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\n  \n 2019\n \n \n (3)\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 \"PlasmaPaper\n  \n \n\n \n \n doi\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 Purpose: The interaction between malignant cells and surrounding healthy tissues is a critical factor in the metastatic progression of breast cancer (BC). Extracellular vesicles, especially exosomes, are known to be involved in inter-cellular communication during cancer progression. In the study presented herein, we aimed to evaluate the role of circulating plasma exosomes in the metastatic dissemination of BC and to investigate the underlying molecular mechanisms of this phenomenon. Methods: Exosomes isolated from plasma of healthy female donors were applied in various concentrations into the medium of MDA-MB-231 and MCF-7 cell lines. Motility and invasive properties of BC cells were examined by random migration and Transwell invasion assays, and the effect of plasma exosomes on the metastatic dissemination of BC cells was demonstrated in an in vivo zebrafish model. To reveal the molecular mechanism of interaction between plasma exosomes and BC cells, a comparison between un-treated and enzymatically modified exosomes was performed, followed by mass spectrometry, gene ontology, and pathway analysis. Results: Plasma exosomes stimulated the adhesive properties, two-dimensional random migration, and transwell invasion of BC cells in vitro as well as their in vivo metastatic dissemination in a dose-dependent manner. This stimulatory effect was mediated by interactions of surface exosome proteins with BC cells and consequent activation of focal adhesion kinase (FAK) signaling in the tumor cells. Conclusions: Plasma exosomes have a potency to stimulate the metastasis-promoting properties of BC cells. This pro-metastatic property of normal plasma exosomes may have impact on the course of the disease and on its prognosis. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.\n
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\n \n\n \n \n \n \n \n \n Inventory of proteoforms as a current challenge of proteomics: Some technical aspects.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Journal of Proteomics, 191: 22-28. 2019.\n cited By 6\n\n\n\n
\n\n\n\n \n \n \"InventoryPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 The main intricacy in the human proteome is that it is tremendously complex and composed from diverse and heterogeneous gene products. These products are called protein species or proteoforms and are the smallest units of the proteome. In pursuit of the comprehensive profiling of the human proteome, significant advances in the technology of so called “Top-Down” mass spectrometry based proteomics, have been made. However, the scale of performance of this approach is still far behind the “Bottom-Up” peptide-centric techniques. The classical two-dimensional electrophoresis (2-DE) as the most powerful and convenient method for separation of proteoforms remains as a superior method in “Top-Down” proteomics. Here, some aspects of approaches for establishing an inventory of proteoforms based on 2-DE and mass spectrometry are discussed. Biological significance: The systematic efforts in the Human Proteome project to map the entire human proteome greatly depend on currently available and emerging techniques and approaches. Here, the possibilities of a visual representation of the human proteome by combination of virtual/experimental 2-DE with protein identification by mass spectrometry or immunologically is discussed. By application of this approach on several profiles of gene products we show its convenience in informative representation of the whole proteome and single gene products, proteoforms (protein species). This approach could be very helpful in the emerging global inventory of all human proteoforms. © 2018 Elsevier B.V.\n
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\n \n\n \n \n \n \n \n \n Structural-functional diversity of p53 proteoforms [СТРУКТУРНО-ФУНКЦИОНАЛЬНОЕ МНОГООБРАЗИЕ ПРОТЕОФОРМ БЕЛКА р53].\n \n \n \n \n\n\n \n Naryzhny, S.; and Legina, O.\n\n\n \n\n\n\n Biomeditsinskaya Khimiya, 65(4): 263-276. 2019.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"Structural-functionalPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Naryzhny2019263,\r\nauthor={Naryzhny, S.N. and Legina, O.K.},\r\ntitle={Structural-functional diversity of p53 proteoforms [СТРУКТУРНО-ФУНКЦИОНАЛЬНОЕ МНОГООБРАЗИЕ ПРОТЕОФОРМ БЕЛКА р53]},\r\njournal={Biomeditsinskaya Khimiya},\r\nyear={2019},\r\nvolume={65},\r\nnumber={4},\r\npages={263-276},\r\ndoi={10.18097/PBMC20196504263},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85071527746&doi=10.18097%2fPBMC20196504263&partnerID=40&md5=c515c112a17fb0eccd1fff6ee112e454},\r\naffiliation={Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Leningrad region, Gatchina, 188300, Russian Federation},\r\nabstract={Protein p53 is one of the most studied proteins. This attention is primarily due to its key role in the cellular mechanisms associated with carcinogenesis. Protein p53 is a transcription factor involved in a wide variety of processes: cell cycle regulation and apoptosis, signaling inside the cell, DNA repair, coordination of metabolic processes, regulation of cell interactions, etc. This multifunctionality