302-5},\r\nnote={cited By 15},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037029033&doi=10.1016%2fS0014-5793%2802%2902302-5&partnerID=40&md5=fcf3c21816d4226e76c96f5a1d63307b},\r\naffiliation={Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, United States; Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States},\r\nabstract={Photoreactive derivatives of yeast tRNA Phe containing 2-azidoadenosine at their 3′ termini were used to trace the movement of tRNA across the 50S subunit during its transit from the P site to the E site of the 70S ribosome. When bound to the P site of poly(U)-programmed ribosomes, deacylated tRNA Phe , Phe-tRNA Phe and N-acetyl-Phe-tRNA Phe probes labeled protein L27 and two main sites within domain V of the 23S RNA. In contrast, deacylated tRNA Phe bound to the E site in the presence of poly(U) labeled protein L33 and a single site within domain V of the 23S rRNA. In the absence of poly(U), the deacylated tRNA Phe probe also labeled protein L1. Cross-linking experiments with vacant 70S ribosomes revealed that deacylated tRNA enters the P site through the E site, progressively labeling proteins L1, L33 and, finally, L27. In the course of this process, tRNA passes through the intermediate P/E binding state. These findings suggest that the transit of tRNA from the P site to the E site involves the same interactions, but in reverse order. Moreover, our results indicate that the final release of deacylated tRNA from the ribosome is mediated by the F site, for which protein L1 serves as a marker. The results also show that the precise placement of the acceptor end of tRNA on the 50S subunit at the P and E sites is influenced in subtle ways both by the presence of aminoacyl or peptidyl moieties and, more surprisingly, by the environment of the anticodon on the 30S subunit. © 2002 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved.},\r\nauthor_keywords={2-Azidoadenosine;  Photoaffinity labeling;  Protein synthesis;  Proteins L1, L27, L33},\r\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 Short-range RNA-RNA crosslinking methods to determine rRNA structure and interactions.\n \n \n \n \n\n\n \n Juzumiene, D.; Shapkina, T.; Kirillov, S.; and Wollenzien, P.\n\n\n \n\n\n\n Methods, 25(3): 333-343. 2001.\n cited By 22\n\n\n\n
\n\n\n\n \n \n $\"Short-range$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Juzumiene2001333,\r\nauthor={Juzumiene, D. and Shapkina, T. and Kirillov, S. and Wollenzien, P.},\r\ntitle={Short-range RNA-RNA crosslinking methods to determine rRNA structure and interactions},\r\njournal={Methods},\r\nyear={2001},\r\nvolume={25},\r\nnumber={3},\r\npages={333-343},\r\ndoi={10.1006/meth.2001.1245},\r\nnote={cited By 22},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035720092&doi=10.1006%2fmeth.2001.1245&partnerID=40&md5=b22dbc658f111c6b28bd54d9c2df9e16},\r\naffiliation={Department of Molecular and Structural Biochemistry, North Carolina State University, 126 Polk Hall, Raleigh, NC, 27695, United States},\r\nabstract={We describe details of procedures to analyze RNA-RNA crosslinks made by far-UV irradiation (< 300 nm) or made by irradiation with near-UV light (320-365 nm) on RNA containing photosensitive nucleotides, in the present case containing 4-thiouridine. Zero-length crosslinks of these types must occur because of the close proximity of the participants through either specific interactions or transient contacts in the folded RNA structure, so they are valuable monitors of the conformation of the RNA. Procedures to produce crosslinks in the 16S ribosomal RNA and between the 16S rRNA and mRNA or tRNA are described. Gel electrophoresis conditions are described that separate the products according to their structure to allow the determination of the number and frequency of the crosslinking products. Gel electrophoresis together with an ultracentrifugation procedure for the efficient recovery of RNA from the polyacrylamide gels allows the purification of molecules containing different crosslinks. These separation techniques allow the analysis of the sites of crosslinking by primer extension and RNA sequencing techniques. The procedures are applicable to other types of RNA molecules with some differences to control levels of crosslinking and separation conditions. © 2001 Elsevier Science USA.},\r\nissn={10462023},\r\npubmed_id={11860287},\r\nlanguage={English},\r\nabbrev_source_title={Methods},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Mechanism of tRNA translocation on the ribosome.\n \n \n \n \n\n\n \n Rodnina, M.; Semenkov, Y.; Savelsbergh, A.; Katunin, V.; Peske, F.; Wilden, B.; and Wintermeyer, W.\n\n\n \n\n\n\n Molecular Biology, 35(4): 559-568. 2001.\n cited By 4\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

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@ARTICLE{Rodnina2001559,\r\nauthor={Rodnina, M.V. and Semenkov, Yu.P. and Savelsbergh, A. and Katunin, V.I. and Peske, F. and Wilden, B. and Wintermeyer, W.},\r\ntitle={Mechanism of tRNA translocation on the ribosome},\r\njournal={Molecular Biology},\r\nyear={2001},\r\nvolume={35},\r\nnumber={4},\r\npages={559-568},\r\ndoi={10.1023/A:1010523026531},\r\nnote={cited By 4},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035385078&doi=10.1023%2fA%3a1010523026531&partnerID=40&md5=3a710f338ca0ee4d9b2c9590624c8723},\r\naffiliation={Institute of Physical Biochemistry, University of Witten/Herdecke, Witten, 58448, Germany; St. Petersburg Nucl. Phys. Institute, Russian Academy of Sciences, Gatchina, 188350, Russian Federation; Institute of Molecular Biology, University of Witten/Herdecke, Witten, 58448, Germany},\r\nabstract={During the translocation step of the elongation cycle of peptide synthesis two tRNAs together with the mRNA move synchronously and rapidly on the ribosome. Translocation is catalyzed by the elongation factor G (EF-G) and requires GTP hydrolysis. The fundamental biochemical features of the process were worked out in the 1970-80s, to a large part by A.S. Spirin and his colleagues. Recent results from pre-steady-state kinetic analysis and cryoelectron microscopy suggest that translocation is a multistep dynamic process that entails large-scale structural rearrangements of both ribosome and EF-G. Kinetic and thermodynamic data, together with the structural information on the conformational changes in the ribosome and EF-G, provide a detailed mechanistic model of translocation and suggest a mechanism of translocation catalysis by EF-G.},\r\nauthor_keywords={Catalysis;  GTPase;  Hybrid states;  Kinetics;  Motor protein;  Protein synthesis;  tRNA translocation},\r\n}

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\n \n\n \n \n \n \n \n \n Mechanism of elongation factor G function in tRNA translocation on the ribosome.\n \n \n \n \n\n\n \n Wintermeyer, W.; Savelsbergh, A.; Semenkov, Y.; Katunin, V.; and Rodnina, M.\n\n\n \n\n\n\n Cold Spring Harbor Symposia on Quantitative Biology, 66: 449-458. 2001.\n cited By 22\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\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Wintermeyer2001449,\r\nauthor={Wintermeyer, W. and Savelsbergh, A. and Semenkov, Y.P. and Katunin, V.I. and Rodnina, M.V.},\r\ntitle={Mechanism of elongation factor G function in tRNA translocation on the ribosome},\r\njournal={Cold Spring Harbor Symposia on Quantitative Biology},\r\nyear={2001},\r\nvolume={66},\r\npages={449-458},\r\ndoi={10.1101/sqb.2001.66.449},\r\nnote={cited By 22},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035787728&doi=10.1101%2fsqb.2001.66.449&partnerID=40&md5=9d776bf4efc1b98eda27060da8631058},\r\naffiliation={Institute of Molecular Biology, University of Witten/Herdecke, 58448 Witten, Germany; Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany; Sankt Petersburg Nucl. Phys. Inst., Russian Academy of Sciences, 188350 Gatchina, Russian Federation},\r\ncorrespondence_address1={Wintermeyer, W.; Institute of Molecular Biology, University of Witten/Herdecke, 58448 Witten, Germany},\r\npublisher={Cold Spring Harbor Laboratory Press},\r\nissn={00917451},\r\ncoden={CSHSA},\r\npubmed_id={12762047},\r\nlanguage={English},\r\nabbrev_source_title={Cold Spring Harbor Symp. Quant. Biol.},\r\ndocument_type={Conference Paper},\r\nsource={Scopus},\r\n}\r\n\r\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 Transit of tRNA through the Escherichia coli ribosome. Cross-linking of the 3' end of tRNA to specific nucleotides of the 23 S ribosomal RNA at the A, P, and E sites.\n \n \n \n \n\n\n \n Wower, J.; Kirillov, S.; Wower, I.; Guven, S.; Hixson, S.; and Zimmermann, R.\n\n\n \n\n\n\n Journal of Biological Chemistry, 275(48): 37887-37894. 2000.\n cited By 34\n\n\n\n
\n\n\n\n \n \n $\"Transit$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Wower200037887,\r\nauthor={Wower, J. and Kirillov, S.V. and Wower, I.K. and Guven, S. and Hixson, S.S. and Zimmermann, R.A.},\r\ntitle={Transit of tRNA through the Escherichia coli ribosome. Cross-linking of the 3' end of tRNA to specific nucleotides of the 23 S ribosomal RNA at the A, P, and E sites},\r\njournal={Journal of Biological Chemistry},\r\nyear={2000},\r\nvolume={275},\r\nnumber={48},\r\npages={37887-37894},\r\ndoi={10.1074/jbc.M005031200},\r\nnote={cited By 34},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034535129&doi=10.1074%2fjbc.M005031200&partnerID=40&md5=a8b23c16b64d3139cf69fc818d6c38ea},\r\naffiliation={Department of Animal and Dairy Sciences, Program in Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849-5415, United States; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, United States; Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina 188350, Russian Federation},\r\nabstract={When bound to Escherichia coli ribosomes and irradiated with near-UV light, various derivatives of yeast tRNA(Phe)Phe containing 2-azidoadenosine at the 3' terminus form cross-links to 23 S rRNA and 56 S subunit proteins in a site-dependent manner. A and P site-bound tRNAs, whose 3' termini reside in the peptidyl transferase center, label primarily nucleotides U2506 and U2585 and protein L27. In contrast, E site-bound tRNA labels nucleotide C2422 and protein L33. The cross-linking patterns confirm the topographical separation of the peptidyl transferase center from the E site domain. The relative amounts of label incorporated into the universally conserved residues U2506 and U2585 depend on the occupancy of the A and P sites by different tRNA ligands and indicates that these nucleotides play a pivotal role in peptide transfer. In particular, the 3'-adenosine of the peptidyl-tRNA analogue, AcPhe-tRNA(Phe), remains in close contact with U2506 regardless of whether its anti-codon is located in the A site or P site. Our findings, therefore, modify and extend the hybrid state model of tRNA-ribosome interaction. We show that the 3'-end of the deacylated tRNA that is formed after transpeptidation does not immediately progress to the E site but remains temporarily in the peptidyl transferase center. In addition, we demonstrate that the E site, defined by the labeling of nucleotide C2422 and protein L33, represents an intermediate state of binding that precedes the entry of deacylated tRNA into the F (final) site from which it dissociates into the cytoplasm.},\r\ncorrespondence_address1={Wower, J.; Dept. of Animal and Dairy Sciences, Program Cell/Molecular Biosciences, Auburn University, Auburn, AL 36849-5415, United States; email: jwower@acesag.auburn.edu},\r\nissn={00219258},\r\ncoden={JBCHA},\r\npubmed_id={10961994},\r\nlanguage={English},\r\nabbrev_source_title={J. Biol. Chem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Energetic contribution of tRNA hybrid state formation to translocation catalysis on the ribosome.\n \n \n \n \n\n\n \n Semenkov, Y.; Rodnina, M.; and Wintermeyer, W.\n\n\n \n\n\n\n Nature Structural Biology, 7(11): 1027-1031. 2000.\n cited By 86\n\n\n\n
\n\n\n\n \n \n $\"Energetic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Semenkov20001027,\r\nauthor={Semenkov, Y.P. and Rodnina, M.V. and Wintermeyer, W.},\r\ntitle={Energetic contribution of tRNA hybrid state formation to translocation catalysis on the ribosome},\r\njournal={Nature Structural Biology},\r\nyear={2000},\r\nvolume={7},\r\nnumber={11},\r\npages={1027-1031},\r\ndoi={10.1038/80938},\r\nnote={cited By 86},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033762347&doi=10.1038%2f80938&partnerID=40&md5=49a1741f4a348c417e91e47234c34592},\r\naffiliation={Institute of Molecular Biology, University of Witten/Herdecke, D-58448 Witten, Germany; Sankt Petersburg Nuclear Physics Institute, Russian Academy of Sciences, 188350 Gatchina, Russian Federation; Institute of Physical Biochemistry, University of Witten/Herdecke, D-58448 Witten, Germany},\r\nabstract={Upon transpeptidylation, the 3' end of aminoacyl-tRNA (aa-tRNA) in the ribosomal A site enters the A/P hybrid state. We report that transpeptidylation of Phe-tRNA to fMetPhe-tRNA on Escherichia coli ribosomes substantially lowers the kinetic stability of the ribosome-tRNA complex and decreases the affinity by 18.9 kJ mol-1. At the same time, the free energy of activation of elongation factor G dependent translocation decreases by 12.5 kJ mol-1, indicating that part of the free energy of transpeptidylation is used to drive translocation kinetically. Thus, the formation of the A/P hybrid state constitutes an important element of the translocation mechanism.},\r\n}

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\n \n\n \n \n \n \n \n \n Puromycin-rRNA interaction sites at the peptidyl transferase center.\n \n \n \n \n\n\n \n Rodriguez-Fonseca, C.; Phan, H.; Long, K.; Porse, B.; Kirillov, S.; Amils, R.; and Garrett, R.\n\n\n \n\n\n\n RNA, 6(5): 744-754. 2000.\n cited By 23\n\n\n\n
\n\n\n\n \n \n $\"Puromycin-rRNA$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Rodriguez-Fonseca2000744,\r\nauthor={Rodriguez-Fonseca, C. and Phan, H. and Long, K.S. and Porse, B.T. and Kirillov, S.V. and Amils, R. and Garrett, R.A.},\r\ntitle={Puromycin-rRNA interaction sites at the peptidyl transferase center},\r\njournal={RNA},\r\nyear={2000},\r\nvolume={6},\r\nnumber={5},\r\npages={744-754},\r\ndoi={10.1017/S1355838200000091},\r\nnote={cited By 23},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034032601&doi=10.1017%2fS1355838200000091&partnerID=40&md5=5ea9b440b79572e4fff8594e873168d3},\r\naffiliation={RNA Regulation Centre, Institute of Molecular Biology, University of Copenhagen, Sølvgade 83H, DK-1307 Copenhagen K, Denmark; Centro de Biología Molecular, Univ. Autónoma de Madrid, Campus de Cantoblanco, E-28049 Madrid, Spain; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, 188350 Gatchina, St. Petersburg, Russian Federation},\r\nabstract={The binding site of puromycin was probed chemically in the peptidyl- transferase center of ribosomes from Escherichia coli and of puromycin- hypersensitive ribosomes from the archaeon Haloferax gibbonsii. Several nucleotides of the 23S rRNAs showed altered chemical reactivities in the presence of puromycin. They include A2439, G2505, and G2553 for E. coli, and G2058, A2503, G2505, and G2553 for Hf. gibbonsil (using the E. coli numbering system). Reproducible enhanced reactivities were also observed at A508 and A1579 within domains I and III, respectively, of E. coli 23S rRNA. In further experiments, puromycin was shown to produce a major reduction in the UV- induced crosslinking of deacylated-(2N3A76)tRNA to U2506 within the P' site of E. coli ribosomes. Moreover, it strongly stimulated the putative UV- induced crosslink between a streptogramin B drug and m2A2503/Ψ2504 at an adjacent site in E. coli 23S rRNA. These data strongly support the concept that puromycin, along with other peptidyl-transferase antibiotics, in particular the streptogramin B drugs, bind to an RNA structural motif that contains several conserved and accessible base moieties of the peptidyl transferase loop region. This streptogramin motif is also likely to provide binding sites for the 3' termini of the acceptor and donor tRNAs. In contrast, the effects at A508 and A1579, which are located at the exit site of the peptide channel, are likely to be caused by a structural effect transmitted along the peptide channel.},\r\nauthor_keywords={23S rRNA;  Peptide channel;  Peptidyl transferase;  Puromycin},\r\ncorrespondence_address1={Garrett, R.A.; RNA Regulation Centre, Institute of Molecular Biology, University of Copenhagen, Solvgade 83H, DK-1307 Copenhagen K, Denmark; email: garrett@mermaid.molbio.ku.dk},\r\nissn={13558382},\r\ncoden={RNARF},\r\npubmed_id={10836795},\r\nlanguage={English},\r\nabbrev_source_title={RNA},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1999\n \n \n (4)\n \n \n