is apparently determined by the fact that p53 is a vivid example of how the same protein can be represented by numerous proteoforms bearing completely different functional loads. By alternative splicing, using different promoters and translation initiation sites, the TP53 gene gives rise to at least 12 isoforms, which can additionally undergo numerous (>200) post-translational modifications. Proteoforms generated due to numerous point mutations in the TP53 gene are adding more complexity to this picture. The proteoforms produced are involved in various processes, such as the regulation of p53 transcriptional activity in response to various factors. This review is devoted to the description of the currently known p53 proteoforms, as well as their possible functionality. © 2019 Russian Academy of Medical Sciences. All rights reserved.},\r\nauthor_keywords={Gene;  Proteoforms;  р53},\r\n}
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\n Protein p53 is one of the most studied proteins. This attention is primarily due to its key role in the cellular mechanisms associated with carcinogenesis. Protein p53 is a transcription factor involved in a wide variety of processes: cell cycle regulation and apoptosis, signaling inside the cell, DNA repair, coordination of metabolic processes, regulation of cell interactions, etc. This multifunctionality is apparently determined by the fact that p53 is a vivid example of how the same protein can be represented by numerous proteoforms bearing completely different functional loads. By alternative splicing, using different promoters and translation initiation sites, the TP53 gene gives rise to at least 12 isoforms, which can additionally undergo numerous (>200) post-translational modifications. Proteoforms generated due to numerous point mutations in the TP53 gene are adding more complexity to this picture. The proteoforms produced are involved in various processes, such as the regulation of p53 transcriptional activity in response to various factors. This review is devoted to the description of the currently known p53 proteoforms, as well as their possible functionality. © 2019 Russian Academy of Medical Sciences. All rights reserved.\n
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\n  \n 2018\n \n \n (5)\n \n \n
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\n \n\n \n \n \n \n \n \n Next Steps on in Silico 2DE Analyses of Chromosome 18 Proteoforms.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Journal of Proteome Research, 17(12): 4085-4096. 2018.\n cited By 1\n\n\n\n
\n\n\n\n \n \n \"NextPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 In the boundaries of the chromosome-centric Human Proteome Project (c-HPP) to obtain information about proteoforms coded by chromosome 18, several cell lines (HepG2, glioblastoma, LEH), normal liver, and plasma were analyzed. In our study, we have been using proteoform separation by two-dimensional electrophoresis (2DE) (a sectional analysis) and a semivirtual 2DE with following shotgun mass spectrometry using LC-ESI-MS/MS. Previously, we published a first draft of this research, where only HepG2 cells were tested. Here, we present the next step using more detailed analysis and more samples. Altogether, confident (2 significant sequences minimum) information about proteoforms of 117 isoforms coded by 104 genes of chromosome 18 was obtained. The 3D-graphs showing distribution of different proteoforms from the same gene in the 2D map were generated. Additionally, a semivirtual 2DE approach has allowed for detecting more proteoforms and estimating their pI more precisely. Data are available via ProteomeXchange with identifier PXD010142. Copyright © 2018 American Chemical Society.\n
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\n \n\n \n \n \n \n \n \n Searching for Specific Markers of Glioblastoma: Analysis of Glioblastoma Cell Proteoforms.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Cell and Tissue Biology, 12(6): 455-459. 2018.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"SearchingPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 Abstract: Using the sectional analysis of two-dimensional electrophoretic gels with liquid chromatography-mass spectrometry, proteoform profiles for individual genes expressed in cancer (glioblastoma) and normal (FLEH) cells were obtained. Profiles of more than 5000 genes were analyzed. It turned out that many genes encoding potential biomarkers of glioblastoma are characterized by sets of proteoforms that are different in normal and cancer cells. These proteoforms could be sources of highly specific markers and targets for therapy. Using a section analysis of two-dimensional electrophoretic gels with liquid chromatography by mass spectrometry, proteoform profiles were obtained for individual genes expressed in cancer (glioblastoma) and normal (FLEH) cells. Profiles of more than 5000 genes were analyzed. It turned out that many genes encoding potential biomarkers of glioblastoma are characterized by sets of proteoforms, which are different in normal and cancer cells. These proteoforms could be sources of highly specific markers and targets for therapy. © 2018, Pleiades Publishing, Ltd.\n