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\n \n\n \n \n \n \n \n \n Thiostrepton inhibits the turnover but not the GTPase of elongation factor G on the ribosome.\n \n \n \n \n\n\n \n Rodnina, M.; Savelsbergh, A.; Matassova, N.; Katunin, V.; Semenkov, Y.; and Wintermeyer, W.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 96(17): 9586-9590. 1999.\n cited By 146\n\n\n\n
\n\n\n\n \n \n $\"Thiostrepton$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Rodnina19999586,\r\nauthor={Rodnina, M.V. and Savelsbergh, A. and Matassova, N.B. and Katunin, V.I. and Semenkov, Y.P. and Wintermeyer, W.},\r\ntitle={Thiostrepton inhibits the turnover but not the GTPase of elongation factor G on the ribosome},\r\njournal={Proceedings of the National Academy of Sciences of the United States of America},\r\nyear={1999},\r\nvolume={96},\r\nnumber={17},\r\npages={9586-9590},\r\ndoi={10.1073/pnas.96.17.9586},\r\nnote={cited By 146},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033578321&doi=10.1073%2fpnas.96.17.9586&partnerID=40&md5=41530c907a9f067ed344e4966dc5c6ba},\r\naffiliation={Institute of Molecular Biology, University of Witten/Herdecke, D-58448 Witten, Germany; Sankt Petersburg Nucl. Phys. Inst., Russian Academy of Sciences, 188350 Gatchina, Russian Federation; Novosibirsk Inst. of Bioorg. Chem., Siberian Branch, Russian Academy of Sciences, Prospect Lavrentieva 8, 630090, Novosibirsk, Russian Federation},\r\nabstract={The region around position 1067 in domain II of 23S rRNA frequently is referred to as the GTPase center of the ribosome. The notion is based on the observation that the binding of the antibiotic thiostrepton to this region inhibited GTP hydrolysis by elongation factor G (EF-G) on the ribosome at the conditions of multiple turnover. In the present work, we have reanalyzed the mechanism of action of thiostrepton. Results obtained by biochemical and fast kinetic techniques show that thiostrepton binding to the ribosome does not interfere with factor binding or with single-round GTP hydrolysis. Rather, the antibiotic inhibits the function of EF-G in subsequent steps, including release of inorganic phosphate from EF-G after GTP hydrolysis, tRNA translocation, and the dissociation of the factor from the ribosome, thereby inhibiting the turnover reaction. Structurally, thiostrepton interferes with EF-G footprints in the α-sarcin stem loop (A2660, A2662) located in domain VI of 23S rRNA. The results indicate that thiostrepton inhibits a structural transition of the 1067 region of 23S rRNA that is important for functions of EF-G after GTP hydrolysis.},\r\ncorrespondence_address1={Wintermeyer, W.; Institute of Molecular Biology, University of Witten/Herdecke, D-58448 Witten, Germany; email: winterme@uni-wh.de},\r\nissn={00278424},\r\ncoden={PNASA},\r\npubmed_id={10449736},\r\nlanguage={English},\r\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Direct crosslinking of the antitumor antibiotic sparsomycin, and its derivatives, to A2602 in the peptidyl transferase center of 23S-like rRNA within ribosome-tRNA complexes.\n \n \n \n \n\n\n \n Porse, B.; Kirillov, S.; Awayez, M.; Ottenheijm, H.; and Garrett, R.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 96(16): 9003-9008. 1999.\n cited By 44\n\n\n\n
\n\n\n\n \n \n $\"Direct$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Porse19999003,\r\nauthor={Porse, B.T. and Kirillov, S.V. and Awayez, M.J. and Ottenheijm, H.C.J. and Garrett, R.A.},\r\ntitle={Direct crosslinking of the antitumor antibiotic sparsomycin, and its derivatives, to A2602 in the peptidyl transferase center of 23S-like rRNA within ribosome-tRNA complexes},\r\njournal={Proceedings of the National Academy of Sciences of the United States of America},\r\nyear={1999},\r\nvolume={96},\r\nnumber={16},\r\npages={9003-9008},\r\ndoi={10.1073/pnas.96.16.9003},\r\nnote={cited By 44},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033529799&doi=10.1073%2fpnas.96.16.9003&partnerID=40&md5=d927b3176e9467e98dc5e272ab07ae58},\r\naffiliation={RNA Regulation Centre, Institute of Molecular Biology, University of Copenhagen, Sølvgade 83H, DK1307 Copenhagen K, Denmark; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, 188350 Gatchina, St. Petersburg, Russian Federation; Organon International, P.O. Box 20, 5340 BH Oss, Netherlands},\r\nabstract={The antitumor antibiotic sparsomycin is a universal and potent inhibitor of peptide bond formation and selectively acts on several human tumors. It binds to the ribosome strongly, at an unknown site, in the presence of an N- blocked donor tRNA substrate, which it stabilizes on the ribosome. Its site of action was investigated by inducing a crosslink between sparsomycin and bacterial, archaeal, and eukaryotic ribosomes complexed with P-site-bound tRNA, on irradiating with low energy ultraviolet light (at 365 nm). The crosslink was localized exclusively to the universally conserved nucleotide A2602 within the peptidyl transferase loop region of 23S-like rRNA by using a combination of a primer extension approach, RNase H fragment analysis, and crosslinking with radioactive [ 125 I]phenol-alanine-sparsomycin. Crosslinking of several sparsomycin derivatives, modified near the sulfoxy group, implicated the modified uracil residue in the rRNA crosslink. The yield of the antibiotic crosslink was weak in the presence of deacylated tRNA and strong in the presence of an N-blocked P-site-bound tRNA, which, as was shown earlier, increases the accessibility of A2602 on the ribosome. We infer that both A2602 and its induced conformational switch are critically important both for the peptidyl transfer reaction and for antibiotic inhibition. This supposition is reinforced by the observation that other antibiotics that can prevent peptide bond formation in vitro inhibit, to different degrees, formation of the crosslink.},\r\nauthor_keywords={[ 125 I] phenol-alanine-sparsomycin;  RNase H analysis;  Sparsomycin-tRNA crosslink},\r\ncorrespondence_address1={Garrett, R.A.; RNA Regulation Centre, Institute of Molecular Biology, University of Copenhagen, Solvgade 83H, DK1307 Copenhagen K, Denmark; email: garrett@mermaid.molbio.ku.dk},\r\nissn={00278424},\r\ncoden={PNASA},\r\npubmed_id={10430885},\r\nlanguage={English},\r\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Peptidyl transferase antibiotics perturb the relative positioning of the 3'-terminal adenosine of P/P'-site-bound tRNA and 23S rRNA in the ribosome.\n \n \n \n \n\n\n \n Kirillov, S.; Porse, B.; and Garrett, R.\n\n\n \n\n\n\n RNA, 5(8): 1003-1013. 1999.\n cited By 25\n\n\n\n
\n\n\n\n \n \n $\"Peptidyl$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Kirillov19991003,\r\nauthor={Kirillov, S.V. and Porse, B.T. and Garrett, R.A.},\r\ntitle={Peptidyl transferase antibiotics perturb the relative positioning of the 3'-terminal adenosine of P/P'-site-bound tRNA and 23S rRNA in the ribosome},\r\njournal={RNA},\r\nyear={1999},\r\nvolume={5},\r\nnumber={8},\r\npages={1003-1013},\r\ndoi={10.1017/S1355838299990568},\r\nnote={cited By 25},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032818296&doi=10.1017%2fS1355838299990568&partnerID=40&md5=c7eeb8b76ab2e68ee58b8e18ac36bb82},\r\naffiliation={RNA Regulation Centre, Institute of Molecular Biology, University of Copenhagen, Sølvgade 83H, DK 1307 Copenhagen, Denmark; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, 188350 Gatchina, St. Petersburg, Russian Federation},\r\nabstract={A range of antibiotic inhibitors that act within the peptidyl transferase center of the ribosome were examined for their capacity to perturb the relative positioning of the 3' end of P/P'-site-bound tRNA and the Escherichia coli ribosome. The 3'-terminal adenosines of deacylated tRNA and N-Ac-Phe-tRNA were derivatized at the 2 position with an azido group and the tRNAs were cross-linked to the ribosome on irradiation with ultraviolet light at 365 nm. The cross-links were localized on the rRNA within extended versions of three previously characterized 23S rRNA fragments F1', F2', and F4' at nucleotides C2601/A2602, U2584/U2585 (F1'), U2506 (F2'), and A2062/C2063 (F4'). Each of these nucleotides lies within the peptidyl transferase loop region of the 23S rRNA. Cross-links were also formed with ribosomal proteins L27 (strong) and L33 (weak), as shown earlier. The antibiotics sparsomycin, chloramphenicol, the streptogramins pristinamycin IA and IIA, gougerotin, lincomycin, and spiramycin were tested for their capacity to alter the identities or yields of each of the cross-links. Although no new cross-links were detected, each of the drugs produced major changes in cross-linking yields, mainly decreases, at one or more rRNA sites but, with the exception of chloramphenicol, did not affect cross-linking to the ribosomal proteins. Moreover, the effects were closely similar for both deacylated and N-Ac-Phe-tRNAs, indicating that the drugs selectively perturb the 3' terminus of the tRNA. The strongest decreases in the rRNA cross-links were observed with pristinamycin IIA and chloramphenicol, which correlates with their both producing complex chemical footprints on 23S rRNA within E. coli ribosomes. Furthermore, gougerotin and pristinamycin IA strongly increased the yields of fragments F2' (U2506) and F4' (U2062/C2063), respectively. The results obtained with an RNAse H approach correlate well with primer extension data implying that cross-linking occurs primarily to the bases. Both sets of data are also consistent with the results of earlier rRNA footprinting experiments on antibiotic-ribosome complexes. It is concluded that the antibiotics perturb the relative positioning of the 3' end of the P/P'-site-bound tRNA and the peptidyl transferase loop region of 23S rRNA.},\r\nauthor_keywords={Antibiotics;  Azido-adenosine;  Peptidyl transferase;  tRNA-ribosome cross- links},\r\ncorrespondence_address1={Garrett, R.A.; RNA Regulation Centre, Institute of Molecular Biology, University of Copenhagen, Solvgade 83H, DK 1307 Copenhagen K, Denmark; email: garrett@mermaid.molbio.ku.dk},\r\nissn={13558382},\r\ncoden={RNARF},\r\npubmed_id={10445875},\r\nlanguage={English},\r\nabbrev_source_title={RNA},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n A range of antibiotic inhibitors that act within the peptidyl transferase center of the ribosome were examined for their capacity to perturb the relative positioning of the 3' end of P/P'-site-bound tRNA and the Escherichia coli ribosome. The 3'-terminal adenosines of deacylated tRNA and N-Ac-Phe-tRNA were derivatized at the 2 position with an azido group and the tRNAs were cross-linked to the ribosome on irradiation with ultraviolet light at 365 nm. The cross-links were localized on the rRNA within extended versions of three previously characterized 23S rRNA fragments F1', F2', and F4' at nucleotides C2601/A2602, U2584/U2585 (F1'), U2506 (F2'), and A2062/C2063 (F4'). Each of these nucleotides lies within the peptidyl transferase loop region of the 23S rRNA. Cross-links were also formed with ribosomal proteins L27 (strong) and L33 (weak), as shown earlier. The antibiotics sparsomycin, chloramphenicol, the streptogramins pristinamycin IA and IIA, gougerotin, lincomycin, and spiramycin were tested for their capacity to alter the identities or yields of each of the cross-links. Although no new cross-links were detected, each of the drugs produced major changes in cross-linking yields, mainly decreases, at one or more rRNA sites but, with the exception of chloramphenicol, did not affect cross-linking to the ribosomal proteins. Moreover, the effects were closely similar for both deacylated and N-Ac-Phe-tRNAs, indicating that the drugs selectively perturb the 3' terminus of the tRNA. The strongest decreases in the rRNA cross-links were observed with pristinamycin IIA and chloramphenicol, which correlates with their both producing complex chemical footprints on 23S rRNA within E. coli ribosomes. Furthermore, gougerotin and pristinamycin IA strongly increased the yields of fragments F2' (U2506) and F4' (U2062/C2063), respectively. The results obtained with an RNAse H approach correlate well with primer extension data implying that cross-linking occurs primarily to the bases. Both sets of data are also consistent with the results of earlier rRNA footprinting experiments on antibiotic-ribosome complexes. It is concluded that the antibiotics perturb the relative positioning of the 3' end of the P/P'-site-bound tRNA and the peptidyl transferase loop region of 23S rRNA.\n

\n\n\n

\n \n\n \n \n \n \n \n \n UV-induced modifications in the peptidyl transferase loop of 23S rRNA dependent on binding of the streptogramin B antibiotic, pristinamycin IA.\n \n \n \n \n\n\n \n Porse, B.; Kirillov, S.; Awayez, M.; and Garrett, R.\n\n\n \n\n\n\n RNA, 5(4): 585-595. 1999.\n cited By 18\n\n\n\n
\n\n\n\n \n \n $\"UV-induced$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Porse1999585,\r\nauthor={Porse, B.T. and Kirillov, S.V. and Awayez, M.J. and Garrett, R.A.},\r\ntitle={UV-induced modifications in the peptidyl transferase loop of 23S rRNA dependent on binding of the streptogramin B antibiotic, pristinamycin IA},\r\njournal={RNA},\r\nyear={1999},\r\nvolume={5},\r\nnumber={4},\r\npages={585-595},\r\ndoi={10.1017/S135583829998202X},\r\nnote={cited By 18},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032899549&doi=10.1017%2fS135583829998202X&partnerID=40&md5=82773b948cc1b6cfbfb3af9cde92e109},\r\naffiliation={RNA Regulation Centre, Institute of Molecular Biology, University of Copenhagen, Copenhagen, Denmark; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, St. Petersburg, Russian Federation; RNA Regulation Centre, Institute of Molecular Biology, University of Copenhagen, Sølvgade 83H, DK1307 Copenhagen K, Denmark},\r\nabstract={The naturally occurring streptogramin B antibiotic, pristinamycin IA, which inhibits peptide elongation, can produce two modifications in 23S rRNA when bound to the Escherichia coli 70S ribosome and irradiated at 365 m. Both drug-induced effects map to highly conserved nucleotides within the functionally important peptidyl transferase loop of 23S rRNA at positions m 2 A2503/Ψ2504 and G2061/A2062. The modification yields are influenced strongly, and differentially, by P-site-bound tRNA and strongly by some of the peptidyl transferase antibiotics tested, with chloramphenicol producing a shift in the latter modification to A2062/C2063. Pristinamycin IA can also produce a modification on binding to deproteinized, mature 23S rRNA, at position U2500/C2501. The same modification occurs on an ~37-nt fragment, encompassing positions ~2496-2532 of the peptidyl transferase loop that was excised from the mature rRNA using RNAse. H. In contrast, no antibiotic- induced effects were observed on in vitro T7 transcripts of full-length 23S rRNA, domain V, or on a fragment extending from positions ~2496-2566, which indicates that one or more posttranscriptional modifications within the sequence Cm-C-U-C-G-m 2 A-Ψ-G 2505 are important for pristinamycin IA binding and/or the antibiotic-dependent modification of 23S rRNA.},\r\nauthor_keywords={23S rRNA;  Peptidyl transferase;  Pristinamycin IA;  RNase H analysis;  rRNA modifications;  Streptogramin B-ribosome interaction},\r\ncorrespondence_address1={Garrett, R.A.; RNA Regulation Centre, Institute of Molecular Biology, University of Copenhagen, Solvgade 83H, DK1307 Copenhagen K, Denmark; email: garrett@mermaid.molbio.ku.dk},\r\nissn={13558382},\r\ncoden={RNARF},\r\npubmed_id={10199574},\r\nlanguage={English},\r\nabbrev_source_title={RNA},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1998\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n Damage to the transforming growth factor TGF-beta type II receptor gene and microsatellite instability in carcinoma cells of the gastrointestinal tract [Povrezhdeniia gena retseptora tipa II transformiruiushchego faktora rosta TGF-beta i mikrosatellitnaia nestabil'nost' genoma v kletkakh kartsinom zheludochno-kishechnogo trakta.].\n \n \n \n \n\n\n \n Vostriukhina, O.; Nikiforova, I.; Shtam, T.; Kantorov, S.; Kovalev, V.; Vasil'ev, S.; Pozharisskii, K.; and Lantsov, V.\n\n\n \n\n\n\n Voprosy onkologii, 44(6): 667-671. 1998.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Damage$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Vostriukhina1998667,\r\nauthor={Vostriukhina, O.A. and Nikiforova, I.F. and Shtam, T.A. and Kantorov, S.L. and Kovalev, V.K. and Vasil'ev, S.V. and Pozharisskii, K.M. and Lantsov, V.A.},\r\ntitle={Damage to the transforming growth factor TGF-beta type II receptor gene and microsatellite instability in carcinoma cells of the gastrointestinal tract [Povrezhdeniia gena retseptora tipa II transformiruiushchego faktora rosta TGF-beta i mikrosatellitnaia nestabil'nost' genoma v kletkakh kartsinom zheludochno-kishechnogo trakta.]},\r\njournal={Voprosy onkologii},\r\nyear={1998},\r\nvolume={44},\r\nnumber={6},\r\npages={667-671},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032235323&partnerID=40&md5=8109709665be565adff9034a57cb1126},\r\naffiliation={B.P. Konstantinov Nuclear Physics Institute, Russian Academy of Sciences, St. Petersburg, Russian Federation},\r\nabstract={In order to compare the frequency of damage to the transforming growth factor TGF-beta receptor type II gene (RII gene) and microsatellite instability (MIN) in oncogenesis of sporadic and hereditary cancer of gastrointestinal tract (GIT), 4 groups of carcinomas were analyzed. They included sporadic gastric (GC), family gastric (FGC), sporadic colorectal (CC) and hereditary nonpolyposis colorectal (HNPCC) carcinomas having appropriate clinical and pathological characteristics. Each group consisted of two types of carcinomas, one of them showing MIN. The RII gene damage occurred in 89% of GC (8 cases out of 9), 86% of CC (6 out of 7), 71% of FGC (5 out of 7), 50% of HNPCC (3 out of 6) for carcinomas coupled with MIN, whereas only in 6% (1 out of 18) of GC and 5% (1 out of 22) of CC for carcinomas without MIN. No damage to RII gene was found in the cases of hereditary carcinomas which did not show MIN though the number of cases analyzed was not sufficient for final conclusions (3 cases of FGC and 3 HNPCC). The data revealed a correlation between the MIN phenotype and mutations in RII gene both for sporadic (p < 0.001) and for hereditary (p < 0.02) cases. For all 4 groups the frequency of RII gene damage was found for early and advanced carcinomas. This suggests that the deficiency of TGF-beta receptor complex in both sporadic and hereditary carcinomas of GIT is revealed at early stages of tumor development and consequently may be responsible for tumor progression. The correlation between RII gene damages and MIN in GIT carcinoma cells suggests that genetic change predetermined the neoplasia of colorectal and gastric epithelium and partially overlapped for both sporadic and hereditary cases.},\r\ncorrespondence_address1={Vostriukhina, O.A.},\r\nissn={05073758},\r\npubmed_id={10087960},\r\nlanguage={Russian},\r\nabbrev_source_title={Vopr Onkol},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Microsatellite instability of genome in cells of sporadic and hereditary carcinoma of the gastrointestinal tract [Mikrosatellitnaia nestabil'nost' genoma v kletkakh sporadicheskikh i nasledstvennykh kartsinom zheludochno-kishechnogo trakta.].\n \n \n \n \n\n\n \n Vostriukhina, O.; Nikiforova, I.; Shtam, T.; Kantorov, S.; Tutaev, K.; Shumakov, A.; Komissarova, S.; Kalinovskii, V.; Vasil'ev, S.; and Kovalev, V.\n\n\n \n\n\n\n Voprosy onkologii, 44(5): 509-514. 1998.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Microsatellite$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Vostriukhina1998509,\r\nauthor={Vostriukhina, O.A. and Nikiforova, I.F. and Shtam, T.A. and Kantorov, S.L. and Tutaev, K.I. and Shumakov, A.R. and Komissarova, S.V. and Kalinovskii, V.P. and Vasil'ev, S.V. and Kovalev, V.K.},\r\ntitle={Microsatellite instability of genome in cells of sporadic and hereditary carcinoma of the gastrointestinal tract [Mikrosatellitnaia nestabil'nost' genoma v kletkakh sporadicheskikh i nasledstvennykh kartsinom zheludochno-kishechnogo trakta.]},\r\njournal={Voprosy onkologii},\r\nyear={1998},\r\nvolume={44},\r\nnumber={5},\r\npages={509-514},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032246181&partnerID=40&md5=98a5bc4c2b4667fd6911b1b0e7b83321},\r\naffiliation={B.P. Konstantinov Institute of Nuclear Physics, Russian Academy of Sciences., Russian Federation},\r\nabstract={Microsatellite instability (MIN) of human genome, i.e. instability of very short (1-5 nt) DNA tandem repeats, points to a deficiency in the mismatch repair system (MMR). To investigate the role of MMR in sporadic and hereditary carcinogenesis in the gastrointestinal tract, four types of carcinomas were compared: sporadic (GC), familial (FGC) gastric carcinoma, sporadic colorectal (CC) and hereditary nonpolyposis colorectal (HNPCC) carcinoma. No significant difference in MIN frequency was found between GC (9 out of 27) (33%) and CC (7 out of 29) (24%). In hereditary carcinoma group, MIN occurrence appeared 2-3 times as high: FGC in 7 out of 10 (70%) and HNPCC in 6 out of 8 patients (75%). No significant differences were recorded in MIN occurrence at early and later stages of the disease in all groups. Therefore, it can be suggested that disorders in the MMR develop at earlier stages of carcinogenesis and may be responsible for tumor progression.},\r\ncorrespondence_address1={Vostriukhina, O.A.},\r\nissn={05073758},\r\npubmed_id={9884704},\r\nlanguage={Russian},\r\nabbrev_source_title={Vopr Onkol},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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