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\n \n\n \n \n \n \n \n \n Comprehensive Analysis of Carbohydrate-Active Enzymes from the Filamentous Fungus Scytalidium candidum 3C.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Biochemistry (Moscow), 83(11): 1399-1410. 2018.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"ComprehensivePaper\n  \n \n\n \n \n doi\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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\n Complete enzymatic degradation of plant polysaccharides is a result of combined action of various carbohydrate-active enzymes (CAZymes). In this paper, we demonstrate the potential of the filamentous fungus Scytalidium candidum 3C for processing of plant biomass. Structural annotation of the improved assembly of S. candidum 3C genome and functional annotation of CAZymes revealed putative gene sequences encoding such proteins. A total of 190 CAZyme-encoding genes were identified, including 104 glycoside hydrolases, 52 glycosyltransferases, 28 oxidative enzymes, and 6 carbohydrate esterases. In addition, 14 carbohydrate-binding modules were found. Glycoside hydrolases secreted during the growth of S. candidum 3C in three media were analyzed with a variety of substrates. Mass spectrometry analysis of the fungal culture liquid revealed the presence of peptides identical to 36 glycoside hydrolases, three proteins without known enzymatic function belonging to the same group of families, and 11 oxidative enzymes. The activity of endohemicellulases was determined using specially synthesized substrates in which the glycosidic bond between monosaccharide residues was replaced by a thiolinkage. During analysis of the CAZyme profile of S. candidum 3C, four β-xylanases from the GH10 family and two β-glucanases from the GH7 and GH55 families were detected, partially purified, and identified. © 2018, Pleiades Publishing, Ltd.\n
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\n \n\n \n \n \n \n \n \n In search of specific markers of glioblastoma: Analysis of proteoforms of glioblastoma cells.\n \n \n \n \n\n\n \n Petrenko, E.; Kopylov, A.; Kleist, O.; Legina, O.; Belyakova, N.; Pantina, R.; and Naryzhny, S.\n\n\n \n\n\n\n Tsitologiya, 60(7): 519-523. 2018.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"InPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Petrenko2018519,\r\nauthor={Petrenko, E.S. and Kopylov, A.T. and Kleist, O.A. and Legina, O.K. and Belyakova, N.V. and Pantina, R.A. and Naryzhny, S.N.},\r\ntitle={In search of specific markers of glioblastoma: Analysis of proteoforms of glioblastoma cells},\r\njournal={Tsitologiya},\r\nyear={2018},\r\nvolume={60},\r\nnumber={7},\r\npages={519-523},\r\ndoi={10.31116/tsitol.2018.07.05},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064618631&doi=10.31116%2ftsitol.2018.07.05&partnerID=40&md5=4fb79a48075054ea3847204606cafb5e},\r\naffiliation={V. N. Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119121, Russian Federation; B. P. Konstantinov Petersburg Nuclear Physics Institute, National Research Centre Kurchatov Institute, Gatchina, Leningrad Region, 188300, Russian Federation},\r\nabstract={Proteins from normal (fibroblasts) and cancer (glioblastoma) human cells were separated by two dimensional gel electrophoresis. Next, a sectional analysis of these gels by mass spectrometry was performed, and profiles of proteoforms coded by more than 5000 genes were obtained. It was found that some proteins have specific for glioblastoma cells proteoforms. We assume that these proteoforms could be used as specific for glioblastoma biomarkers. © 2018 Sankt Peterburg. All rights reserved.},\r\nauthor_keywords={Biomarker;  Glioblastoma;  Mass spectrometry;  Proteoforma;  Proteome;  Two dimensional electrophoresis},\r\ncorrespondence_address1={Naryzhny, S.N.; V. N. Orekhovich Research Institute of Biomedical ChemistryRussian Federation; email: naryzhnyy_sn@pnpi.nrcki.ru},\r\npublisher={Sankt Peterburg},\r\nissn={00413771},\r\ncoden={TSITA},\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 Proteins from normal (fibroblasts) and cancer (glioblastoma) human cells were separated by two dimensional gel electrophoresis. Next, a sectional analysis of these gels by mass spectrometry was performed, and profiles of proteoforms coded by more than 5000 genes were obtained. It was found that some proteins have specific for glioblastoma cells proteoforms. We assume that these proteoforms could be used as specific for glioblastoma biomarkers. © 2018 Sankt Peterburg. All rights reserved.\n
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\n \n\n \n \n \n \n \n \n Quaternary Structures of Human Cytoplasmic and Nuclear PCNA Are the Same.\n \n \n \n \n\n\n \n Belyakova, N.; Pantina, R.; Kovalev, R.; Filatov, M.; and Naryzhny, S.\n\n\n \n\n\n\n Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry, 12(1): 39-42. 2018.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"QuaternaryPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Belyakova201839,\r\nauthor={Belyakova, N.V. and Pantina, R.A. and Kovalev, R.A. and Filatov, M.V. and Naryzhny, S.N.},\r\ntitle={Quaternary Structures of Human Cytoplasmic and Nuclear PCNA Are the Same},\r\njournal={Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry},\r\nyear={2018},\r\nvolume={12},\r\nnumber={1},\r\npages={39-42},\r\ndoi={10.1134/S199075081801002X},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85042775026&doi=10.1134%2fS199075081801002X&partnerID=40&md5=5c507aecac55632ff5640f00b0f7139c},\r\naffiliation={Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Leningrad region, Gatchina, 188300, Russian Federation},\r\nabstract={Properties and mechanisms of PCNA (proliferating cell nuclear antigen) functions have been investigated for a long time and are studied in great detail. As follows from its name, most known PCNA functions (DNA replication, DNA repair, DNA recombination and others) are connected with cell proliferation and localization of this protein in nuclei. In addition, there is good reason to believe that PCNA also performs some functions in the cytoplasm. However, the possible role and mechanisms of PCNA action in the cytoplasm require careful study and clarification. Interestingly, such cells as neutrophils differ in that they are non-dividing on one hand and on the other hand contain a rather large amount of PCNA, which is localized only in the cytoplasm, that is, they are an ideal model for the study of cytoplasmic PCNA. Using cross-linkages with formaldehyde, we showed that this cytoplasmic PCNA is cross-linked in a similar way, that is, organized in the same way as the nuclear PCNA that is present in the proliferating cells. Previously, we showed that PCNA in such cells is organized into a dynamic complex of double trimer on the basis of the back-toback principle. Apparently, such organization of this hub-protein allows it to better coordinate the processes taking place in the cytoplasm as well. © 2018, Pleiades Publishing, Ltd.},\r\nauthor_keywords={cytoplasm;  double trimer;  monomer;  neutrophil;  PCNA;  structure},\r\ncorrespondence_address1={Naryzhny, S.N.; Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov InstituteRussian Federation; email: snaryzhny@mail.ru},\r\npublisher={Pleiades Publishing},\r\nissn={19907508},\r\nlanguage={English},\r\nabbrev_source_title={Biochem. (Moscow) Suppl. Ser. B Biomed. Chem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n Properties and mechanisms of PCNA (proliferating cell nuclear antigen) functions have been investigated for a long time and are studied in great detail. As follows from its name, most known PCNA functions (DNA replication, DNA repair, DNA recombination and others) are connected with cell proliferation and localization of this protein in nuclei. In addition, there is good reason to believe that PCNA also performs some functions in the cytoplasm. However, the possible role and mechanisms of PCNA action in the cytoplasm require careful study and clarification. Interestingly, such cells as neutrophils differ in that they are non-dividing on one hand and on the other hand contain a rather large amount of PCNA, which is localized only in the cytoplasm, that is, they are an ideal model for the study of cytoplasmic PCNA. Using cross-linkages with formaldehyde, we showed that this cytoplasmic PCNA is cross-linked in a similar way, that is, organized in the same way as the nuclear PCNA that is present in the proliferating cells. Previously, we showed that PCNA in such cells is organized into a dynamic complex of double trimer on the basis of the back-toback principle. Apparently, such organization of this hub-protein allows it to better coordinate the processes taking place in the cytoplasm as well. © 2018, Pleiades Publishing, Ltd.\n
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\n \n\n \n \n \n \n \n \n Heterologous expression in Pichia pastoris and biochemical characterization of the unmodified sulfatase from Fusarium proliferatum LE1.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Protein Engineering, Design and Selection, 30(7): 477-488. 2017.\n cited By 2\n\n\n\n
\n\n\n\n \n \n \"HeterologousPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 Sulfatases are a family of enzymes (sulfuric ester hydrolases, EC 3.1.6.-) that catalyze the hydrolysis of a wide array of sulfate esters. To date, despite the discovery of many sulfatase genes and the accumulation of data on numerous sulfated molecules, the number of characterized enzymes that are key players in sulfur metabolism remains extremely limited. While mammalian sulfatases are well studied due to their involvement in a wide range of normal and pathological biological processes, lower eukaryotic sulfatases, especially fungal sulfatases, have not been thoroughly investigated at the biochemical and structural level. In this paper, we describe the molecular cloning of Fusarium prolifera-tum sulfatase (F.p.Sulf-6His), its recombinant expression in Pichia pastoris as a soluble and active cytosolic enzyme and its detailed characterization. Gel filtration and native electrophoretic experiments showed that this recombinant enzyme exists as a tetramer in solution. The enzyme is thermo-sensitive, with an optimal temperature of 25°C. The optimal pH value for the hydrolysis of sulfate esters and stability of the enzyme was 6.0. Despite the absence of the post-translational modification of cysteine into Cα-formylglycine, the recombinant F.p.Sulf-6His has remarkably stable catalytic activity against p-nitrophenol sulfate, with kcat = 0.28 s-1 and Km = 2.45 mM, which indicates potential use in the desulfating processes. The currently proposed enzymatic mechanisms of sulfate ester hydrolysis do not explain the appearance of catalytic activity for the unmodified enzyme. According to the available models, the unmodified enzyme is not able to perform multiple catalytic acts; therefore, the enzymatic mechanism of sulfate esters hydrolysis remains to be fully elucidated. © The Author 2017. Published by Oxford University Press.\n