\n

\n \n 1997\n \n \n (2)\n \n \n

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\n \n \n

\n \n\n \n \n \n \n \n \n Purpuromycin: An antibiotic inhibiting tRNA aminoacylation.\n \n \n \n \n\n\n \n Kirillov, S.; Vitali, L.; Goldstein, B.; Monti, F.; Semenkov, Y.; Makhno, V.; Ripa, S.; Pon, C.; and Gualerzi, C.\n\n\n \n\n\n\n RNA, 3(8): 905-913. 1997.\n cited By 27\n\n\n\n
\n\n\n\n \n \n $\"Purpuromycin:$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Kirillov1997905,\r\nauthor={Kirillov, S. and Vitali, L.A. and Goldstein, B.P. and Monti, F. and Semenkov, Y. and Makhno, V. and Ripa, S. and Pon, C.L. and Gualerzi, C.O.},\r\ntitle={Purpuromycin: An antibiotic inhibiting tRNA aminoacylation},\r\njournal={RNA},\r\nyear={1997},\r\nvolume={3},\r\nnumber={8},\r\npages={905-913},\r\nnote={cited By 27},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030753165&partnerID=40&md5=3ab611344e578c15f2b6ab4b909c8014},\r\naffiliation={Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC), Italy; Lepetit Research Center, 21040 Gerenzano (VA), Italy; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, 188350 Gathina, Russian Federation},\r\nabstract={Purpuromycin, an antibiotic produced by Actinoplanes lanthinogenes, had been reported previously to inhibit protein synthesis. In the present report, we demonstrate that the mechanism of action of this antibiotic is quite novel in that it binds with fairly high affinity to all tRNAs, inhibiting their acceptor capacity. Although more than one molecule of purpuromycin is bound to each tRNA molecule, the inhibitory activity of this antibiotic was found to be selective for the tRNA acceptor function; in fact, after the aminoacylation step, purpuromycin was found to affect none of the other tested functions of tRNA (interaction with the ribosomal P- and A-sites and interaction with translation factors). Accordingly, purpuromycin was found to inhibit protein synthesis only when translation depended on the aminoacylation of tRNA and not when the system was supplemented with pre- formed aminoacyl-tRNAs. Because purpuromycin did not interfere with the ATP- PP(1) exchange reaction of the synthetase or with the initial interaction of the enzyme with its tRNA substrate, the basis for the inhibition of aminoacylation is presumably the formation of a nonproductive synthetase- tRNA complex in the presence of purpuromycin in which the tRNA is unable to be charged with the corresponding amino acid.},\r\nauthor_keywords={Aminoacyl-tRNA synthetase;  Antibiotics;  Protein synthesis;  tRNA},\r\ncorrespondence_address1={Gualerzi, C.O.; Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC), Italy; email: gualerzi@cambio.unicam.it},\r\nissn={13558382},\r\ncoden={RNARF},\r\npubmed_id={9257649},\r\nlanguage={English},\r\nabbrev_source_title={RNA},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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

\n\n\n

\n \n\n \n \n \n \n \n \n Movement of the 3'-end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n FEBS Letters, 406(3): 223-233. 1997.\n cited By 44\n\n\n\n
\n\n\n\n \n \n $\"Movement$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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\n\n\n\n\n\n

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

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\n \n \n

\n \n\n \n \n \n \n \n \n Peptidyl transferase and the movement of transfer RNA across the escherichia cou rffiosome.\n \n \n \n \n\n\n \n Wower, J.; Kirillov, S.; Wower, I.; Hixson, S.; and Zimmcrmann, R.\n\n\n \n\n\n\n FASEB Journal, 10(6): A1369. 1996.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Peptidyl$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Wower1996,\r\nauthor={Wower, J. and Kirillov, S.V. and Wower, I. and Hixson, S.S. and Zimmcrmann, R.A.},\r\ntitle={Peptidyl transferase and the movement of transfer RNA across the escherichia cou rffiosome},\r\njournal={FASEB Journal},\r\nyear={1996},\r\nvolume={10},\r\nnumber={6},\r\npages={A1369},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33749152111&partnerID=40&md5=ab686eb39b321a95a546547ebdea4d3e},\r\naffiliation={University of Massachusetts, Amherst, MA 01003, United States},\r\nabstract={The 3'-terminus of tRNA plays an essential role in tRNA-ribosome interactions and formation of the peptide bond. We have traced its movement across the E. coli ribosome during the elongation cycle of translation using photoreactive tRNA probes in which the 3' terminal adenosine was substituted with 2-azidoadenosine. Photoreactive tRNA labeled five segments (F1-F5) of 23S rRNA and four 50S ribosomal proteins. The distribution of labeling was distinct for each of the three classical tRNA binding sites. A and P site-bound tRNA labeled segments Fl, F2 and F5 of the 23S rRNA and protein L27. E site bound-tRNA exclusively labeled protein L33. Analysis of photoaffinity labeling patterns as the tRNA is translocated from the A to the P site and then from the P to the E site revealed several new intermediate states of tRNA binding. To study the role of L27, the protein most frequently labeled by tRNA substituted with 2-azidoadenosine at the 3' end, we have constructed an E. coli strain in which the gene for L27 has been replaced by a kanamycinresistance marker. Deletion of protein L27 led to an impairment in the assembly of 50S ribosomal subunits, and both affected tRNA binding to the A site and the kinetics of peptide bond formation. Photoaffinity experiments suggested that some functions of protein L27 might be compensated by protein L33. We are using the data obtained from these studies to derive a dynamic model of tRNA-ribosome complexes during protein synthesis.},\r\ncorrespondence_address1={Wower, J.; University of Massachusetts, Amherst, MA 01003, United States},\r\nissn={08926638},\r\ncoden={FAJOE},\r\nlanguage={English},\r\nabbrev_source_title={FASEB J.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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

\n\n\n

\n \n\n \n \n \n \n \n \n The \"allosteric three-site model\" of elongation cannot be confirmed in a well-defined ribosome system from Escherichia coli.\n \n \n \n \n\n\n \n Semenkov, Y.; Rodnina, M.; and Wintermeyer, W.\n\n\n \n\n\n\n Proceedings of the National Academy of Sciences of the United States of America, 93(22): 12183-12188. 1996.\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

@ARTICLE{Semenkov199612183,\r\nauthor={Semenkov, Y.P. and Rodnina, M.V. and Wintermeyer, W.},\r\ntitle={The "allosteric three-site model" of elongation cannot be confirmed in a well-defined ribosome system from Escherichia coli},\r\njournal={Proceedings of the National Academy of Sciences of the United States of America},\r\nyear={1996},\r\nvolume={93},\r\nnumber={22},\r\npages={12183-12188},\r\ndoi={10.1073/pnas.93.22.12183},\r\nnote={cited By 67},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029959815&doi=10.1073%2fpnas.93.22.12183&partnerID=40&md5=7ce2c9fe57de69e5fe4b98a43a61e6e9},\r\naffiliation={St. Petersburg Nucl. Phys. Institute, Russian Academy of Sciences, 188350 Gatchina, Russian Federation; Institute of Molecular Biology, University of Witten/Herdecke, D-58448 Witten, Germany},\r\nabstract={For the functional role of the ribosomal tRNA exit (E) site, two different models have been proposed. It has been suggested that transient E-site binding of the tRNA leaving the peptidyl (P) site promotes elongation factor G (EF-G)-dependent translocation by lowering the energetic barrier of tRNA release [Lill, R., Robertson, J. M. &amp; Wintermeyer, W. (1989) EMBO J. 8, 3933-3938]. The alternative "allosteric three-site model" [Nierhaus, K. H. (1990) Biochemistry 29, 4997-5008] features stable, codon-dependent tRNA binding to the E site and postulates a coupling between E and aminoacyl (A) sites that regulates the tRNA binding affinity of the two sites in an anticooperative manner. Extending our testing of the two conflicting models, we have performed translocation experiments with fully active ribosomes programmed with heteropolymeric mRNA. The results confirm that the deacylated tRNA released from the P site is bound to the E site in a kinetically labile fashion, and that the affinity of binding, i.e., the occupancy of the E site, is increased by Mg2+ or polyamines. At conditions of high E-site occupancy in the posttranslocation complex, filling the A site with aminoacyl-tRNA had no influence on the E site, i.e., there was no detectable anticooperative coupling between the two sites, provided that second-round translocation was avoided by removing EF-G. On the basis of these results, which are entirely consistent with our previous results, we consider the allosteric three-site model of elongation untenable. Rather, as proposed earlier, the E site-bound state of the leaving tRNA is a transient intermediate and, as such, is a mechanistic feature of the classic two-state model of the elongating ribosome.},\r\nauthor_keywords={Elongation factor G;  Exit site;  Protein synthesis;  Translocation},\r\ncorrespondence_address1={Wintermeyer, W.; Institute of Molecular Biology, University of Witten/Herdecke, D-58448 Witten, Germany},\r\npublisher={National Academy of Sciences},\r\nissn={00278424},\r\ncoden={PNASA},\r\npubmed_id={8901554},\r\nlanguage={English},\r\nabbrev_source_title={Proc. Natl. Acad. Sci. U. S. A.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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

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\n \n\n \n \n \n \n \n \n Peptidyl transferase and beyond.\n \n \n \n \n\n\n \n Wower, J.; Wower, I.; Kirillov, S.; Rosen, K.; Hixson, S.; and Zimmermann, R.\n\n\n \n\n\n\n Biochemistry and cell biology = Biochimie et biologie cellulaire, 73(11-12): 1041-1047. 1995.\n cited By 32\n\n\n\n
\n\n\n\n \n \n $\"Peptidyl$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Wower19951041,\r\nauthor={Wower, J. and Wower, I.K. and Kirillov, S.V. and Rosen, K.V. and Hixson, S.S. and Zimmermann, R.A.},\r\ntitle={Peptidyl transferase and beyond.},\r\njournal={Biochemistry and cell biology = Biochimie et biologie cellulaire},\r\nyear={1995},\r\nvolume={73},\r\nnumber={11-12},\r\npages={1041-1047},\r\ndoi={10.1139/o95-111},\r\nnote={cited By 32},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029402925&doi=10.1139%2fo95-111&partnerID=40&md5=985aa6122fb85343ff3c1efcc18b0fc2},\r\naffiliation={Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, 01003-4505, United States},\r\nabstract={The peptidyl transferase center of the Escherichia coli ribosome encompasses a number of 50S-subunit proteins as well as several specific segments of the 23S rRNA. Although our knowledge of the role that both ribosomal proteins and 23S rRNA play in peptide bond formation has steadily increased, the location, organization, and molecular structure of the peptidyl transferase center remain poorly defined. Over the past 10 years, we have developed a variety of photoaffinity reagents and strategies for investigating the topography of tRNA binding sites on the ribosome. In particular, we have used the photoreactive tRNA probes to delineate ribosomal components in proximity to the 3' end of tRNA at the A, P, and E sites. In this article, we describe recent experiments from our laboratory which focus on the identification of segments of the 23S rRNA at or near the peptidyl transferase center and on the functional role of L27, the 50S-subunit protein most frequently labeled from the acceptor end of A- and P-site tRNAs. In addition, we discuss how these results contribute to a better understanding of the structure, organization, and function of the peptidyl transferase center.},\r\ncorrespondence_address1={Wower, J.},\r\nissn={08298211},\r\npubmed_id={8722019},\r\nlanguage={English},\r\nabbrev_source_title={Biochem. Cell Biol.},\r\ndocument_type={Review},\r\nsource={Scopus},\r\n}\r\n\r\n

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

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\n \n\n \n \n \n \n \n \n Structural elements of rpsO mRNA involved in the modulation of translational initiation and regulation of E.coli ribosomal protein S15.\n \n \n \n \n\n\n \n Philippe, C.; Bénard, L.; Eyermann, F.; Cachia, C.; Kirillov, S.; Portier, C.; Ehresmann, B.; and Ehresmann, C.\n\n\n \n\n\n\n Nucleic Acids Research, 22(13): 2538-2546. 1994.\n cited By 18\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

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@ARTICLE{Philippe19942538,\r\nauthor={Philippe, C. and Bénard, L. and Eyermann, F. and Cachia, C. and Kirillov, S.V. and Portier, C. and Ehresmann, B. and Ehresmann, C.},\r\ntitle={Structural elements of rpsO mRNA involved in the modulation of translational initiation and regulation of E.coli ribosomal protein S15},\r\njournal={Nucleic Acids Research},\r\nyear={1994},\r\nvolume={22},\r\nnumber={13},\r\npages={2538-2546},\r\ndoi={10.1093/nar/22.13.2538},\r\nnote={cited By 18},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0028179103&doi=10.1093%2fnar%2f22.13.2538&partnerID=40&md5=de1a6ed60790133c17461010ad111f4d},\r\naffiliation={UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084-Strasbourg cedex, France; Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005-Paris, France; Laboratoire de Biophysique, Faculté de Pharmacie, 7 boulevard Jeanne d'Arc, 21000 Dijon, France; Laboratory of Protein Biosynthesis, Nuclear Physic Institut, 188350 Gatchina, St Petersbourg district, Russian Federation},\r\nabstract={Previous experiments showed that S15 inhibits its own translation by binding to its mRNA in a region overlapping the ribosome loading site. This binding was postulated to stabilize a pseudoknot structure that exists in equilibrium with two stem-loops and to trap the ribosome on its mRNA loading site in a transitory state. In this study, we investigated the effect of mutations in the translational operator on: the binding of protein S15, the formation of the 30S/mRNA/tRNAMett ternary initiation complex, the ability of S15 to inhibit the formation of this ternary complex. The results were compared to in vivo expression and repression rates. The results show that (1) the pseudoknot is required for S15 recognition and translational control; (2) mRNA and 16S rRNA efficiently compete for S15 binding and 16S rRNA suppresses the ability of S15 to inhibit the formation of the active ternary complex; (3) the ribosome binds more efficiently to the pseudoknot than to the stem-loop; (4) sequences located between nucleotides 12 to 47 of the S15 coding phase enhances the efficiency of ribosome binding in vitro; this is correlated with enhanced in vivo expression and regulation rates. © 1994 Oxford University Press.},\r\nfunding_details={Centre National de la Recherche ScientifiqueUA1139, UPR 9002},\r\n}

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\n \n\n \n \n \n \n \n \n Purification of fMET-tRNAfMET by Fast Protein Liquid Chromatography.\n \n \n \n \n\n\n \n Rodnina, M.; Semenkov, Y.; and Wintermeyer, W.\n\n\n \n\n\n\n Analytical Biochemistry, 219(2): 380-381. 1994.\n cited By 44\n\n\n\n
\n\n\n\n \n \n $\"Purification$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Rodnina1994380,\r\nauthor={Rodnina, M.V. and Semenkov, Y.P. and Wintermeyer, W.},\r\ntitle={Purification of fMET-tRNAfMET by Fast Protein Liquid Chromatography},\r\njournal={Analytical Biochemistry},\r\nyear={1994},\r\nvolume={219},\r\nnumber={2},\r\npages={380-381},\r\ndoi={10.1006/abio.1994.1282},\r\nnote={cited By 44},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0028175534&doi=10.1006%2fabio.1994.1282&partnerID=40&md5=f2c6f8166a07026a42d59549b43aa789},\r\naffiliation={Univ Witten Herdecke, Inst Molek Biol, D 58448 Witten, Germany and Russian Acad Sci, Inst Nucl Phys, Gatchina 188350, Russia},\r\ncorrespondence_address1={Rodnina, M.V.},\r\nissn={00032697},\r\ncoden={ANBCA},\r\npubmed_id={8080098},\r\nlanguage={English},\r\nabbrev_source_title={Anal. Biochem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Interaction of deacylated tRNA with the P site of Escherichia coli ribosomes. Role of modified nucleotide in codon- anticodon interaction.\n \n \n \n \n\n\n \n Katunin, V.; Soboleva, N.; Makhno, V.; Sedelnikova, E.; Zhenodarova, S.; and Kirillov, S.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 28(1): 66-75. 1994.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Interaction$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Katunin199466,\r\nauthor={Katunin, V.I. and Soboleva, N.G. and Makhno, V.I. and Sedelnikova, E.A. and Zhenodarova, S.M. and Kirillov, S.V.},\r\ntitle={Interaction of deacylated tRNA with the P site of Escherichia coli ribosomes. Role of modified nucleotide in codon- anticodon interaction},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1994},\r\nvolume={28},\r\nnumber={1},\r\npages={66-75},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0028306695&partnerID=40&md5=68e2dad0fa12c3f6e33f54dd5db8fb1f},\r\naffiliation={St. Petersb. Nuclear Physics Inst., Russian Academy of Sciences, Gatchina 188350, Russian Federation},\r\nabstract={The method of anticodon loop replacement has been used to make derivatives of yeast tRNA((G(m)AAY(Phe)) with the substitution at the 37 position (tRNA(GAAA)(Phe)), and at both the anticodon (tRNA(GCAG)(Phe)) and the 37 position. A quantitative study of the interaction of various types of yeast deacylated tRNA: tRNA(G(m)(AAY)(Phe), tRNA(GAAA)(Phe), tRNA(GCAG)(Phe), and tRNA(-Y)(Phe) with the P site of the 70S ribosome·poly(U) complex was carried out at different Mg2+ concentrations and temperatures. The replacement of the Y base on the nonmodified adenosine decreases the interaction enthalphy from 39 to 24 kcal/mole, whereas the complete removal of the Y base reduces the interaction enthalpy to 16 kcal/mole. The replacement of the second letter of the anticodon (A) with cytosine leads to a drop in the enthalpy to 6 kcal/mole, which is typical of tRNA interaction with the P site in the absence of poly(U) the affinity of tRNA(-Y)(Phe) for the P site of the 70S ribosome is 5 times lower that the affinity of tRNA(G(m)AAY(Phe)) and tRNA(GCAG)(Phe). Thus, in the ribosome the mofified nucleotide not only stabilizes the codon-anticodon interaction owing to the stacking interaction with the stack of codon- anticodon bases, but also lowers the free energy of binding as a result of the interaction of the modified nucleotide itself with the hydrophobic center of the P site on the ribosome.},\r\ncorrespondence_address1={Katunin, V.I.; St. Petersb. Nuclear Physics Inst., Russian Academy of Sciences, Gatchina 188350, Russian Federation},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={8145756},\r\nlanguage={Russian},\r\nabbrev_source_title={MOL. BIOL.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Effect of the nucleotide-37 on the interaction of tRNAPhe with the P site of Escherichia coli ribosomes.\n \n \n \n \n\n\n \n Katunin, V.; Soboleva, N.; Mahkno, V.; Sedelnikova, E.; Zhenodarova, S.; and Kirillov, S.\n\n\n \n\n\n\n Biochimie, 76(1): 51-57. 1994.\n cited By 8\n\n\n\n
\n\n\n\n \n \n $\"Effect$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Katunin199451,\r\nauthor={Katunin, V. and Soboleva, N. and Mahkno, V. and Sedelnikova, E. and Zhenodarova, S. and Kirillov, S.},\r\ntitle={Effect of the nucleotide-37 on the interaction of tRNAPhe with the P site of Escherichia coli ribosomes},\r\njournal={Biochimie},\r\nyear={1994},\r\nvolume={76},\r\nnumber={1},\r\npages={51-57},\r\ndoi={10.1016/0300-9084(94)90062-0},\r\nnote={cited By 8},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0028213557&doi=10.1016%2f0300-9084%2894%2990062-0&partnerID=40&md5=28e38efb03ea6c49c3f74fdc2487ab60},\r\naffiliation={Petersburg Nuclear Physics Institute, Russian Academy of Science, 188350 Gatchina, Leningrad Region, Russian Federation; Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, 142292 Puschino, Moscow Region, Russian Federation},\r\nabstract={The method of anticodon loop replacement has been used to make derivatives of yeast tRNAPhe with the substitution at position 37 (tRNAGAAAPhe) and at the anticodon(tRNAGCAGPhe). A quantitative study of the interaction of various types of deacylated yeast tRNAPhe (tRNA+YPhe, tRNAGAAAPhe, tRNA-yPhe) with the P site of the [70S ribosome*poly(U)]-complex was carried out at different Mg2+ concentrations and temperatures. The presence and nature of the nucleotide situated at the 3′-end of the anticodon are essential for such interaction in E coli ribosomes. Replacement of thee Y base with the unmodified adenosine decreases the interation enthalpy from 39 kcal/mol to 24 kcal/mol, whereas its removal reduces the interaction enthalpy to 16 kcal/mol. Replacement of the second anticodon nucleotide, adenosine, with cytosine further reduces the enthalphy to 6 kcal/mol, which is typical of tRNA-P site interaction in the absence of poly(U). In the absence of poly(U) the affinity of tRNA-YPhe for the P site of the 70S ribosome is five times lower than the affinity of tRNA+YPhe or tRNAGCAGPhe. Thus, in the ribosome the modified nucleotide stabilizes the codon-anticodon interaction through its stacking interaction with the codon-anticodon base stack. In addition, this decreases the free energy of binding as a result of the interaction of the modified nucleotide itself with the hydrophobic center of the P site. © 1994.},\r\nauthor_keywords={70S ribosome;  codon-anticodon interaction;  Escherichia coli;  modified nucleotide;  tRNAPhe},\r\ncorrespondence_address1={Katunin, V.; Petersburg Nuclear Physics Institute, Russian Academy of Science, 188350 Gatchina, Leningrad Region, Russian Federation},\r\nissn={03009084},\r\ncoden={BICMB},\r\npubmed_id={7518255},\r\nlanguage={English},\r\nabbrev_source_title={Biochimie},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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