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\n \n\n \n \n \n \n \n \n Dataset of protein species from human liver.\n \n \n \n \n\n\n \n Naryzhny, S.; Maynskova, M.; Zgoda, V.; and Archakov, A.\n\n\n \n\n\n\n Data in Brief, 12: 584-588. 2017.\n cited By 3\n\n\n\n
\n\n\n\n \n \n \"DatasetPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Naryzhny2017584,\r\nauthor={Naryzhny, S. and Maynskova, M. and Zgoda, V. and Archakov, A.},\r\ntitle={Dataset of protein species from human liver},\r\njournal={Data in Brief},\r\nyear={2017},\r\nvolume={12},\r\npages={584-588},\r\ndoi={10.1016/j.dib.2017.04.051},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85019123043&doi=10.1016%2fj.dib.2017.04.051&partnerID=40&md5=5072bbc78c4994665c53af85e0accfea},\r\naffiliation={Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow, 119121, Russian Federation; B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center “Kurchatov Institute”, 1 Orlova roscha, Gatchina, Leningrad Region  188300, Russian Federation},\r\nabstract={This article contains data related to the research article entitled “Zipf׳s law in proteomics” (Naryzhny et al., 2017) [1]. The protein composition in the human liver or hepatocarcinoma (HepG2) cells extracts was estimated using a filter-aided sample preparation (FASP) protocol. The protein species/proteoform composition in the human liver was determined by two-dimensional electrophoresis (2-DE) followed by Electrospray Ionization Liquid Chromatography-Tandem Mass Spectrometry (ESI LC-MS/MS). In the case of two-dimensional electrophoresis (2-DE), the gel was stained with Coomassie Brilliant Blue R350, and image analysis was performed with ImageMaster 2D Platinum software (GE Healthcare). The 96 sections in the 2D gel were selected and cut for subsequent ESI LC-MS/MS and protein identification. If the same protein was detected in different sections, it was considered to exist as different protein species/proteoforms. A list of human liver proteoforms detected in this way is presented. © 2017 The Authors},\r\ncorrespondence_address1={Naryzhny, S.; Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Pogodinskaya 10, Russian Federation; email: snaryzhny@mail.ru},\r\npublisher={Elsevier Inc.},\r\nissn={23523409},\r\nlanguage={English},\r\nabbrev_source_title={Data Brief},\r\ndocument_type={Data Paper},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n This article contains data related to the research article entitled “Zipf׳s law in proteomics” (Naryzhny et al., 2017) [1]. The protein composition in the human liver or hepatocarcinoma (HepG2) cells extracts was estimated using a filter-aided sample preparation (FASP) protocol. The protein species/proteoform composition in the human liver was determined by two-dimensional electrophoresis (2-DE) followed by Electrospray Ionization Liquid Chromatography-Tandem Mass Spectrometry (ESI LC-MS/MS). In the case of two-dimensional electrophoresis (2-DE), the gel was stained with Coomassie Brilliant Blue R350, and image analysis was performed with ImageMaster 2D Platinum software (GE Healthcare). The 96 sections in the 2D gel were selected and cut for subsequent ESI LC-MS/MS and protein identification. If the same protein was detected in different sections, it was considered to exist as different protein species/proteoforms. A list of human liver proteoforms detected in this way is presented. © 2017 The Authors\n
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\n \n\n \n \n \n \n \n \n Corrigendum to “Characterization of a new α-L-fucosidase isolated from Fusarium proliferatum LE1 that is regioselective to α-(1 → 4)-L-fucosidic linkage in the hydrolysis of α-L-fucobiosides” [Biochimie (2017) 132C (54–65)] (S0300908416303029) (10.1016/j.biochi.2016.10.014).\n \n \n \n \n\n\n \n Shvetsova, S.; Shabalin, K.; Bobrov, K.; Ivanen, D.; Ustyuzhanina, N.; Krylov, V.; Nifantiev, N.; Naryzhny, S.; Zgoda, V.; Eneyskaya, E.; and Kulminskaya, A.\n\n\n \n\n\n\n Biochimie, 137: 198. 2017.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"CorrigendumPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Shvetsova2017198,\r\nauthor={Shvetsova, S.V. and Shabalin, K.A. and Bobrov, K.S. and Ivanen, D.R. and Ustyuzhanina, N.E. and Krylov, V.B. and Nifantiev, N.E. and Naryzhny, S.N. and Zgoda, V.G. and Eneyskaya, E.V. and Kulminskaya, A.A.},\r\ntitle={Corrigendum to “Characterization of a new α-L-fucosidase isolated from Fusarium proliferatum LE1 that is regioselective to α-(1 → 4)-L-fucosidic linkage in the hydrolysis of α-L-fucobiosides” [Biochimie (2017) 132C (54–65)] (S0300908416303029) (10.1016/j.biochi.2016.10.014)},\r\njournal={Biochimie},\r\nyear={2017},\r\nvolume={137},\r\npages={198},\r\ndoi={10.1016/j.biochi.2017.04.007},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018899144&doi=10.1016%2fj.biochi.2017.04.007&partnerID=40&md5=c6e162583a61b1d5dcf12b5dd03029b4},\r\naffiliation={National Research Center «Kurchatov Institute», B.P. Konstantinov Petersburg Nuclear Physics Institute, Orlova Roscha, Gatchina, 188300, Russian Federation; Department of Medical Physics, Peter the Great St. Petersburg Polytechnic University, Chlopina Str. 5, St. Petersburg, 195251, Russian Federation; Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya Str., 29, St. Petersburg, 195251, Russian Federation; N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47, Leninsky Pr., Moscow, 119991, Russian Federation; Institute of Biomedical Chemistry, Pogodinskaya 10, Moscow, 119121, Russian Federation},\r\nabstract={The authors would like to inform readers of needed clarifications to this article: 1. page 55, the second column, line 12: pNPαGal instead of pNP αGal.2. page 59, section 3.3, references to Figure 2 should be to Figure 3. Line 6: Fig. 2A should be Fig. 3A; line 10: Fig. 2B should be Fig. 3B; line 11: Fig. 2C should be Fig. 3C; line 14: Fig. 2D should be Fig. 3D.3. page 61, section 3.5, lines 3 and 4: in the sentence starting “The highest affinity …” the numbering of fucobiosides should be corrected and should read “The highest affinity was observed for the L-Fuc-α-(1→4)-L-Fuc-α-OPr and the lowest one was for the L-Fuc-α-(1→3)-L-Fuc-α-OPr”.4. page 63, Acknowledgments: please remove Table 2S and add Fig. 3S in line 8. It should read: … syntheses of the p-nitrophenyl glycoside substrates and the experiments depicted in Figs. 4–6, 1S and 3S, Tables 1 and 5 as well as sample preparation for gene sequencing and analysis were supported by the RSF grant 16-14-00109; …The authors wish to apologise for any inconvenience caused. © 2017},\r\ncorrespondence_address1={Kulminskaya, A.A.; Laboratory of Enzymology, National Research Center «Kurchatov Institute», B.P. Konstantinov Petersburg Nuclear Physics Institute, Orlova roscha, Russian Federation; email: kulm@omrb.pnpi.spb.ru},\r\npublisher={Elsevier B.V.},\r\nissn={03009084},\r\ncoden={BICMB},\r\npubmed_id={28434920},\r\nlanguage={English},\r\nabbrev_source_title={Biochimie},\r\ndocument_type={Erratum},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n The authors would like to inform readers of needed clarifications to this article: 1. page 55, the second column, line 12: pNPαGal instead of pNP αGal.2. page 59, section 3.3, references to Figure 2 should be to Figure 3. Line 6: Fig. 2A should be Fig. 3A; line 10: Fig. 2B should be Fig. 3B; line 11: Fig. 2C should be Fig. 3C; line 14: Fig. 2D should be Fig. 3D.3. page 61, section 3.5, lines 3 and 4: in the sentence starting “The highest affinity …” the numbering of fucobiosides should be corrected and should read “The highest affinity was observed for the L-Fuc-α-(1→4)-L-Fuc-α-OPr and the lowest one was for the L-Fuc-α-(1→3)-L-Fuc-α-OPr”.4. page 63, Acknowledgments: please remove Table 2S and add Fig. 3S in line 8. It should read: … syntheses of the p-nitrophenyl glycoside substrates and the experiments depicted in Figs. 4–6, 1S and 3S, Tables 1 and 5 as well as sample preparation for gene sequencing and analysis were supported by the RSF grant 16-14-00109; …The authors wish to apologise for any inconvenience caused. © 2017\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 \"AggregationPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 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.\n
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\n \n\n \n \n \n \n \n \n Quaternary structures of human cytoplasmic and nuclear PCNA are the same.\n \n \n \n \n\n\n \n Belyakova, N.; Pantina, R.; Kovalev, R.; Filatov, M.; and Naryzhny, S.\n\n\n \n\n\n\n Biomeditsinskaya Khimiya, 63(4): 356-360. 2017.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"QuaternaryPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Belyakova2017356,\r\nauthor={Belyakova, N.V. and Pantina, R.A. and Kovalev, R.A. and Filatov, M.V. and Naryzhny, S.N.},\r\ntitle={Quaternary structures of human cytoplasmic and nuclear PCNA are the same},\r\njournal={Biomeditsinskaya Khimiya},\r\nyear={2017},\r\nvolume={63},\r\nnumber={4},\r\npages={356-360},\r\ndoi={10.18097/PBMC20176304356},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028754223&doi=10.18097%2fPBMC20176304356&partnerID=40&md5=ce5cadb78677efafb3f40f9a9cf8706b},\r\naffiliation={Petersburg Nuclear Physics Institute NRC Kurchatov Institute, Leningrad Region (PNPI), Gatchina, 188300, Russian Federation},\r\nabstract={Properties and mechanisms of PCNA (proliferating cell nuclear antigen) functions have been investigated for a long time and are studied in great detail. As follows from its name, most known PCNA functions (DNA replication, DNA repair, DNA recombination and others) are connected with cell proliferation and localization of this protein in nuclei. In addition, there is good reason to believe that PCNA also performs some functions in the cytoplasm. However, the possible role and mechanisms of PCNA action in the cytoplasm require careful study and clarification. Interestingly, such cells as neutrophils differ in that they are non-dividing on one hand and on the other hand contain a rather large amount of PCNA, which is localized only in the cytoplasm, that is, they are an ideal model for the study of cytoplasmic PCNA. Using cross-linkages with formaldehyde, we showed that this cytoplasmic PCNA is cross-linked in a similar way, that is, organized in the same way as the nuclear PCNA that is present in the proliferating cells. Previously, we showed that PCNA in such cells is organized into a dynamic complex of double trimer on the basis of the back-to-back principle (Naryzhny S.N. et al. (2005) J. Biol. Chem., 280, 13888). Apparently, such organization of this hub-protein allows it to better coordinate the processes taking place in the cytoplasm as well.