\n

\n \n 1992\n \n \n (2)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Puromycin reaction for the A site-bound peptidyl-tRNA.\n \n \n \n \n\n\n \n Semenkov, Y.; Shapkina, T.; Makhno, V.; and Kirillov, S.\n\n\n \n\n\n\n FEBS Letters, 296(2): 207-210. 1992.\n cited By 36\n\n\n\n
\n\n\n\n \n \n $\"Puromycin$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Semenkov1992207,\r\nauthor={Semenkov, Yu. and Shapkina, T. and Makhno, V. and Kirillov, S.},\r\ntitle={Puromycin reaction for the A site-bound peptidyl-tRNA},\r\njournal={FEBS Letters},\r\nyear={1992},\r\nvolume={296},\r\nnumber={2},\r\npages={207-210},\r\ndoi={10.1016/0014-5793(92)80380-Y},\r\nnote={cited By 36},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0026548529&doi=10.1016%2f0014-5793%2892%2980380-Y&partnerID=40&md5=00cc8ce7c3bb426712820f1f692b1b7e},\r\naffiliation={B.P. Konstantinov Petersburg Nuclear Physics Institute, Academy of Sciences, 188350 Gatchina, Saint Petersburg district, USSR},\r\nabstract={AcPhe 2 -tRNA Phe synthesized in 70S ribosomes after consecutive binding of AcPhe-tRNA Phe at the P sites and EF-Tu-directed binding of Phe-tRNA Phe at the A sites is able to react quantitatively with puromycin in the absence of EF-G. A detailed study of the kinetics of the puromycin reaction, its comparison with that of spontaneous translocation, the use of antibiotic viomycin as an effective inhibitor of spontaneous translocation revealed that, besides spontaneous translocation, this peptidyl-tRNA could react with puromycin being located at the A site. This leads to the conclusion that the transpeptidation reaction per se triggers conformational changes in the ribosomal complex bringing the 3′-end of a newly synthesized peptidyl-tRNA nearer to the peptidyl-site of the peptidyltransferase center. This is detected functionally as the ability of such an A site bound peptidyl-tRNA to react with puromycin. This reaction is highly pronounced at elevated (25°C) temperature but can be hardly detected at 0°C. © 1992.},\r\nauthor_keywords={70S Ribosome;  A site;  Puromycin reaction;  Spontaneous translocation;  Viomycin},\r\ncorrespondence_address1={Kirillov, S.},\r\nissn={00145793},\r\ncoden={FEBLA},\r\npubmed_id={1733779},\r\nlanguage={English},\r\nabbrev_source_title={FEBS Lett.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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

\n\n\n

\n \n\n \n \n \n \n \n \n Puromycin reaction of the A-site bound peptidyl-tRNA.\n \n \n \n \n\n\n \n Semenkov, Y.; Shapkina, T.; and Kirillov, S.\n\n\n \n\n\n\n Biochimie, 74(5): 411-417. 1992.\n cited By 27\n\n\n\n
\n\n\n\n \n \n $\"Puromycin$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Semenkov1992411,\r\nauthor={Semenkov, Y.P. and Shapkina, T.G. and Kirillov, S.V.},\r\ntitle={Puromycin reaction of the A-site bound peptidyl-tRNA},\r\njournal={Biochimie},\r\nyear={1992},\r\nvolume={74},\r\nnumber={5},\r\npages={411-417},\r\ndoi={10.1016/0300-9084(92)90080-X},\r\nnote={cited By 27},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0026665859&doi=10.1016%2f0300-9084%2892%2990080-X&partnerID=40&md5=d9336bcea930fd757f3c941fc5f4b8a1},\r\naffiliation={BP Konstantinov Nuclear Physics Institute, Russian Academy of Sciences, 188350 Gatchina, Leningrad Region, Russia},\r\nabstract={AcPhe 2 -tRNA Phe which appears in ribosomes after consecutive binding of AcPhe-tRNA Phe at the P sites and EF-Tu-directed binding of Phe-tRNA Phe at the A sites is able to react quantitatively with puromycin in the absence of EF-G. One could readily explain this fact to be the consequence of spontaneous translocation. However, a detailed study of kinetics of puromycin reaction carried out with the use of viomycin (inhibitor of translocation) and the P-site test revealed that, apart from spontaneous translocation, this peptidyl-tRNA could react with puromycin being located at the A site. This leads to the conclusion that the transpeptidation reaction triggers conformational changes in the A-site ribosomal complex bringing the 3′-end of a newly synthesized peptidyl-tRNA nearer to the peptidyl site of peptidyltransferase center. This is detected functionally as a highly pronounced ability of such a peptidyl-tRNA to react with puromycin. © 1992.},\r\nauthor_keywords={70S ribosome;  A site;  puromycin;  translocation;  viomycin},\r\ncorrespondence_address1={Semenkov, Y.P.},\r\nissn={03009084},\r\ncoden={BICMB},\r\npubmed_id={1322179},\r\nlanguage={English},\r\nabbrev_source_title={Biochimie},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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

\n

\n \n 1989\n \n \n (1)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Interaction of tRNA with the A and P sites of rabbit‐liver 80S ribosomes and their 40S subunits.\n \n \n \n \n\n\n \n RODNINA, M.; EL'SKAYA, A.; SEMENKOV, Y.; and KIRILLOV, S.\n\n\n \n\n\n\n European Journal of Biochemistry, 185(3): 563-568. 1989.\n cited By 21\n\n\n\n
\n\n\n\n \n \n $\"Interaction$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{RODNINA1989563,\r\nauthor={RODNINA, M.V. and EL'SKAYA, A.V. and SEMENKOV, Y.P. and KIRILLOV, S.V.},\r\ntitle={Interaction of tRNA with the A and P sites of rabbit‐liver 80S ribosomes and their 40S subunits},\r\njournal={European Journal of Biochemistry},\r\nyear={1989},\r\nvolume={185},\r\nnumber={3},\r\npages={563-568},\r\ndoi={10.1111/j.1432-1033.1989.tb15150.x},\r\nnote={cited By 21},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0024377256&doi=10.1111%2fj.1432-1033.1989.tb15150.x&partnerID=40&md5=6637a2e9b8a2e5a5d5ea92991c84839c},\r\naffiliation={Institute of Molecular Biology and Genetics, Kiev; B. P. Konstantinov Nuclear Physics Institute, Leningrad},\r\nabstract={The interaction between tRNA and rabbit liver 80S ribosomes and 40S subunits was studied using a nitrocellulose membrane filtration technique. Binding of the different tRNA forms (aminoacyl‐, peptidyl‐ or deacylated) to poly(U)‐programmed 40S subunits and 80S ribosomes was found to be a cooperative process. The association constants of AcPhe‐tRNAPhe for the A and P sites of 80S ribosomes and the cooperativity constant were measured at different temperature and Mg2+ concentration. The AcPhe‐tRNAPhe association constant for the P site was shown to be between 2 × 107 M−1 and 2 × 108 M−1 at 25–37°C and 5–20 mM Mg2+, while the affinity for the A site was 10–100‐fold lower. The cooperativity constant was shown to decrease with the increase of incubation temperature and the decrease of Mg2+ concentration. The affinity of AcPhe‐tRNAPhe for the A site of 80S ribosomes was shown to depend upon the codon specificity of tRNA at the P site. The cooperativity of the tRNA interaction with 80S ribosomes was suggested to be mostly contributed by the association with the 40S subunit and result from the correct codon‐anticodon pairing at the P site. The data presented imply a codon‐anticodon interaction at the P site of eukaryotic 80S ribosomes. Copyright © 1989, Wiley Blackwell. All rights reserved},\r\ncorrespondence_address1={EL'SKAYA, A.V.; Institute of Molecular Biology and Genetics, Kiev, 150},\r\nissn={00142956},\r\npubmed_id={2591377},\r\nlanguage={English},\r\nabbrev_source_title={Eur. J. Biochem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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

\n

\n \n 1988\n \n \n (2)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n A modified method of isolation of \"tight\" 70S ribosomes from Escherichia coli highly active at different stages of the elongation cycle [Modifitsirovannyǐ sposob polucheniia \"tight\" 70S ribosom iz Escherichia coli, vysokoaktivnykh v otdel'nykh stadiiakh tsikla élongatsii.].\n \n \n \n \n\n\n \n Makhno, V.; Peshin, N.; Semenkov, I.; and Kirillov, S.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 22(3): 670-679. 1988.\n cited By 22\n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Makhno1988670,\r\nauthor={Makhno, V.I. and Peshin, N.N. and Semenkov, I.P. and Kirillov, S.V.},\r\ntitle={A modified method of isolation of "tight" 70S ribosomes from Escherichia coli highly active at different stages of the elongation cycle [Modifitsirovannyǐ sposob polucheniia "tight" 70S ribosom iz Escherichia coli, vysokoaktivnykh v otdel'nykh stadiiakh tsikla élongatsii.]},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1988},\r\nvolume={22},\r\nnumber={3},\r\npages={670-679},\r\nnote={cited By 22},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0024008492&partnerID=40&md5=bf3149ceb87758712f297126de60198e},\r\nabstract={The functional activity of the wide-spread "tight" 70S ribosomes is usually equal to 55-80%. We show here that the inactive fraction of this type of ribosomes is virtually blocked by residual endogenous RNA's. These RNA's are shown to be removable by introducing an additional stage in the isolation procedure including: 1. short heating (15 min, 37 degrees C) of "tight" 70S under dissociation conditions, i. e. in a buffer containing 3 mM MgCl2 and 200 mM NH4Cl; 2. washing off endogenous RNA's on a sucrose density gradient in the same buffer; 3. final selection of purified "tight" 70S on the sucrose gradient containing 5 mM MgCl2 and 50 mM NH4Cl. "Tight" 70S ribosomes isolated by such a procedure are 90-100% active with respect to tRNA binding (including the factor-dependent one), peptide bond synthesis and translocation.},\r\ncorrespondence_address1={Makhno, V.I.},\r\nissn={00268984},\r\npubmed_id={3054495},\r\nlanguage={Russian},\r\nabbrev_source_title={Mol Biol (Mosk)},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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

\n\n\n

\n \n\n \n \n \n \n \n \n Number of tRNA binding sites on 80 S ribosomes and their subunits.\n \n \n \n \n\n\n \n Rodnina, M.; El'skaya, A.; Semenkov, Y.; and Kirillov, S.\n\n\n \n\n\n\n FEBS Letters, 231(1): 71-74. 1988.\n cited By 14\n\n\n\n
\n\n\n\n \n \n $\"Number$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Rodnina198871,\r\nauthor={Rodnina, M.V. and El'skaya, A.V. and Semenkov, Yu.P. and Kirillov, S.V.},\r\ntitle={Number of tRNA binding sites on 80 S ribosomes and their subunits},\r\njournal={FEBS Letters},\r\nyear={1988},\r\nvolume={231},\r\nnumber={1},\r\npages={71-74},\r\ndoi={10.1016/0014-5793(88)80705-1},\r\nnote={cited By 14},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0024284248&doi=10.1016%2f0014-5793%2888%2980705-1&partnerID=40&md5=8cea7310dc9df12b2f9b19fecf00524a},\r\naffiliation={Institute of Molecular Biology and Genetics, USSR Academy of Sciences, ul. Zabolotnogo, 24, Kiev 252627 USSR; Konstantinov Nuclear Physics Institute, USSR Academy of Sciences, Gatchina, Leningrad district 188350, Russian Federation},\r\nabstract={The ability of rabbit liver ribosomes and their subunits to form complexes with different forms of tRNA Phe (aminoacyl-, peptidyl- and deacylated) was studied using the nitrocellulose membrane filtration technique. The 80 S ribosomes were shown to have two binding sites for aminoacyl- or peptidyl-tRNA and three binding sites for deacylated tRNA. The number of tRNA binding sites on 80 S ribosomes or 40 S subunits is constant at different Mg 2+ concentrations (5-20 mM). Double reciprocal or Scatchard plot analysis indicates that the binding of Ac-Phe-tRNA Phe to the ribosomal sites is a cooperative process. The third site on the 80 S ribosome is formed by its 60 S subunit, which was shown to have one codon-independent binding site specific for deacylated tRNA. © 1988.},\r\nauthor_keywords={40 S subunit;  60 S subunit;  80 S ribosome;  tRNA binding site},\r\ncorrespondence_address1={Rodnina, M.V.},\r\nissn={00145793},\r\ncoden={FEBLA},\r\npubmed_id={3360133},\r\nlanguage={English},\r\nabbrev_source_title={FEBS Lett.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1987\n \n \n (1)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Effect of the concentration ratio of bi- and monovalent ions on the functional activity of 30S ribosome subunits of Escherichia coli [Vliianie sootnosheniia kontsentratsii dvukh- i odnovalentnykh kationov na funktsional'nuiu aktivnost' 30S subchastits ribosom Escherichia coli.].\n \n \n \n \n\n\n \n Zhuchenko, O.; Semenkov, I.; and Kirillov, S.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 21(1): 266-274. 1987.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Effect$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Zhuchenko1987266,\r\nauthor={Zhuchenko, O.P. and Semenkov, I.P. and Kirillov, S.V.},\r\ntitle={Effect of the concentration ratio of bi- and monovalent ions on the functional activity of 30S ribosome subunits of Escherichia coli [Vliianie sootnosheniia kontsentratsii dvukh- i odnovalentnykh kationov na funktsional'nuiu aktivnost' 30S subchastits ribosom Escherichia coli.]},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1987},\r\nvolume={21},\r\nnumber={1},\r\npages={266-274},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0023073531&partnerID=40&md5=7a363df02ccaf461f3d1901a10e89c39},\r\nabstract={Experiments on poly(U)-dependent binding of Phe-tRNAPhe to 30S subunits revealed the existence of a critical [Mg2+]/[NH4+] ratio in a medium (approximately 0.05-0.1) with respect to the binding capacity of subunits. If the ratio is greater than the critical one, 30S subunits undergo reversible inactivation even at the highest Mg2+ concentrations (up to 20 mM). The stronger is the deviation from the [Mg2+]/[NH4+] value = 0.05-0.1, the greater are both the rate and extent of such an inactivation. Two sites for tRNA in initially active 30S subunits have been shown to be inactivated in an interdependent way. On the other hand, a progressive decrease of [Mg2+]/[NH4+] ratio in a medium (from the value of 0.05 and lower) does not produce inactivation, but rather results in reduced affinity constants of Phe-tRNAPhe for active sites of 30S subunits.},\r\ncorrespondence_address1={Zhuchenko, O.P.},\r\nissn={00268984},\r\npubmed_id={3553898},\r\nlanguage={Russian},\r\nabbrev_source_title={Mol Biol (Mosk)},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1986\n \n \n (1)\n \n \n

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\n \n \n

\n \n\n \n \n \n \n \n \n Extension of watson’s model for the elongation cycle of protein biosynthesis.\n \n \n \n \n\n\n \n Kirillov, S.; and Semenkov, Y.\n\n\n \n\n\n\n Journal of Biomolecular Structure and Dynamics, 4(2): 263-269. 1986.\n cited By 20\n\n\n\n
\n\n\n\n \n \n $\"Extension$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Kirillov1986263,\r\nauthor={Kirillov, S.V. and Semenkov, Y.P.},\r\ntitle={Extension of watson’s model for the elongation cycle of protein biosynthesis},\r\njournal={Journal of Biomolecular Structure and Dynamics},\r\nyear={1986},\r\nvolume={4},\r\nnumber={2},\r\npages={263-269},\r\ndoi={10.1080/07391102.1986.10506345},\r\nnote={cited By 20},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0023001328&doi=10.1080%2f07391102.1986.10506345&partnerID=40&md5=55580d48ab70422dc90c5d7fcd58c2b9},\r\naffiliation={B. P. Konstantinov Nuclear Physics Institute of the USSR Academy of Sciences, Gatchina, Leningrad, 188350, Russian Federation},\r\nabstract={The scheme for the elongation cycle of protein biosynthesis is proposed based on modern quantitative data on the interactions of mRNA and different functional forms of tRNAwith 70S ribosomes and their 30S and 50S subunits. This scheme takes into account recently discovered third ribosomal (E) site with presumable exit function. The E site is introduced into 70S ribosome by its 50S subunit, the codon-anticodon interaction does not take place at the E site, and the affinity of tRNA for the E site is considerably lower than that for the P site. On the other hand, the P and A sites are located mainly on a 30S subunit, the codon-anticodon interactions being realized on both these sites. An mRNA molecule is placed exclusively on a 30S subunit where it makes U-tum. The proposed scheme does not contradict to any data but includes all main postulates of the initial Watson’s model (J. D. Watson, Bull Soc. Chim. Biol 46, 1399 (1964), and is considered as a natural extension of the later according to modem experimental data. © Taylor & Francis Group, LLC.},\r\nissn={07391102},\r\npubmed_id={3271444},\r\nlanguage={English},\r\nabbrev_source_title={J. Biomol. Struct. Dyn.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1985\n \n \n (2)\n \n \n