},\r\nauthor_keywords={Cytoplasm;  Double trimer;  Monomer;  Neutrophil;  PCNA;  Structure},\r\npublisher={Russian Academy of Medical Sciences},\r\nissn={23106905},\r\npubmed_id={28862608},\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 Properties and mechanisms of PCNA (proliferating cell nuclear antigen) functions have been investigated for a long time and are studied in great detail. As follows from its name, most known PCNA functions (DNA replication, DNA repair, DNA recombination and others) are connected with cell proliferation and localization of this protein in nuclei. In addition, there is good reason to believe that PCNA also performs some functions in the cytoplasm. However, the possible role and mechanisms of PCNA action in the cytoplasm require careful study and clarification. Interestingly, such cells as neutrophils differ in that they are non-dividing on one hand and on the other hand contain a rather large amount of PCNA, which is localized only in the cytoplasm, that is, they are an ideal model for the study of cytoplasmic PCNA. Using cross-linkages with formaldehyde, we showed that this cytoplasmic PCNA is cross-linked in a similar way, that is, organized in the same way as the nuclear PCNA that is present in the proliferating cells. Previously, we showed that PCNA in such cells is organized into a dynamic complex of double trimer on the basis of the back-to-back principle (Naryzhny S.N. et al. (2005) J. Biol. Chem., 280, 13888). Apparently, such organization of this hub-protein allows it to better coordinate the processes taking place in the cytoplasm as well.\n
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\n \n\n \n \n \n \n \n \n A semi-virtual two dimensional gel electrophoresis: IF–ESI LC-MS/MS.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n MethodsX, 4: 260-264. 2017.\n cited By 2\n\n\n\n
\n\n\n\n \n \n \"APaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 A method for increasing the productivity of ESI LC-MS/MS (electrospray ionization-liquid chromatography-tandem mass spectrometry) was proposed and applied. After IF (isoelectric focusing) of the sample using IPG (immobilized pH gradient) strip, the strip was cut to sections, and every section was treated according to trypsinolysis protocol for MS/MS analysis. The peptides produced were further analyzed by ESI LC-MS/MS. The procedure allows to:• identify many more proteins and proteoforms compared to shotgun analysis of extracts.• build a semi-virtual 2DE map of identified proteins. © 2017 The Authors\n
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\n \n\n \n \n \n \n \n \n Multiomics study of HepG2 cell line proteome.\n \n \n \n \n\n\n \n Poverennaya, E.; Kiseleva, O.; Ponomarenko, E.; Naryzhny, S.; Zgoda, V.; and Lisitsa, A.\n\n\n \n\n\n\n Biomeditsinskaya Khimiya, 63(5): 373-378. 2017.\n cited By 1\n\n\n\n
\n\n\n\n \n \n \"MultiomicsPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Poverennaya2017373,\r\nauthor={Poverennaya, E.V. and Kiseleva, O.I. and Ponomarenko, E.A. and Naryzhny, S.N. and Zgoda, V.G. and Lisitsa, A.V.},\r\ntitle={Multiomics study of HepG2 cell line proteome},\r\njournal={Biomeditsinskaya Khimiya},\r\nyear={2017},\r\nvolume={63},\r\nnumber={5},\r\npages={373-378},\r\ndoi={10.18097/PBMC20176305373},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85033215527&doi=10.18097%2fPBMC20176305373&partnerID=40&md5=94ea687ebe4dd828c734e5220ad350c2},\r\naffiliation={Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121, Russian Federation},\r\nabstract={Current proteomic studies are generally focused on the most abundant proteoforms encoded by canonical nucleic sequences. Transcriptomic and proteomic data, accumulated in a variety of postgenome sources and coupled with state-of-art analytical technologies, allow to start the identification of aberrant (non-canonical) proteoforms. The main sources of aberrant proteoforms are alternative splicing, single nucleotide polymorphism, and post-translational modifications. The aim of this work was to estimate the heterogeneity of HepG2 proteome. We suggested multiomics approach, which combines transcriptomic (RNAseq) and proteomic (2DE-MS/MS) methods, as a promising strategy to explore the proteome.},\r\nauthor_keywords={Alternative splicing;  Post-translational modification;  Proteoform;  Proteome;  Single amino acid polymorphism;  Transcriptome;  Transcriptoproteome},\r\ncorrespondence_address1={Kiseleva, O.I.; Institute of Biomedical Chemistry, 10 Pogodinskaya str., Russian Federation; email: olly.kiseleva@gmail.com},\r\npublisher={Russian Academy of Medical Sciences},\r\nissn={23106905},\r\npubmed_id={29080867},\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 Current proteomic studies are generally focused on the most abundant proteoforms encoded by canonical nucleic sequences. Transcriptomic and proteomic data, accumulated in a variety of postgenome sources and coupled with state-of-art analytical technologies, allow to start the identification of aberrant (non-canonical) proteoforms. The main sources of aberrant proteoforms are alternative splicing, single nucleotide polymorphism, and post-translational modifications. The aim of this work was to estimate the heterogeneity of HepG2 proteome. We suggested multiomics approach, which combines transcriptomic (RNAseq) and proteomic (2DE-MS/MS) methods, as a promising strategy to explore the proteome.\n