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\n \n \n

\n \n\n \n \n \n \n \n \n 40 S subunits from rat liver ribosomes contain two codon-dependent sites for transfer RNA.\n \n \n \n \n\n\n \n Semenkov, Y.; Kirillov, S.; and Stahl, J.\n\n\n \n\n\n\n FEBS Letters, 193(1): 105-108. 1985.\n cited By 15\n\n\n\n
\n\n\n\n \n \n $\"40$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Semenkov1985105,\r\nauthor={Semenkov, Yu.P. and Kirillov, S.V. and Stahl, J.},\r\ntitle={40 S subunits from rat liver ribosomes contain two codon-dependent sites for transfer RNA},\r\njournal={FEBS Letters},\r\nyear={1985},\r\nvolume={193},\r\nnumber={1},\r\npages={105-108},\r\ndoi={10.1016/0014-5793(85)80088-0},\r\nnote={cited By 15},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0022373758&doi=10.1016%2f0014-5793%2885%2980088-0&partnerID=40&md5=ac122dfb7967b0dbce00b2b2f6cde85d},\r\naffiliation={B.P. Konstantinov Nuclear Physics Institute, USSR Academy of Sciences, Gatchina, Leningrad district 188350, Russian Federation; Central Institute of Molecular Biology, Department of Cell Physiology, GDR Academy of Sciences, 1115 Berlin-Buch, Germany},\r\nabstract={40 S subunits from rat liver ribosomes are able to bind, after heat activation, two molecules of either Phe-tRNA phe , Ac-Phe-tRNA phe or deacylated tRNA phe . Addition of 60 S subunits to the quaternary complex 40 S·poly(U)·(Phe-tRNA phe ) 2 results in quantitative formation of (Phe) 2 -tRNA phe . This indicates that the two binding sites for tRNA on 40 S subunits should be considered as the constituent of P and A sites of 80 S ribosomes. © 1985.},\r\nauthor_keywords={40 S subunit;  Association constant;  Binding site;  Eukaryotic ribosome;  Poly(U);  tRNA},\r\ncorrespondence_address1={Stahl, J.; Central Institute of Molecular Biology, Department of Cell Physiology, GDR Academy of Sciences, 1115 Berlin-Buch, Germany},\r\nissn={00145793},\r\ncoden={FEBLA},\r\npubmed_id={4065329},\r\nlanguage={English},\r\nabbrev_source_title={FEBS Lett.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The effect of GTP hydrolysis and transpeptidation on the arrangement of aminoacyl-tRNA at the A-site of Escherichia coli 70 S ribosomes.\n \n \n \n \n\n\n \n Vladimirov, S.; Graifer, D.; Karpova, G.; Semenkov, Y.; Makhno, V.; and Kirillov, S.\n\n\n \n\n\n\n FEBS Letters, 181(2): 367-372. 1985.\n cited By 11\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Vladimirov1985367,\r\nauthor={Vladimirov, S.N. and Graifer, D.M. and Karpova, G.G. and Semenkov, Yu.P. and Makhno, V.I. and Kirillov, S.V.},\r\ntitle={The effect of GTP hydrolysis and transpeptidation on the arrangement of aminoacyl-tRNA at the A-site of Escherichia coli 70 S ribosomes},\r\njournal={FEBS Letters},\r\nyear={1985},\r\nvolume={181},\r\nnumber={2},\r\npages={367-372},\r\ndoi={10.1016/0014-5793(85)80294-5},\r\nnote={cited By 11},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0021960322&doi=10.1016%2f0014-5793%2885%2980294-5&partnerID=40&md5=6e836e46953170e55e9e2f84949d0984},\r\naffiliation={Institute of Bioorganic Chemistry, Siberian Division, the USSR Academy of Sciences, Novosibirsk, 630090, Russian Federation; B.P. Konstantinov Nuclear Physics Institute, the USSR Academy of Sciences, Gatchina, Leningrad District 188350, Russian Federation},\r\nabstract={From the affinity labelling of 70 S ribosomes with a photoreactive derivative of Phe-tRNA phe bearing an arylazido group on guanine residues, it has been found that different sets of ribosomal proteins are labelled in the course of three successive steps of EF-Tu-dependent binding of aminoacyl-tRNA derivative at the A-site. Proteins S5, S7, S8, S16, S17, L9, L14, L15 and L24 were labelled before GTP hydrolysis; proteins S5, S7, S9, S11, S14, S18, S19, S21, L9, L21 and L29 - after GTP hydrolysis; proteins S2, S5, S7, S21, L11 and L23 - after GTP hydrolysis and transpeptidation. © 1985.},\r\nauthor_keywords={A-site;  Aminoacyl-tRNA derivative Ribosomal protein;  Elongation factor Tu;  Photoaffinity labelling;  Ribosome},\r\ncorrespondence_address1={Vladimirov, S.N.; Institute of Bioorganic Chemistry, Siberian Division, the USSR Academy of Sciences, Novosibirsk, 630090, Russian Federation},\r\nissn={00145793},\r\ncoden={FEBLA},\r\npubmed_id={2578985},\r\nlanguage={English},\r\nabbrev_source_title={FEBS Lett.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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

\n

\n \n 1984\n \n \n (3)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Transfer RNA-binding to ribosomes (Review).\n \n \n \n \n\n\n \n Kirillov, S.; and Semenkov, Y.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 18(5): 1249-1263. 1984.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Transfer$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Kirillov19841249,\r\nauthor={Kirillov, S.V. and Semenkov, Y.P.},\r\ntitle={Transfer RNA-binding to ribosomes (Review)},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1984},\r\nvolume={18},\r\nnumber={5},\r\npages={1249-1263},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0021499203&partnerID=40&md5=f6640915ede43c2469839eed89dce1e9},\r\naffiliation={B.P. Konstantinov Leningrad Institute of Nuclear Physics, Academy of Sciences of the USSR, Gatchina, Leningrad Region},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={6390173},\r\nlanguage={Russian},\r\nabbrev_source_title={MOL. BIOL.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Influence of antibiotic edeine on tRNA binding to the A, P and E sites of Escherichia coli ribosomes.\n \n \n \n \n\n\n \n Semenkov, Y.; Makhno, V.; Makarov, E.; and Kirillov, S.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 18(5): 1348-1351. 1984.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Influence$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Semenkov19841348,\r\nauthor={Semenkov, Y.P. and Makhno, V.I. and Makarov, E.M. and Kirillov, S.V.},\r\ntitle={Influence of antibiotic edeine on tRNA binding to the A, P and E sites of Escherichia coli ribosomes},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1984},\r\nvolume={18},\r\nnumber={5},\r\npages={1348-1351},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0021719141&partnerID=40&md5=3bfa308b6b620907cc84bced3d0eba9c},\r\naffiliation={B.P. Konstantinov Leningrad Institute of Nuclear Physics, Academy of Sciences of the USSR, Gatchina, Leningrad Region},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={6209550},\r\nlanguage={Russian},\r\nabbrev_source_title={MOL. BIOL.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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\n \n\n \n \n \n \n \n \n Binding of yeast phenylalanine tRNA with ribosomes of Escherichia coli. Effect of removal of the modified base adjacent to the 3' end of the anticodon in codon-anticodon interaction.\n \n \n \n \n\n\n \n Katunin, V.; and Kirillov, S.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 18(6): 1486-1496. 1984.\n cited By 3\n\n\n\n
\n\n\n\n \n \n $\"Binding$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Katunin19841486,\r\nauthor={Katunin, V.I. and Kirillov, S.V.},\r\ntitle={Binding of yeast phenylalanine tRNA with ribosomes of Escherichia coli. Effect of removal of the modified base adjacent to the 3' end of the anticodon in codon-anticodon interaction},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1984},\r\nvolume={18},\r\nnumber={6},\r\npages={1486-1496},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0021678975&partnerID=40&md5=c96dad869d64a620059c901a7204455e},\r\naffiliation={B.P. Konstantinov Institute of Nuclear Physics, Academy of Sciences of the USSR, Gatchina, Leningrad Region},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={6084167},\r\nlanguage={Russian},\r\nabbrev_source_title={MOL. BIOL.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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

\n

\n \n 1983\n \n \n (3)\n \n \n

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\n \n \n

\n \n\n \n \n \n \n \n \n Quantitative study of interaction of deacylated tRNA with Escherichia coli ribosomes. Role of 50 S subunits in formation of the E site.\n \n \n \n \n\n\n \n Kirillov, S.; Makarov, E.; and Semenkov, Y.\n\n\n \n\n\n\n FEBS Letters, 157(1): 91-94. 1983.\n cited By 81\n\n\n\n
\n\n\n\n \n \n $\"Quantitative$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Kirillov198391,\r\nauthor={Kirillov, S.V. and Makarov, E.M. and Semenkov, Yu.P.},\r\ntitle={Quantitative study of interaction of deacylated tRNA with Escherichia coli ribosomes. Role of 50 S subunits in formation of the E site},\r\njournal={FEBS Letters},\r\nyear={1983},\r\nvolume={157},\r\nnumber={1},\r\npages={91-94},\r\ndoi={10.1016/0014-5793(83)81122-3},\r\nnote={cited By 81},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020534216&doi=10.1016%2f0014-5793%2883%2981122-3&partnerID=40&md5=ab1383a0ed2da9252e2777bd1c40ddb0},\r\naffiliation={B.P. Konstantinov Nuclear Physics Institute, USSR Academy of Sciences, Gatchina, Leningrad district 188350, Russian Federation},\r\nabstract={The 30 S subunit contains 2 sites for tRNA binding (Phe-tRNA, AcPhe-tRNA, tRNA Phe OH ) with the functional properties of D and A sites of the 70 S ribosome after attachment of 50 S subunit. The third (E) site specific for deacylated tRNA is introduced into 70 S ribosome by its 50 S subunit. The E-site binding of tRNA Phe OH is not sensitive to either tetracycline and edeine, and practically codon-independent. The affinity constant of tRNA Phe OH for the E site is 2-3 orders of magnitude lower than that for the D site. © 1983.},\r\nauthor_keywords={Antibiotic, tetracycline, edeine;  Deacylated tRNA-ribosome interaction;  Ribosome, exit site;  Site distribution, between subunits},\r\ncorrespondence_address1={Kirillov, S.V.; B.P. Konstantinov Nuclear Physics Institute, USSR Academy of Sciences, Gatchina, Leningrad district 188350, Russian Federation},\r\nissn={00145793},\r\ncoden={FEBLA},\r\npubmed_id={6345196},\r\nlanguage={English},\r\nabbrev_source_title={FEBS Lett.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Correlation between biological activity of 30 S subunits of escherichia coli ribosomes and their conformation changes revealed by optical mixing spectroscopy.\n \n \n \n \n\n\n \n Dobitchin, P.; Kirillov, S.; Noskin, V.; and Peshin, N.\n\n\n \n\n\n\n Biophysical Chemistry, 17(2): 165-169. 1983.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Correlation$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Dobitchin1983165,\r\nauthor={Dobitchin, P.D. and Kirillov, S.V. and Noskin, V.A. and Peshin, N.N.},\r\ntitle={Correlation between biological activity of 30 S subunits of escherichia coli ribosomes and their conformation changes revealed by optical mixing spectroscopy},\r\njournal={Biophysical Chemistry},\r\nyear={1983},\r\nvolume={17},\r\nnumber={2},\r\npages={165-169},\r\ndoi={10.1016/0301-4622(83)80010-6},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020586988&doi=10.1016%2f0301-4622%2883%2980010-6&partnerID=40&md5=6fb641fb17efc9c7066ad7e97957131c},\r\naffiliation={B.P. Konstantinov Nuclear Physics Institute, the Academy of Sciences, the U.S.S.R., Gatchina, Leningrad District 188350, Russian Federation},\r\nabstract={Spectral analysis of light scattered from solutions of 30 S subunits was performed by the method of regularization of the inverse spectral problem. The subunits observed under ionic conditions which preserved their biological activity (200 mM NH4Cl at 1 mM MgCl2) revealed a monodisperse pattern of scattering with diffusion constant D = (1.83 ± 0.10) × 10-7 cm2 s. The polydispersity and compaction of 30 S subunits were observed under inactivation ionic conditions (30 mM NH4Cl at 1 mM MgCl2). The number of compacted particles correlates with the irreversible loss of biological activity, the ability of 30 S subunits to bind specific tRNA. © 1983.},\r\nauthor_keywords={(E.coli ribosome);  Conformational change;  Optical mixing spectroscopy},\r\ncorrespondence_address1={Dobitchin, P.D.; B.P. Konstantinov Nuclear Physics Institute, the Academy of Sciences, the U.S.S.R., Gatchina, Leningrad District 188350, Russian Federation},\r\nissn={03014622},\r\ncoden={BICIA},\r\npubmed_id={6340749},\r\nlanguage={English},\r\nabbrev_source_title={Biophys. Chem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Localization of 5' and 3' ends of the ribosome-bound segment of template polynucleotides by immune electron microscopy.\n \n \n \n \n\n\n \n Evstafieva, A.; Shatsky, I.; Bogdanov, A.; Semenkov, Y.; and Vasiliev, V.\n\n\n \n\n\n\n The EMBO journal, 2(5): 799-804. 1983.\n cited By 36\n\n\n\n
\n\n\n\n \n \n $\"Localization$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Evstafieva1983799,\r\nauthor={Evstafieva, A.G. and Shatsky, I.N. and Bogdanov, A.A. and Semenkov, Y.P. and Vasiliev, V.D.},\r\ntitle={Localization of 5' and 3' ends of the ribosome-bound segment of template polynucleotides by immune electron microscopy.},\r\njournal={The EMBO journal},\r\nyear={1983},\r\nvolume={2},\r\nnumber={5},\r\npages={799-804},\r\nnote={cited By 36},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0021092757&partnerID=40&md5=51835e04e6144e4fa5321f82bd08277a},\r\naffiliation={A.N. Belozersky Laboratory of Molecular Biology and Bioorganic Chemistry, Moscow State University., Russian Federation},\r\nabstract={Poly(U) with an average chain length of 40-70 nucleotides was modified at the 5'- or 3'-terminal residues with 2,4-dinitrophenyl derivatives. The modified poly(U) was used to form 30S.poly(U) or 70S.poly(U).Phe-tRNA complexes. Localization of the 5' and 3' ends of the template polynucleotide on the 30S subunit and the 70S ribosome was performed by immune electron microscopy using antibodies against dinitrophenyl haptens. The 5' and 3' ends of poly(U) (putative entry and exit sites of the message) were found in the same region both on the 30S subunit and the 70S ribosome. They were located on the dorsal side of the 30S subunit between the head and the body near the groove bordering the side ledge (platform). Comparison of the size of this region with the possible length of the polynucleotide chain covered by the ribosome allowed us to suggest that the message makes a 'U-turn" (or forms a 'loop') as it passes through the ribosome.},\r\ncorrespondence_address1={Evstafieva, A.G.},\r\nissn={02614189},\r\npubmed_id={11584834},\r\nlanguage={English},\r\nabbrev_source_title={EMBO J.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1982\n \n \n (7)\n \n \n

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\n \n\n \n \n \n \n \n \n Non-exclusion principle of Ac-Phe-tRNA Phe interaction with the donor and acceptor sites of Escherichia coli ribosomes.\n \n \n \n \n\n\n \n Kirillov, S.; and Semenkov, Y.\n\n\n \n\n\n\n FEBS Letters, 148(2): 235-238. 1982.\n cited By 33\n\n\n\n
\n\n\n\n \n \n $\"Non-exclusion$ Paper\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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@ARTICLE{Kirillov1982235,\r\nauthor={Kirillov, S.V. and Semenkov, Yu.P.},\r\ntitle={Non-exclusion principle of Ac-Phe-tRNA Phe interaction with the donor and acceptor sites of Escherichia coli ribosomes},\r\njournal={FEBS Letters},\r\nyear={1982},\r\nvolume={148},\r\nnumber={2},\r\npages={235-238},\r\ndoi={10.1016/0014-5793(82)80814-4},\r\nnote={cited By 33},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020446681&doi=10.1016%2f0014-5793%2882%2980814-4&partnerID=40&md5=32cf73ccf60978926cb5e720196f3c9e},\r\naffiliation={B.P. Konstantinov Nuclear Physics Institute, USSR Academy of Sciences, Gatchina, Leningrad district 188350, Russian Federation},\r\nauthor_keywords={Ac-Phe-tRNA Phe Non-exclusion principle;  Elongation;  Ribosome acceptor site;  Ribosome donor site;  tRNA-ribosome interaction},\r\ncorrespondence_address1={Kirillov, S.V.; B.P. Konstantinov Nuclear Physics Institute, USSR Academy of Sciences, Gatchina, Leningrad district 188350, Russian Federation},\r\nissn={00145793},\r\ncoden={FEBLA},\r\npubmed_id={6759165},\r\nlanguage={English},\r\nabbrev_source_title={FEBS Lett.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Kinetic aspects of tetracycline action on the acceptor (A) site of Escherichia coli ribosomes.\n \n \n \n \n\n\n \n Semenkov, Y.; Makarov, E.; Makhno, V.; and Kirillov, S.\n\n\n \n\n\n\n FEBS Letters, 144(1): 125-129. 1982.\n cited By 31\n\n\n\n
\n\n\n\n \n \n $\"Kinetic$ Paper\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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@ARTICLE{Semenkov1982125,\r\nauthor={Semenkov, Yu.P. and Makarov, E.M. and Makhno, V.I. and Kirillov, S.V.},\r\ntitle={Kinetic aspects of tetracycline action on the acceptor (A) site of Escherichia coli ribosomes},\r\njournal={FEBS Letters},\r\nyear={1982},\r\nvolume={144},\r\nnumber={1},\r\npages={125-129},\r\ndoi={10.1016/0014-5793(82)80584-X},\r\nnote={cited By 31},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020468152&doi=10.1016%2f0014-5793%2882%2980584-X&partnerID=40&md5=307251417cc69abf16bdbe62f2416744},\r\naffiliation={B.P. Konstantinov Nuclear Physics Institute, USSR, Academy of Sciences, Gatchina, Leningrad district 188350, Russian Federation},\r\ncorrespondence_address1={Semenkov, Yu.P.; B.P. Konstantinov Nuclear Physics Institute, USSR, Academy of Sciences, Gatchina, Leningrad district 188350, Russian Federation},\r\nissn={00145793},\r\ncoden={FEBLA},\r\npubmed_id={7049736},\r\nlanguage={English},\r\nabbrev_source_title={FEBS Lett.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Quantitative study of kanamycin action on different functions of Escherichia coli ribosomes.\n \n \n \n \n\n\n \n Semenkov, Y.; Katunin, V.; Makarov, E.; and Kirillov, S.\n\n\n \n\n\n\n FEBS Letters, 144(1): 121-124. 1982.\n cited By 5\n\n\n\n
\n\n\n\n \n \n $\"Quantitative$ Paper\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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@ARTICLE{Semenkov1982121,\r\nauthor={Semenkov, Yu.P. and Katunin, V.I. and Makarov, E.M. and Kirillov, S.V.},\r\ntitle={Quantitative study of kanamycin action on different functions of Escherichia coli ribosomes},\r\njournal={FEBS Letters},\r\nyear={1982},\r\nvolume={144},\r\nnumber={1},\r\npages={121-124},\r\ndoi={10.1016/0014-5793(82)80583-8},\r\nnote={cited By 5},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020383572&doi=10.1016%2f0014-5793%2882%2980583-8&partnerID=40&md5=028cf443b521cc36af0ae2044054c4f8},\r\naffiliation={B.P. Konstantinov Nuclear Physics Institute, USSR, Academy of Sciences, Gatchina, Leningrad district 188350, Russian Federation},\r\ncorrespondence_address1={Semenkov, Yu.P.; B.P. Konstantinov Nuclear Physics Institute, USSR, Academy of Sciences, Gatchina, Leningrad district 188350, Russian Federation},\r\nissn={00145793},\r\ncoden={FEBLA},\r\npubmed_id={7049735},\r\nlanguage={English},\r\nabbrev_source_title={FEBS Lett.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Study on the conformational state of Escherichia coli tRNA-Phe in solution by ESR-spectometry without modulation [Izuchenie konformatsionnoǐ situatsii v vodnykh rastvorakh spin-mechenoǐ tRNA-Phe iz Escherichia coli bezomduliatsionnym metodom EPR.].\n \n \n \n \n\n\n \n Bondarev, G.; Isaev-Ivanov, V.; Isaeva-Ivanova, L.; Kirillov, S.; and Kleǐner, A.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 16(2): 352-362. 1982.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Study$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Bondarev1982352,\r\nauthor={Bondarev, G.N. and Isaev-Ivanov, V.V. and Isaeva-Ivanova, L.S. and Kirillov, S.V. and Kleǐner, A.R.},\r\ntitle={Study on the conformational state of Escherichia coli tRNA-Phe in solution by ESR-spectometry without modulation [Izuchenie konformatsionnoǐ situatsii v vodnykh rastvorakh spin-mechenoǐ tRNA-Phe iz Escherichia coli bezomduliatsionnym metodom EPR.]},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1982},\r\nvolume={16},\r\nnumber={2},\r\npages={352-362},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020108887&partnerID=40&md5=737d07719caa6d071f7b656012d89f83},\r\nabstract={ESR-spectrometry without modulation of the magnetic field was used for registering the EST spectral line shape (with shape distortion about 0.1 percent) of spin-labeled Escherichia coli tRNAPhe. The analysis of line shape of two different spin-labels in position 8 (S4U) revealed that tRNAPhe in solution always exists as a mixture of at least two conformers, the equilibria between conformers being dependent on pH, concentration of magnesium and the biological state of tRNA (deacylated, aminoacyl- or peptidyl-tRNA). There are no large structural rearrangements upon aminoacylation or peptidylation of tRNA, the observed small changes of spectral line shape are due to the changes in conformational equilibria.},\r\ncorrespondence_address1={Bondarev, G.N.},\r\nissn={00268984},\r\npubmed_id={6175894},\r\nlanguage={Russian},\r\nabbrev_source_title={Mol Biol (Mosk)},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Study on conformational states of Escherichia coli tRNAPhe in solution by a modulation-free ESR-spectrometer.\n \n \n \n \n\n\n \n Bondarev, G.; Isaev-Ivanov, V.; Isaeva-Ivanova, L.; Kirillov, S.; Kleiner, A.; Lepekhin, A.; Odinzov, V.; and Fomichev, V.\n\n\n \n\n\n\n Nucleic Acids Research, 10(3): 1113-1126. 1982.\n cited By 2\n\n\n\n
\n\n\n\n \n \n $\"Study$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Bondarev19821113,\r\nauthor={Bondarev, G.N. and Isaev-Ivanov, V.V. and Isaeva-Ivanova, L.S. and Kirillov, S.V. and Kleiner, A.R. and Lepekhin, A.F. and Odinzov, V.B. and Fomichev, V.N.},\r\ntitle={Study on conformational states of Escherichia coli tRNAPhe in solution by a modulation-free ESR-spectrometer},\r\njournal={Nucleic Acids Research},\r\nyear={1982},\r\nvolume={10},\r\nnumber={3},\r\npages={1113-1126},\r\ndoi={10.1093/nar/10.3.1113},\r\nnote={cited By 2},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020480097&doi=10.1093%2fnar%2f10.3.1113&partnerID=40&md5=69e930e30c6b63173943f327db31e733},\r\naffiliation={B.P.Konstantinov Nuclear Physics Institute of Academy of Sciences of USSR, Gatchina, Leningrad district 188350, Russian Federation},\r\nabstract={A modulationfree Electron Spin Resonance spectrometer was used for the registration of spectral absorption lines of a spin-labeled Escherichia coli phenylalanine tRNA in solution with low (less than 0.1%) line shape distortion. The analysis of line shape of two different spin-labels introduced into position 8 revealed that phenylalanine tRNA in solution exists as a mixture of two conformers, the equilibria between conformers being dependent on pH, concentration of magnesium and functional state of tRNA (deacylated, aminoacylated or peptidylated). There are no overall structural rearrangements upon aminoacylation or peptidylation of tRNA. The observed small changes of spectral line shape can be assigned to shifts in conformational equilibria. © 1982 IRL Press Limited.},\r\ncorrespondence_address1={Bondarev, G.N.; B.P.Konstantinov Nuclear Physics Institute of Academy of Sciences of USSR, Gatchina, Leningrad district 188350, Russian Federation},\r\nissn={03051048},\r\ncoden={NARHA},\r\npubmed_id={6278435},\r\nlanguage={English},\r\nabbrev_source_title={Nucleic Acids Res.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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

\n\n\n

\n \n\n \n \n \n \n \n \n Relationship between the conformational change observed by the method of optical mixing spectroscopy and the biological activity of 30S ribosomal subunits from Escherichia coli.\n \n \n \n \n\n\n \n Dobychin, P.; Kirillov, S.; Noskin, V.; and Peshin, N.\n\n\n \n\n\n\n Molecular Biology, 16(3 I): 422-427. 1982.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Relationship$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Dobychin1982422,\r\nauthor={Dobychin, P.D. and Kirillov, S.V. and Noskin, V.A. and Peshin, N.N.},\r\ntitle={Relationship between the conformational change observed by the method of optical mixing spectroscopy and the biological activity of 30S ribosomal subunits from Escherichia coli},\r\njournal={Molecular Biology},\r\nyear={1982},\r\nvolume={16},\r\nnumber={3 I},\r\npages={422-427},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020422203&partnerID=40&md5=27357fc4acde1005344eda986db95cdc},\r\naffiliation={B.P. Konstantinov Leningrad Inst. Nucl. Phys., Acad. Sci. USSR, Gatchina},\r\nissn={00268933},\r\ncoden={MOLBB},\r\nlanguage={English},\r\nabbrev_source_title={MOL. BIOL.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Correlation between biological activity of 30S subunits of Escherichia coli ribosomes and their conformational changes revealed by mixing optical spectroscopy.\n \n \n \n \n\n\n \n Dobichin, P.; Kirillov, S.; Noskin, V.; and Peshin, N.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 16(3): 535-540. 1982.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Correlation$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Dobichin1982535,\r\nauthor={Dobichin, P.D. and Kirillov, S.V. and Noskin, V.A. and Peshin, N.N.},\r\ntitle={Correlation between biological activity of 30S subunits of Escherichia coli ribosomes and their conformational changes revealed by mixing optical spectroscopy},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1982},\r\nvolume={16},\r\nnumber={3},\r\npages={535-540},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0019996685&partnerID=40&md5=f74e012f0164fdbe43f13a4af3828ba4},\r\naffiliation={B.P. Konstantinov Inst. Nucl. Phys., Acad. Sci. USSR, Gatchina, Leningrad Reg., Russian Federation},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={7048066},\r\nlanguage={Russian},\r\nabbrev_source_title={MOL. BIOL.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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

\n

\n \n 1981\n \n \n (3)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Mechanism of codon-anticodon interaction in ribosomes. Interaction of aminoacyl-tRNA with 70S ribosomes in the absence of elongation factor EF-Tu and GTP [Mekhanizm kodon-antikodonnogo vsaimodeǐstviia v ribosomakh. Vzaimodeǐstvie aminoatsil-tRNA s 70S ribosomami Escherichia coli v otsutstvie faktora élongatsii EF-Tu i GTP.].\n \n \n \n \n\n\n \n Kemkhadze, K.; Odintsov, V.; Makhno, V.; Semenkov, I.; and Kirillov, S.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 15(4): 779-789. 1981.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Mechanism$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Kemkhadze1981779,\r\nauthor={Kemkhadze, K.S. and Odintsov, V.B. and Makhno, V.I. and Semenkov, I.P. and Kirillov, S.V.},\r\ntitle={Mechanism of codon-anticodon interaction in ribosomes. Interaction of aminoacyl-tRNA with 70S ribosomes in the absence of elongation factor EF-Tu and GTP [Mekhanizm kodon-antikodonnogo vsaimodeǐstviia v ribosomakh. Vzaimodeǐstvie aminoatsil-tRNA s 70S ribosomami Escherichia coli v otsutstvie faktora élongatsii EF-Tu i GTP.]},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1981},\r\nvolume={15},\r\nnumber={4},\r\npages={779-789},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0019589026&partnerID=40&md5=3d86002998938c1f0dba1c337dc846fc},\r\nabstract={Purified Phe-tRNAPhe revealed higher affinity to the donor (D) site of vacant 70S . poly(U) complex than to the acceptor (A) site, independent on Mg2+ concentration. As a result, in excess of ribosomes Phe-tRNAPhe binds exclusively to the D site. This was proved using the tests in the presence of tetracycline and puromycin. Preferential binding of Phe-tRNAPhe to the D site was used to measure equilibrium association constants of this interaction at different temperatures and Mg2+ concentrations. A large value of reaction enthalpy (ca. -26 Kcal/mole) was found.},\r\ncorrespondence_address1={Kemkhadze, K.S.},\r\nissn={00268984},\r\npubmed_id={6912382},\r\nlanguage={Russian},\r\nabbrev_source_title={Mol Biol (Mosk)},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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

\n\n\n

\n \n\n \n \n \n \n \n \n Mechanism of codon-anticodon interaction in ribosomes. Comparative study of interaction of Phe-tRNA Phe and N-acetyl-Phe-tRNA Phe with the donor site of Escherichia coli ribosomes.\n \n \n \n \n\n\n \n Kirillov, S.; Katunin, V.; and Semenkov, Y.\n\n\n \n\n\n\n FEBS Letters, 125(1): 15-19. 1981.\n cited By 12\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\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Kirillov198115,\r\nauthor={Kirillov, S.V. and Katunin, V.I. and Semenkov, Yu.P.},\r\ntitle={Mechanism of codon-anticodon interaction in ribosomes. Comparative study of interaction of Phe-tRNA Phe and N-acetyl-Phe-tRNA Phe with the donor site of Escherichia coli ribosomes},\r\njournal={FEBS Letters},\r\nyear={1981},\r\nvolume={125},\r\nnumber={1},\r\npages={15-19},\r\ndoi={10.1016/0014-5793(81)80986-6},\r\nnote={cited By 12},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0019875918&doi=10.1016%2f0014-5793%2881%2980986-6&partnerID=40&md5=77c90fc035ec0f4e9ba051a4cbc739b2},\r\naffiliation={B. P. Konstantinov Nuclear Physics Institute, USSR Academy of Sciences, Gatchina, Leningrad district 188350, Russian Federation},\r\ncorrespondence_address1={Kirillov, S.V.; B. P. Konstantinov Nuclear Physics Institute, USSR Academy of Sciences, Gatchina, Leningrad district 188350, Russian Federation},\r\nissn={00145793},\r\ncoden={FEBLA},\r\npubmed_id={7014251},\r\nlanguage={English},\r\nabbrev_source_title={FEBS Lett.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Quantitative study of the interaction of aminoacyl-tRNA with the a site of Escherichia coli ribosomes. Equilibrium and kinetic parameters of binding in the absence of EF-Tu factor and GTP.\n \n \n \n \n\n\n \n Kemkhadze, K.; Odintsov, V.; Semenkov, Y.; and Kirillov, S.\n\n\n \n\n\n\n FEBS Letters, 125(1): 10-14. 1981.\n cited By 15\n\n\n\n
\n\n\n\n \n \n $\"Quantitative$ Paper\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{Kemkhadze198110,\r\nauthor={Kemkhadze, K.Sh. and Odintsov, V.B. and Semenkov, Yu.P. and Kirillov, S.V.},\r\ntitle={Quantitative study of the interaction of aminoacyl-tRNA with the a site of Escherichia coli ribosomes. Equilibrium and kinetic parameters of binding in the absence of EF-Tu factor and GTP},\r\njournal={FEBS Letters},\r\nyear={1981},\r\nvolume={125},\r\nnumber={1},\r\npages={10-14},\r\ndoi={10.1016/0014-5793(81)80985-4},\r\nnote={cited By 15},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0019514267&doi=10.1016%2f0014-5793%2881%2980985-4&partnerID=40&md5=410ed076ccb45ec765aa99bd3d433a97},\r\naffiliation={B. P. Konstantinov Nuclear Physics Institute, USSR, Academy of Sciences, Gatchina, Leningrad District 188350, Russian Federation; I. S. Beritashvili Institute of Physiology, Academy of Sciences, Georgian SSR Tbilisi,, Russian Federation},\r\ncorrespondence_address1={Kemkhadze, K.Sh.; I. S. Beritashvili Institute of Physiology, Academy of Sciences, Georgian SSR Tbilisi,, Russian Federation},\r\nissn={00145793},\r\ncoden={FEBLA},\r\npubmed_id={7014250},\r\nlanguage={English},\r\nabbrev_source_title={FEBS Lett.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n\n\n\n

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

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\n \n 1980\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Comparative study of the interaction of polyuridylic acid with 30S subunits and 70S ribosomes of Escherichia coli.\n \n \n \n \n\n\n \n Katunin, V.; Semenkov, Y.; Makhno, V.; and Kirillov, S.\n\n\n \n\n\n\n Nucleic Acids Research, 8(2): 403-421. 1980.\n cited By 22\n\n\n\n
\n\n\n\n \n \n $\"Comparative$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Katunin1980403,\r\nauthor={Katunin, V.I. and Semenkov, Y.P. and Makhno, V.I. and Kirillov, S.V.},\r\ntitle={Comparative study of the interaction of polyuridylic acid with 30S subunits and 70S ribosomes of Escherichia coli},\r\njournal={Nucleic Acids Research},\r\nyear={1980},\r\nvolume={8},\r\nnumber={2},\r\npages={403-421},\r\ndoi={10.1093/nar/8.2.403},\r\nnote={cited By 22},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0018848986&doi=10.1093%2fnar%2f8.2.403&partnerID=40&md5=849e2d6525166d9a80380bab77fcdd7f},\r\naffiliation={B.P.Konstantinov Nuclear Physics Institute, Academy of Sciences of the USSR, Gatchina, Leningrad district 188350, Russian Federation},\r\nabstract={Fractionated polyuridylic acid with an average chain length of 55 nucleotides forms binary complexes with 30S subunits with a stoichiometry of I:I. These complexes are heterogeneous in stability. The more stable one is characterized by an association constant K 2 = 5.5×I0 9 M -I , and the less stable-by K I = IO 6 ×M -I , at 20 mM Mg 2+ , 200 mM NH + 4 and 0°C. The main reason for this heterogeneity is the presence or absence of the ribosomal protein SI in the subunits. Decrease of Mg 2+ concentration down to 5 mM hardly changes the K 2 values but reduction of the NH + 4 concentration to 50 mM results in a 25-fold increase of K 2 . Association constants K 2 for the stable complex, i.e. in the presence of SI protein, were measured at different temperatures ( 0 - 30°C ) and the thermodynamic parameters of binding ( δH°, δS°, δG° ) were determined.Analogous experiments were made with 70S ribosomes. K 2 values as well δH°, δS°, δG° appeared the same both for 30S and 70S ribosomes in all conditions examined. This is strong evidence that the 50s subunits do not contribute to the interaction of poly(U) with the complete 70S ribosomes. © 1980 IRL Press Limited.},\r\ncorrespondence_address1={Katunin, V.I.; B.P.Konstantinov Nuclear Physics Institute, Academy of Sciences of the USSR, Gatchina, Leningrad district 188350, Russian Federation},\r\nissn={03051048},\r\ncoden={NARHA},\r\npubmed_id={6999461},\r\nlanguage={English},\r\nabbrev_source_title={Nucleic Acids Res.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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

\n\n\n

\n \n\n \n \n \n \n \n \n Mechanism of codon-anticodon interaction in ribosomes. Direct functional evidence that isolated 30S subunits contain two codon-specific binding sites for transfer RNA.\n \n \n \n \n\n\n \n Kirillov, S.; Makhno, V.; and Semenkov, Y.\n\n\n \n\n\n\n Nucleic Acids Research, 8(1): 183-196. 1980.\n cited By 51\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

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@ARTICLE{Kirillov1980183,\r\nauthor={Kirillov, S.V. and Makhno, V.I. and Semenkov, Y.P.},\r\ntitle={Mechanism of codon-anticodon interaction in ribosomes. Direct functional evidence that isolated 30S subunits contain two codon-specific binding sites for transfer RNA},\r\njournal={Nucleic Acids Research},\r\nyear={1980},\r\nvolume={8},\r\nnumber={1},\r\npages={183-196},\r\ndoi={10.1093/nar/8.1.183},\r\nnote={cited By 51},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0019322015&doi=10.1093%2fnar%2f8.1.183&partnerID=40&md5=df00af9105d87fbedf871791f2e6762e},\r\naffiliation={B.P. Konstantinov Nuclear Physics Institute, Academy of Sciences of the USSR, Gatchina, Leningrad district 188350, Russian Federation},\r\nabstract={308 subunits were isolated capable to bind simultaneously two molecules of Phe-tRNAPhe (or N-Acetyl-Phe-tRNAPhe), both poly(U) dependent. The site with higher affinity to was identified as P site. tRNA binding to this site was not inhibited by low concentrations of tetracycline (2×10-5M) and, on the other hand, N-Acetyl-Phe-tRNAPhe, initially prebound to the 30S·poly(U) complex in the presence of tetraoycline, reacted with puromycin quantitatively after addition of 50S subunits. The site with lower affinity to tRNA revealed features of the A site: tetracycline fully inhibited the binding of both Phe-tRNAPhe and N-Acetyl-Phe-tRNAPhe. Binding of two molecules of Phe-tRNAPhe to the 30S·poly(U) complex followed by the addition of 50s subunits resulted in the formation of (Phe)2-tRNAPhe in 75-90% of the reassociated 70S ribosomes.These results prove that isolated 30S subunits contain two physically distinct centers for the binding of specific aminoacyl- (or peptidyl-) tRNA. Addition of 50S subunits results in the formatfon of whole 70S ribosomes with usual donor and acceptor sites. © 1980 IRL Press Limited.},\r\ncorrespondence_address1={Kirillov, S.V.; B.P. Konstantinov Nuclear Physics Institute, Academy of Sciences of the USSR, Gatchina, Leningrad district 188350, Russian Federation},\r\nissn={03051048},\r\ncoden={NARHA},\r\npubmed_id={6986612},\r\nlanguage={English},\r\nabbrev_source_title={Nucleic Acids Res.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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

\n\n\n

\n \n\n \n \n \n \n \n \n Mechanism of codon—anticodon interaction in ribosomes: Codon—anticodon interaction of aminoacyl-tRNA at the ribosomal donor site.\n \n \n \n \n\n\n \n Kirillov, S.; Kemkhadze, K.; Makarov, E.; Makhno, V.; Odintsov, V.; and Semenkov, Y.\n\n\n \n\n\n\n FEBS Letters, 120(2): 221-224. 1980.\n cited By 21\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\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{Kirillov1980221,\r\nauthor={Kirillov, S.V. and Kemkhadze, K.Sh. and Makarov, E.M. and Makhno, V.I. and Odintsov, V.B. and Semenkov, Yu.P.},\r\ntitle={Mechanism of codon—anticodon interaction in ribosomes: Codon—anticodon interaction of aminoacyl-tRNA at the ribosomal donor site},\r\njournal={FEBS Letters},\r\nyear={1980},\r\nvolume={120},\r\nnumber={2},\r\npages={221-224},\r\ndoi={10.1016/0014-5793(80)80302-4},\r\nnote={cited By 21},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0019316077&doi=10.1016%2f0014-5793%2880%2980302-4&partnerID=40&md5=82566c6c5d79765eab8509f0923bd77f},\r\naffiliation={B.P. Konstantinov Nuclear Physics Institute, USSR Academy of Sciences, Gatchina, Leningrad district, 188350; I.S. Beritashvili Institute of Physiology, Georgian SSR Academy of Sciences, Tbilisi},\r\ncorrespondence_address1={Kirillov, S.V.; B.P. Konstantinov Nuclear Physics Institute, USSR Academy of Sciences, Gatchina, Leningrad district, 188350},\r\nissn={00145793},\r\npubmed_id={6904302},\r\nlanguage={English},\r\nabbrev_source_title={FEBS Lett.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1979\n \n \n (4)\n \n \n

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\n \n\n \n \n \n \n \n \n Quantitative study of the interaction of polyuridylic acid with the 30S subparticles of Escherichia coli ribosomes.\n \n \n \n \n\n\n \n Kirillov, S.; Katunin, V.; Makhno, V.; and Semenkov Yu., P.\n\n\n \n\n\n\n Molecular Biology, 13(3 II): 525-530. 1979.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Quantitative$ 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

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@ARTICLE{Kirillov1979525,\r\nauthor={Kirillov, S.V. and Katunin, V.I. and Makhno, V.I. and Semenkov Yu., P.},\r\ntitle={Quantitative study of the interaction of polyuridylic acid with the 30S subparticles of Escherichia coli ribosomes},\r\njournal={Molecular Biology},\r\nyear={1979},\r\nvolume={13},\r\nnumber={3 II},\r\npages={525-530},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0018595269&partnerID=40&md5=731b609c370beb9af33b6d6f164edbd4},\r\naffiliation={B.P. Konstantinov Leningrad Inst. Nucl. Phys., Acad. Sci. USSR, Leningrad, Russian Federation},\r\nissn={00268933},\r\ncoden={MOLBB},\r\nlanguage={English},\r\nabbrev_source_title={MOL. BIOL.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n\n\n\n

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\n \n\n \n \n \n \n \n \n Quantitative studies of interaction of polyurolitic acid with 30S subunits of ribosome of Escherichia coli.\n \n \n \n \n\n\n \n Kirillov, S.; Katunin, V.; Machno, V.; and Semenkov Yu., P.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 13(3): 690-697. 1979.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Quantitative$ 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

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@ARTICLE{Kirillov1979690,\r\nauthor={Kirillov, S.V. and Katunin, V.I. and Machno, V.I. and Semenkov Yu., P.},\r\ntitle={Quantitative studies of interaction of polyurolitic acid with 30S subunits of ribosome of Escherichia coli},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1979},\r\nvolume={13},\r\nnumber={3},\r\npages={690-697},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0018375423&partnerID=40&md5=d0cc15585293325f32bd05f909361228},\r\naffiliation={B.P. Konstantinov Inst. Nucl. Phys., Acad. Scis USSR, Gatchina, Russian Federation},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={379617},\r\nlanguage={Russian},\r\nabbrev_source_title={MOL. BIOL.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Nature of heterogeneity of 30S ribosomal subunits in vitro. II. Two types of inactivation of 30S subunits of Escherichia col in ribosomes.\n \n \n \n \n\n\n \n Peshin, N.; and Kirillov, S.\n\n\n \n\n\n\n Molecular Biology, 13(4): 569-576. 1979.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Nature$ 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

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@ARTICLE{Peshin1979569,\r\nauthor={Peshin, N.N. and Kirillov, S.V.},\r\ntitle={Nature of heterogeneity of 30S ribosomal subunits in vitro. II. Two types of inactivation of 30S subunits of Escherichia col in ribosomes},\r\njournal={Molecular Biology},\r\nyear={1979},\r\nvolume={13},\r\nnumber={4},\r\npages={569-576},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0018607671&partnerID=40&md5=c75b7a30eeebdecc504471de7b603126},\r\naffiliation={B.P. Konstantinov Leningrad Inst. Nucl. Phys., Acad. Sci. USSR, Leningrad, Russian Federation},\r\nissn={00268933},\r\ncoden={MOLBB},\r\nlanguage={English},\r\nabbrev_source_title={MOL. BIOL.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The nature of heterogeneity of the 30S ribosomal subunits in vitro. II. Two types of inactivation of the 30S subunits of Escherichia coli ribosomes.\n \n \n \n \n\n\n \n Peshin, N.; and Kirillov, S.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 13(4): 752-760. 1979.\n cited By 2\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Peshin1979752,\r\nauthor={Peshin, N.N. and Kirillov, S.V.},\r\ntitle={The nature of heterogeneity of the 30S ribosomal subunits in vitro. II. Two types of inactivation of the 30S subunits of Escherichia coli ribosomes},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1979},\r\nvolume={13},\r\nnumber={4},\r\npages={752-760},\r\nnote={cited By 2},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0018422672&partnerID=40&md5=94bf246ca7e6f509a23da3bf7e0f586d},\r\naffiliation={B.P. Konstantinov Inst. Nucl. Phys., Acad. Sci. USSR, Gatchina},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={381895},\r\nlanguage={Russian},\r\nabbrev_source_title={MOL. BIOL.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1978\n \n \n (8)\n \n \n

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\n \n\n \n \n \n \n \n \n Separation of ribosomal subunits of escherichia coli by sepharose chromatography using reverse salt gradient.\n \n \n \n \n\n\n \n Kirillov, S.; Makhno, V.; Peshin, N.; and Semenkov, Y.\n\n\n \n\n\n\n Nucleic Acids Research, 5(11): 4305-4316. 1978.\n cited By 9\n\n\n\n
\n\n\n\n \n \n $\"Separation$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Kirillov19784305,\r\nauthor={Kirillov, S.V. and Makhno, V.I. and Peshin, N.N. and Semenkov, Y.P.},\r\ntitle={Separation of ribosomal subunits of escherichia coli by sepharose chromatography using reverse salt gradient},\r\njournal={Nucleic Acids Research},\r\nyear={1978},\r\nvolume={5},\r\nnumber={11},\r\npages={4305-4316},\r\ndoi={10.1093/nar/5.11.4305},\r\nnote={cited By 9},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0018179978&doi=10.1093%2fnar%2f5.11.4305&partnerID=40&md5=dad86821502f087e64d51da73e7a64b7},\r\naffiliation={Leningrad Institute of Nuclear Physics, Academy of Sciences of USSR, Gatchina, Leningrad district 188350, Russian Federation},\r\nabstract={A mixture of 30 S and 50 S subunits quantitatively adsorbs on a column of Sepharose-4B from the buffer: 0.02 M Tris-HCl, pH 7.5, containing 1.5 M (NH4)2SO4. During elution by reverse gradient of ammonium sulphate (1.5 - 0.05 M) the subunits are eluted at different salt concentrations. Complete separation of subunits is attained in the absence of Mg2+ ions.The 30 S subunits prepared from 70 S ribosomes according to this procedure are fully active in the codon-dependent binding of a specific aminoacyl-tRNA. After their reassociation with 50 S subunits isolated by zonal centrifugation, the resulting 70 S ribosomes are active in polypeptide synthesis at the same degree as control 70 S ribosomes in which both types of subunits were prepared by zonal centrifugation. The initial 70 S ribosomes for the chromatographic separation into subunits can be obtained by their pelleting from a crude extract with subsequent washing with concentrated solutions of NH4Cl in the ultracentrifuge, or by salt fractionation of the crude extract according to a slightly modified procedure of Kurland1. © 1978 Information Retrieval Limited 1 Falconberg Court London W1V 5FG England.},\r\ncorrespondence_address1={Kirillov, S.V.; Leningrad Institute of Nuclear Physics, Academy of Sciences of USSR, Gatchina, Leningrad district 188350, Russian Federation},\r\nissn={03051048},\r\ncoden={NARHA},\r\npubmed_id={364425},\r\nlanguage={English},\r\nabbrev_source_title={Nucleic Acids Res.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Interaction of N-acetyl-phenylalanyl-tRNA Phe with 70S ribosomes of escherichia coli.\n \n \n \n \n\n\n \n Odinzov, V.; and Kirillov, S.\n\n\n \n\n\n\n Nucleic Acids Research, 5(10): 3871-3880. 1978.\n cited By 31\n\n\n\n
\n\n\n\n \n \n $\"Interaction$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\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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@ARTICLE{Odinzov19783871,\r\nauthor={Odinzov, V.B. and Kirillov, S.V.},\r\ntitle={Interaction of N-acetyl-phenylalanyl-tRNA Phe with 70S ribosomes of escherichia coli},\r\njournal={Nucleic Acids Research},\r\nyear={1978},\r\nvolume={5},\r\nnumber={10},\r\npages={3871-3880},\r\ndoi={10.1093/nar/5.10.3871},\r\nnote={cited By 31},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0018071747&doi=10.1093%2fnar%2f5.10.3871&partnerID=40&md5=10818e6be2ca38bf0bafe0ef947009bc},\r\naffiliation={Leningrad Institute of Nuclear Physics, Academy of Sciences of USSR, Gatchina, Leningrad District 188350, Russian Federation},\r\nabstract={The interaction of N-Acetyl-Phe-tRNA Phe with 70 S ribosomes is a reversible process in the absence as well as in the presence of messenger. The equilibrium binding constants of these interactions were measured at different magnesium concentrations and temperatures and thermodynamical quantities computed. The enthalpy of the formation of complexes with the P site of ribosomes is larger by 6,000 cal/mol in the presence of poly (U) than in the presence of poly (C) or in total absence of messenger. Free energy differences are rather small, the association constants differ less than one order of magnitude. The association constant of N-Acetyl-Phe-tRNA Phe with the A site of ribosomes is 30 - 50 times lower than with the P site even in the presence of poly (U). © 1978 Information Retrieval Limited.},\r\ncorrespondence_address1={Odinzov, V.B.; Leningrad Institute of Nuclear Physics, Academy of Sciences of USSR, Gatchina, Leningrad District 188350, Russian Federation},\r\nissn={03051048},\r\ncoden={NARHA},\r\npubmed_id={364420},\r\nlanguage={English},\r\nabbrev_source_title={Nucleic Acids Res.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The interconversion of conformers of phenylalanyl-tRNA with different affinity to 70S ribosomes of Escherichia coli.\n \n \n \n \n\n\n \n Kirillov, S.; and Odinzov, V.\n\n\n \n\n\n\n Nucleic Acids Research, 5(5): 1501-1514. 1978.\n cited By 5\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

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@ARTICLE{Kirillov19781501,\r\nauthor={Kirillov, S.V. and Odinzov, V.B.},\r\ntitle={The interconversion of conformers of phenylalanyl-tRNA with different affinity to 70S ribosomes of Escherichia coli},\r\njournal={Nucleic Acids Research},\r\nyear={1978},\r\nvolume={5},\r\nnumber={5},\r\npages={1501-1514},\r\ndoi={10.1093/nar/5.5.1501},\r\nnote={cited By 5},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0017826109&doi=10.1093%2fnar%2f5.5.1501&partnerID=40&md5=112372a28a4bed72d2bbfe6c30a5710f},\r\naffiliation={Leningrad Institute of Nudear Physics, Academy of Sciences of USSR, Gatchina, Leningrad district 188350, Russian Federation},\r\nabstract={Earlier the existence of two conformers of Phe-tRNAPhe of E.coli was demonstrated because one of them yields complexes with 70S·poly(U) of extremely high affinity and the other with at least a 105 lower binding constant1. We denote the first conformer as HAC (high affinity conformer) and the second as LAC (low affinity conformer). This high difference in binding constants was used for studying the process of reversible interconversion of conformers of Phe-tRNAPhe. The transition kinetics of LAC to HAC in conditions when the latter is stable (in the presence of magnesium ions) was studied and a high value of activation energy (35 kcal/mole) found. The interconversion is the first order reaction and equilibrium does not depend of overall Phe-tRNA concentration. © 1978 Information Retrieval Limited.},\r\ncorrespondence_address1={Kirillov, S.V.; Leningrad Institute of Nudear Physics, Academy of Sciences of USSR, Gatchina, Leningrad district 188350, Russian Federation},\r\nissn={03051048},\r\ncoden={NARHA},\r\npubmed_id={351562},\r\nlanguage={English},\r\nabbrev_source_title={Nucleic Acids Res.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The Mechanism of Codon‐Anticodon Interaction in Ribosomes: Quantitative Study of Codon‐Dependent Binding of tRNA to the 30‐S Ribosomal Subunits of Escherichia coli.\n \n \n \n \n\n\n \n KIRILLOV, S.; MAKHNO, V.; and SEMENKOV, Y.\n\n\n \n\n\n\n European Journal of Biochemistry, 89(1): 297-304. 1978.\n cited By 25\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

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@ARTICLE{KIRILLOV1978297,\r\nauthor={KIRILLOV, S.V. and MAKHNO, V.I. and SEMENKOV, Y.P.},\r\ntitle={The Mechanism of Codon‐Anticodon Interaction in Ribosomes: Quantitative Study of Codon‐Dependent Binding of tRNA to the 30‐S Ribosomal Subunits of Escherichia coli},\r\njournal={European Journal of Biochemistry},\r\nyear={1978},\r\nvolume={89},\r\nnumber={1},\r\npages={297-304},\r\ndoi={10.1111/j.1432-1033.1978.tb20927.x},\r\nnote={cited By 25},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0017845412&doi=10.1111%2fj.1432-1033.1978.tb20927.x&partnerID=40&md5=c6cde655727eb9d2acdcaa2171f36271},\r\naffiliation={Leningrad Institute of Nuclear Physics, Akademiya Nauk S.S.S.R, Oblasti, 188350},\r\nabstract={The formation of a ternary complex 30‐S‐subunit · poly(U) · tRNAPhe is discussed and the conditions for its correct description by Langmuir's isotherm are deduced. The affinity constant of the binary complex 30‐S‐subunit · poly(U) is measured. The reversibility of binding of tRNAPhe to the complex 30‐S‐subunit · poly(U) is proved in a direct way. The main reason for the heterogeneity of ternary complexes was found to be due to the ability of high‐molecular‐weight poly(U) to form complicated aggregates with 30‐S subunits. If a fraction of poly(U) of moderate molecular weight (30000) is used, then the ternary complexes are homogeneous in stability and yield the same affinity constants for deacylated, aminoacylated and peptidyl‐tRNAPhe (1×108 M‐1 at 20 mM Mg2+, 200 mM NH4+ and 0 °C). Ribosomal protein S1 increases the binding constant of poly(U) with 30‐S subunits but does not change the binding constant of tRNAPhe with the 30‐S‐subunit · poly(U) complex. All 30‐S subunits, even partially stripped of S1 protein, are active in the binding of both poly(U) and tRNAPhe. Copyright © 1978, Wiley Blackwell. All rights reserved},\r\ncorrespondence_address1={KIRILLOV, S.V.; Leningrad Institute of Nuclear Physics, Akademiya Nauk S.S.S.R, Oblasti, 188350},\r\nissn={00142956},\r\npubmed_id={359329},\r\nlanguage={English},\r\nabbrev_source_title={Eur. J. Biochem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The reason for the heterogeneity of the 30S ribosomal subunits in vitro. I. Effect of high centrifugal fields during isolation of the 30S subunits on its ability to bind tRNA specifically.\n \n \n \n \n\n\n \n Kirillov, S.; Makhno, V.; Peshin, N.; and Semenkov Yu., P.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 12(3): 602-611. 1978.\n cited By 7\n\n\n\n
\n\n\n\n \n \n $\"The$ 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

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@ARTICLE{Kirillov1978602,\r\nauthor={Kirillov, S.V. and Makhno, V.I. and Peshin, N.N. and Semenkov Yu., P.},\r\ntitle={The reason for the heterogeneity of the 30S ribosomal subunits in vitro. I. Effect of high centrifugal fields during isolation of the 30S subunits on its ability to bind tRNA specifically},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1978},\r\nvolume={12},\r\nnumber={3},\r\npages={602-611},\r\nnote={cited By 7},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0017963459&partnerID=40&md5=28d7b26548ff9b087028b8199b5d71cd},\r\naffiliation={B.P. Konstantinov Inst. Nucl. Phys., Acad. Sci. USSR, Gatchina},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={248137},\r\nlanguage={Russian},\r\nabbrev_source_title={MOL. BIOL.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n The Mechanism of Codon‐Anticodon Interaction in Ribosomes: Heterogeneity of tRNA Complexes with 70‐S Ribosomes of Escherichia coli.\n \n \n \n \n\n\n \n KIRILLOV, S.; MAKHNO, V.; ODINZOV, V.; and SEMENKOV, Y.\n\n\n \n\n\n\n European Journal of Biochemistry, 89(1): 305-313. 1978.\n cited By 13\n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

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@ARTICLE{KIRILLOV1978305,\r\nauthor={KIRILLOV, S.V. and MAKHNO, V.I. and ODINZOV, V.B. and SEMENKOV, Y.P.},\r\ntitle={The Mechanism of Codon‐Anticodon Interaction in Ribosomes: Heterogeneity of tRNA Complexes with 70‐S Ribosomes of Escherichia coli},\r\njournal={European Journal of Biochemistry},\r\nyear={1978},\r\nvolume={89},\r\nnumber={1},\r\npages={305-313},\r\ndoi={10.1111/j.1432-1033.1978.tb20928.x},\r\nnote={cited By 13},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0017881557&doi=10.1111%2fj.1432-1033.1978.tb20928.x&partnerID=40&md5=b314eedffcb8102aa4e701201aa04eb3},\r\naffiliation={Leningradskij Institut Yadernoj Fiziki imeni B. P. Konstantinova, Akademiya Nauk S.S.S.R, Gatchina, 188350},\r\nabstract={It was shown that at 20 mM Mg 2+ and 0 or 20 °C each 70‐S ribosome binds non‐enzymatically about one Phe‐tRNA Phe molecule in the A site if poly(U) is used as messenger. Only a minor amount of ribosomes (never exceeding 15%) and after long incubation binds a second molecule of Phe‐tRNA Phe and forms diphenylalanyl‐tRNA. If the Phe‐tRNA Phe preparation contains nonspecific deacylated tRNA, the latter is always bound in the P site up to one molecule per 70‐S ribosome. The association constant for this non‐specific tRNA binding is equal to (1.4 ± 0.3) × 10 7 M ‐1 and is independent of the messenger poly(U) and the fiilling of the A site by a specific aminoacyl‐tRNA. It was found that the codon‐dependent binding of Phe‐tRNA Phe in the A site is reversible, but two different types of complexes are formed with drastic differences of binding constants. This heterogeneity is due to the presence of two conformers of Phe‐tRNA Phe . The equilibrium of the two Phe‐tRNA Phe conformers depends on Mg 2+ and can be shifted if tRNA is heated and Mg 2+ added or sequestered by complexing agents. One type of Phe‐tRNA Phe yields complexes with 70‐S ribosomes showing extremely high affinity constants (higher than 10 11 M ‐1 ). The second conformer is characterized by a comparatively low binding constant about 5 × 10 6 M ‐1 . In the binding of both species to 30‐S subunits no difference is seen. A big difference in the behaviour of both Phe‐tRNA Phe conformers is found also in the absence of messenger RNA. The association constant of Phe‐tRNA Phe (high‐affinity conformer) to 70‐S ribosomes is about 3 × 10 8 M ‐1 , but for the low‐affinity conformer is hundred times lower. Copyright © 1978, Wiley Blackwell. All rights reserved},\r\ncorrespondence_address1={KIRILLOV, S.V.; Leningradskij Institut Yadernoj Fiziki imeni B. P. Konstantinova, Akademiya Nauk S.S.S.R, Gatchina, 188350},\r\nissn={00142956},\r\npubmed_id={359330},\r\nlanguage={English},\r\nabbrev_source_title={Eur. J. Biochem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Separation of the 30S and 50S subparticles of the ribosomes of Escherichia coli by hydrophobic chromatography on sepharose-4B.\n \n \n \n \n\n\n \n Kirillov, S.; Makhno, V.; Peshin, N.; and Semenkov Yu., P.\n\n\n \n\n\n\n Doklady Biochemistry, 237(1-6): 352-354. 1978.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Separation$ 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

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@ARTICLE{Kirillov1978352,\r\nauthor={Kirillov, S.V. and Makhno, V.I. and Peshin, N.N. and Semenkov Yu., P.},\r\ntitle={Separation of the 30S and 50S subparticles of the ribosomes of Escherichia coli by hydrophobic chromatography on sepharose-4B},\r\njournal={Doklady Biochemistry},\r\nyear={1978},\r\nvolume={237},\r\nnumber={1-6},\r\npages={352-354},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0017809337&partnerID=40&md5=f6650e59bd348aae821a04aa9536a508},\r\naffiliation={B.P. Konstantinov Leningrad Inst. Nucl. Phys., Acad. Sci. USSR, Leningrad, Russian Federation},\r\nissn={00124958},\r\ncoden={DBIOA},\r\nlanguage={English},\r\nabbrev_source_title={DOKL. BIOCHEM.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Inactivation of the 30S subparticles of the ribosomes in the centrifugal field of an ultracentrifuge.\n \n \n \n \n\n\n \n Bresler, S.; Kirillov, S.; and Makhno, V.\n\n\n \n\n\n\n Doklady Biochemistry, 236(1-6): 284-287. 1978.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Inactivation$ 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

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@ARTICLE{Bresler1978284,\r\nauthor={Bresler, S.E. and Kirillov, S.V. and Makhno, V.I.},\r\ntitle={Inactivation of the 30S subparticles of the ribosomes in the centrifugal field of an ultracentrifuge},\r\njournal={Doklady Biochemistry},\r\nyear={1978},\r\nvolume={236},\r\nnumber={1-6},\r\npages={284-287},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0017803724&partnerID=40&md5=09928bbb4d70bbf88d25f30de17b2716},\r\naffiliation={B.P. Konstantinov Leningrad Inst. Nucl. Phys., Acad. Sci. USSR, Gatchina},\r\nissn={00124958},\r\ncoden={DBIOA},\r\nlanguage={English},\r\nabbrev_source_title={DOKL. BIOCHEM.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1977\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Influence of the molecular weight of polyuridylic acid and the presence of the ribosomal protein SI on the stability of a complex of transfer RNA with the small subparticle of the ribosomes.\n \n \n \n \n\n\n \n Kirillov, S.; Makhno, V.; and Semenkov, Y.\n\n\n \n\n\n\n Doklady Biochemistry, 229(1-6): 334-337. 1977.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Influence$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Kirillov1977334,\r\nauthor={Kirillov, S.V. and Makhno, V.I. and Semenkov, Y.P.},\r\ntitle={Influence of the molecular weight of polyuridylic acid and the presence of the ribosomal protein SI on the stability of a complex of transfer RNA with the small subparticle of the ribosomes},\r\njournal={Doklady Biochemistry},\r\nyear={1977},\r\nvolume={229},\r\nnumber={1-6},\r\npages={334-337},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0017577781&partnerID=40&md5=947f7a9173c5aa0ee394f3c4cd3c9e0a},\r\naffiliation={B.P. Konstantinov Leningrad Inst. Nucl. Phys., Gatchina, Russia},\r\nissn={00124958},\r\ncoden={DBIOA},\r\nlanguage={English},\r\nabbrev_source_title={DOKL. BIOCHEM.},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Separation of the 30 S and 50 S subparticles of Escherichia coli ribosomes by hydrophobic chromatography on sepharose-4B [Razdelenie 30 S i 50 S subchastits ribosom Escherichia coli gidrofobnoǐ khromatografieǐ na sefaroze-4B.].\n \n \n \n \n\n\n \n Kirillov, S.; Makhno, V.; Peshin, N.; and Semenkov, I.\n\n\n \n\n\n\n Doklady Akademii nauk SSSR, 237(3): 725-727. 1977.\n cited By 1\n\n\n\n
\n\n\n\n \n \n $\"Separation$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Kirillov1977725,\r\nauthor={Kirillov, S.V. and Makhno, V.I. and Peshin, N.N. and Semenkov, I.P.},\r\ntitle={Separation of the 30 S and 50 S subparticles of Escherichia coli ribosomes by hydrophobic chromatography on sepharose-4B [Razdelenie 30 S i 50 S subchastits ribosom Escherichia coli gidrofobnoǐ khromatografieǐ na sefaroze-4B.]},\r\njournal={Doklady Akademii nauk SSSR},\r\nyear={1977},\r\nvolume={237},\r\nnumber={3},\r\npages={725-727},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0017647115&partnerID=40&md5=5c0297c1b790cf18b48d6f99970cf2bd},\r\ncorrespondence_address1={Kirillov, S.V.},\r\nissn={00023264},\r\npubmed_id={338274},\r\nlanguage={Russian},\r\nabbrev_source_title={Dokl Akad Nauk SSSR},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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\n \n\n \n \n \n \n \n \n Inactivation of 30S ribosomal subunits in the centrifugal field of the ultracentrifuge [Inaktivatsiia 30S subchastits ribosom v tsentrobezhnom pole ul'tratsentrifugi.].\n \n \n \n \n\n\n \n Bresler, S.; Kirillov, S.; Makhno, V.; Peshin, N.; and Semenkov, I.\n\n\n \n\n\n\n Doklady Akademii nauk SSSR, 236(2): 467-470. 1977.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Inactivation$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Bresler1977467,\r\nauthor={Bresler, S.E. and Kirillov, S.V. and Makhno, V.I. and Peshin, N.N. and Semenkov, I.P.},\r\ntitle={Inactivation of 30S ribosomal subunits in the centrifugal field of the ultracentrifuge [Inaktivatsiia 30S subchastits ribosom v tsentrobezhnom pole ul'tratsentrifugi.]},\r\njournal={Doklady Akademii nauk SSSR},\r\nyear={1977},\r\nvolume={236},\r\nnumber={2},\r\npages={467-470},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0017355028&partnerID=40&md5=5e2b29596ea5a22077b617f9fbfa558e},\r\ncorrespondence_address1={Bresler, S.E.},\r\nissn={00023264},\r\npubmed_id={913236},\r\nlanguage={Russian},\r\nabbrev_source_title={Dokl Akad Nauk SSSR},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1976\n \n \n (3)\n \n \n

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\n \n\n \n \n \n \n \n \n Isolation and study of some properties of the highly active 30S and 50S Escherichia coli ribosomal subunits.\n \n \n \n \n\n\n \n Semenkov, Y.; Makhno, V.; and Kirillov, S.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 10(4): 620-628. 1976.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Isolation$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Semenkov1976620,\r\nauthor={Semenkov, Y.P. and Makhno, V.I. and Kirillov, S.V.},\r\ntitle={Isolation and study of some properties of the highly active 30S and 50S Escherichia coli ribosomal subunits.},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1976},\r\nvolume={10},\r\nnumber={4},\r\npages={620-628},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0016978404&partnerID=40&md5=6520c4cd393fe0bccd3375af52ad58ad},\r\nabstract={A method for the isolation of highly active Escherichia coli ribosomal subunits has been described and used to obtain 30S subunits, which are fully active in the cistron-specific binding of tRNA, and reassociated 70S ribosomes, which are at least 35% active in the synthesis of polypeptides. The dissociation constants (Kd) of the 30S-poly(U)-tRNAPhe complex, which proved to be practically identical for tRNAPhe in the deacylated and aminoacylated forms, as well as for the chemically synthesized peptidyl-tRNA, have been measured. Changes in the binding conditions (temperatures from 0 to 30 degrees, Mg2+ concentrations from 20 to 5 mM, and NH4+ concentrations from 200 to 50mM) have a significant effect on the value of Kd without altering the number of active 30S subunits. It has been shown that the codon-specific binding of tRNA to the 30S subunits is completely reversible. The 30S subunits are not only not inactivated after a single act of binding of a tRNA molecule, but are capable of undergoing this process repeatedly without any appreciable loss in activity.},\r\ncorrespondence_address1={Semenkov, Y.P.},\r\nissn={00268984},\r\npubmed_id={799255},\r\nlanguage={English},\r\nabbrev_source_title={Mol Biol (Mosk)},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Isolation and investigation of some properties of highly active 30S and 50S ribosomal subunits of Escherichia coli (Russian).\n \n \n \n \n\n\n \n Semenkov, Y.; Makhno, N.; and Kirillov, S.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 10(4): 754-763. 1976.\n cited By 17\n\n\n\n
\n\n\n\n \n \n $\"Isolation$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Semenkov1976754,\r\nauthor={Semenkov, Y.P. and Makhno, N.I. and Kirillov, S.V.},\r\ntitle={Isolation and investigation of some properties of highly active 30S and 50S ribosomal subunits of Escherichia coli (Russian)},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1976},\r\nvolume={10},\r\nnumber={4},\r\npages={754-763},\r\nnote={cited By 17},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0017127969&partnerID=40&md5=815f62d6bc085bc7da5f5ba9e755236e},\r\naffiliation={B.P. Konstantinov Inst. Nucl. Phys., Acad. Sci. USSR, Leningrad, Russian Federation},\r\nissn={00268984},\r\ncoden={MOBIB},\r\nlanguage={Russian},\r\nabbrev_source_title={MOL. BIOL.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n\n \n \n \n \n \n \n Effect of the molecular weight of polyuridylic acid and the presence of ribosomal protein S1 on the stability of the complex of transport RNA with small ribosomal subunits [Vliianie molekuliarnogo vesa poliuridilovoǐ kisloty i prisutstviia ribosomnogo belka S1 na stabil'nost' kompleksa transportnoǐ RNK s maloǐ subchastitseǐ ribosom].\n \n \n \n \n\n\n \n Kirillov, S.; Makhno, V.; and Semenkov, I.\n\n\n \n\n\n\n Doklady Akademii nauk SSSR, 229(2): 488-491. 1976.\n cited By 9\n\n\n\n
\n\n\n\n \n \n $\"Effect$ Paper\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@ARTICLE{Kirillov1976488,\r\nauthor={Kirillov, S.V. and Makhno, V.I. and Semenkov, I.P.},\r\ntitle={Effect of the molecular weight of polyuridylic acid and the presence of ribosomal protein S1 on the stability of the complex of transport RNA with small ribosomal subunits [Vliianie molekuliarnogo vesa poliuridilovoǐ kisloty i prisutstviia ribosomnogo belka S1 na stabil'nost' kompleksa transportnoǐ RNK s maloǐ subchastitseǐ ribosom]},\r\njournal={Doklady Akademii nauk SSSR},\r\nyear={1976},\r\nvolume={229},\r\nnumber={2},\r\npages={488-491},\r\nnote={cited By 9},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0016914906&partnerID=40&md5=097790ab37dba19b3b52231928306fa1},\r\ncorrespondence_address1={Kirillov, S.V.},\r\nissn={00023264},\r\npubmed_id={971660},\r\nlanguage={Russian},\r\nabbrev_source_title={Dokl Akad Nauk SSSR},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1975\n \n \n (2)\n \n \n

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\n \n\n \n \n \n \n \n \n Non-enzymatic specific (codon-dependent) binding of tRNA with isolated 30S ribosomal subunits. Measurement of the dissociation constant of the complex [Nefermentativnoe spetsificheskoe (kodon-zavisimoe) sviazyvanie tRNK s izolirovannoǐ 30S ribosomnoǐ sub'edinitseǐ. Izmerenie konstant dissotsiatsii kompleksa].\n \n \n \n \n\n\n \n Bresler, S.; Vlasov, G.; Kirillov, S.; Semenkov, I.; and Makhno, V.\n\n\n \n\n\n\n Doklady Akademii nauk SSSR, 220(3): 719-722. 1975.\n cited By 7\n\n\n\n
\n\n\n\n \n \n $\"Non-enzymatic$ 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

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@ARTICLE{Bresler1975719,\r\nauthor={Bresler, S.E. and Vlasov, G.P. and Kirillov, S.V. and Semenkov, I.P. and Makhno, V.I.},\r\ntitle={Non-enzymatic specific (codon-dependent) binding of tRNA with isolated 30S ribosomal subunits. Measurement of the dissociation constant of the complex [Nefermentativnoe spetsificheskoe (kodon-zavisimoe) sviazyvanie tRNK s izolirovannoǐ 30S ribosomnoǐ sub'edinitseǐ. Izmerenie konstant dissotsiatsii kompleksa]},\r\njournal={Doklady Akademii nauk SSSR},\r\nyear={1975},\r\nvolume={220},\r\nnumber={3},\r\npages={719-722},\r\nnote={cited By 7},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-17144440772&partnerID=40&md5=de48e7afe0a0aaee1574710584accdf1},\r\ncorrespondence_address1={Bresler, S.E.},\r\nissn={00023264},\r\npubmed_id={1089511},\r\nlanguage={Russian},\r\nabbrev_source_title={Dokl Akad Nauk SSSR},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

\n

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\n \n\n \n \n \n \n \n \n Nonenzymatic specific (codon dependent) bonding of tRNA to an isolated 30S ribosomal subunit measurement of the dissociation constants of the complex.\n \n \n \n \n\n\n \n Bresler, S.; Vlasov, G.; and Kirillov, S.\n\n\n \n\n\n\n Doklady Biochemistry, 220(1-6): 26-28. 1975.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Nonenzymatic$ 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

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@ARTICLE{Bresler197526,\r\nauthor={Bresler, S.E. and Vlasov, G.P. and Kirillov, S.V.},\r\ntitle={Nonenzymatic specific (codon dependent) bonding of tRNA to an isolated 30S ribosomal subunit measurement of the dissociation constants of the complex},\r\njournal={Doklady Biochemistry},\r\nyear={1975},\r\nvolume={220},\r\nnumber={1-6},\r\npages={26-28},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0016743116&partnerID=40&md5=8ac5f67c7024c1058cefba9bab97d68d},\r\naffiliation={B. P. Konstantinov Leningrad Inst. Nucl. Phys., Acad. Sci. USSR, Gatchina},\r\nissn={00124958},\r\ncoden={DBIOA},\r\nlanguage={English},\r\nabbrev_source_title={DOKL. BIOCHEM.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1971\n \n \n (1)\n \n \n

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\n \n\n \n \n \n \n \n \n Binding of synthetic peptidyl-tRNA to the ribosomes and enzymatic synthesis of the polypeptide chain.\n \n \n \n \n\n\n \n Semenkov, Y.; Kirillov, S.; Makhno, V.; Shvartsman, A.; and Bresler, S.\n\n\n \n\n\n\n Molecular Biology, 5(5): 587-594. 1971.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"Binding$ 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

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@ARTICLE{Semenkov1971587,\r\nauthor={Semenkov, Y.P. and Kirillov, S.V. and Makhno, V.I. and Shvartsman, A.L. and Bresler, S.E.},\r\ntitle={Binding of synthetic peptidyl-tRNA to the ribosomes and enzymatic synthesis of the polypeptide chain.},\r\njournal={Molecular Biology},\r\nyear={1971},\r\nvolume={5},\r\nnumber={5},\r\npages={587-594},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0015113228&partnerID=40&md5=7dca58af673afa9c5c178f9443a2a6b6},\r\ncorrespondence_address1={Semenkov, Y.P.},\r\nissn={00268933},\r\npubmed_id={4949527},\r\nlanguage={English},\r\nabbrev_source_title={Mol Biol},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n

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\n \n 1964\n \n \n (1)\n \n \n

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\n \n\n \n \n \n \n \n \n INVESTIGATION OF AN INTERMEDIATE COMPOUND FORMED BY A NEWLY SYNTHESIZED [ISSLEDOVANIE PROMEZHUTOCHNOGO SOEDINENIIA VNOV' SINTEZIROVANNOGO].\n \n \n \n \n\n\n \n BRESLER, S.; VASILEVA, N.; GRAEVSKAIA, R.; KIRILLOV, S.; and SAMINSKII, E.\n\n\n \n\n\n\n Biokhimiia (Moscow, Russia), 29: 353-362. 1964.\n cited By 0\n\n\n\n
\n\n\n\n \n \n $\"INVESTIGATION$ 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

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@ARTICLE{BRESLER1964353,\r\nauthor={BRESLER, S.E. and VASILEVA, N.N. and GRAEVSKAIA, R.A. and KIRILLOV, S.V. and SAMINSKII, E.M.},\r\ntitle={INVESTIGATION OF AN INTERMEDIATE COMPOUND FORMED BY A NEWLY SYNTHESIZED [ISSLEDOVANIE PROMEZHUTOCHNOGO SOEDINENIIA VNOV' SINTEZIROVANNOGO]},\r\njournal={Biokhimiia (Moscow, Russia)},\r\nyear={1964},\r\nvolume={29},\r\npages={353-362},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-78651201828&partnerID=40&md5=2043a6a838368ebfb534f1eb32351c07},\r\ncorrespondence_address1={BRESLER, S.E.},\r\nissn={03209725},\r\npubmed_id={14207652},\r\nlanguage={Russian},\r\nabbrev_source_title={Biokhimiia},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n

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