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\n \n\n \n \n \n \n \n \n Characterization of a new α-L-fucosidase isolated from Fusarium proliferatum LE1 that is regioselective to α-(1 → 4)-L-fucosidic linkage in the hydrolysis of α-L-fucobiosides.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Biochimie, 132: 54-65. 2017.\n cited By 5\n\n\n\n
\n\n\n\n \n \n \"CharacterizationPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 Here, we report the biochemical characterization of a novel α-L-fucosidase with broad substrate specificity (FpFucA) isolated from the mycelial fungus Fusarium proliferatum LE1. Highly purified α-L-fucosidase was obtained from several chromatographic steps after growth in the presence of L-fucose. The purified α-L-fucosidase appeared to be a monomeric protein of 67 ± 1 kDa that was able to hydrolyze the synthetic substrate p-nitrophenyl α-L-fucopyranoside (pNPFuc), with Km = 1.1 ± 0.1 mM and kcat = 39.8 ± 1.8 s−1. L-fucose, 1-deoxyfuconojirimycin and tris(hydroxymethyl)aminomethane inhibited pNPFuc hydrolysis, with inhibition constants of 0.2 ± 0.05 mM, 7.1 ± 0.05 nM, and 12.2 ± 0.1 mM, respectively. We assumed that the enzyme belongs to subfamily A of the GH29 family (CAZy database) based on its ability to hydrolyze practically all fucose-containing oligosaccharides used in the study and the phylogenetic analysis. We found that this enzyme was a unique α-L-fucosidase that preferentially hydrolyzes the α-(1 → 4)-L-fucosidic linkage present in α-L-fucobiosides with different types of linkages. As a retaining glycosidase, FpFucA is capable of catalyzing the transglycosylation reaction with alcohols (methanol, ethanol, and 1-propanol) and pNP-containing monosaccharides as acceptors. These features make the enzyme an important tool that can be used in the various modifications of valuable fucose-containing compounds. © 2016\n
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\n \n\n \n \n \n \n \n \n Towards the full realization of 2DE power.\n \n \n \n \n\n\n \n Naryzhny, S.\n\n\n \n\n\n\n Proteomes, 4(4). 2016.\n cited By 6\n\n\n\n
\n\n\n\n \n \n \"TowardsPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Naryzhny2016,\r\nauthor={Naryzhny, S.},\r\ntitle={Towards the full realization of 2DE power},\r\njournal={Proteomes},\r\nyear={2016},\r\nvolume={4},\r\nnumber={4},\r\ndoi={10.3390/proteomes4040033},\r\nart_number={33},\r\nnote={cited By 6},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-85033220492&doi=10.3390%2fproteomes4040033&partnerID=40&md5=289382547a6981ecd112456c19e58e9d},\r\naffiliation={Institute of Biomedical Chemistry, Pogodinskaya 10, Moscow, 119121, Russian Federation; B. P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center 'Kurchatov Institute', Leningrad region, Gatchina, 188300, Russian Federation},\r\nabstract={Here, approaches that allow disclosure of the information hidden inside and outside of two-dimensional gel electrophoresis (2DE) are described. Experimental identification methods, such as mass spectrometry of high resolution and sensitivity (MALDI-TOF MS and ESI LC-MS/MS) and immunodetection (Western and Far-Western) in combination with bioinformatics (collection of all information about proteoforms), move 2DE to the next level of power. The integration of these technologies will promote 2DE as a powerful methodology of proteomics technology. © 2016 by the authors.},\r\nauthor_keywords={Bioinformatics;  Mass-spectrometry;  Proteoforms;  Two-dimensional gel electrophoresis},\r\ncorrespondence_address1={Naryzhny, S.; Institute of Biomedical Chemistry, Pogodinskaya 10, Russian Federation; email: snaryzhny@mail.ru},\r\npublisher={MDPI AG},\r\nissn={22277382},\r\nlanguage={English},\r\nabbrev_source_title={Proteomes},\r\ndocument_type={Review},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
\n\n\n
\n Here, approaches that allow disclosure of the information hidden inside and outside of two-dimensional gel electrophoresis (2DE) are described. Experimental identification methods, such as mass spectrometry of high resolution and sensitivity (MALDI-TOF MS and ESI LC-MS/MS) and immunodetection (Western and Far-Western) in combination with bioinformatics (collection of all information about proteoforms), move 2DE to the next level of power. The integration of these technologies will promote 2DE as a powerful methodology of proteomics technology. © 2016 by the authors.\n
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\n \n\n \n \n \n \n \n \n Virtual-Experimental 2DE Approach in Chromosome-Centric Human Proteome Project.\n \n \n \n \n\n\n \n Naryzhny, S.; Maynskova, M.; Zgoda, V.; Ronzhina, N.; Kleyst, O.; Vakhrushev, I.; and Archakov, A.\n\n\n \n\n\n\n Journal of Proteome Research, 15(2): 525-530. 2016.\n cited By 12\n\n\n\n
\n\n\n\n \n \n \"Virtual-ExperimentalPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Naryzhny2016525,\r\nauthor={Naryzhny, S.N. and Maynskova, M.A. and Zgoda, V.G. and Ronzhina, N.L. and Kleyst, O.A. and Vakhrushev, I.V. and Archakov, A.I.},\r\ntitle={Virtual-Experimental 2DE Approach in Chromosome-Centric Human Proteome Project},\r\njournal={Journal of Proteome Research},\r\nyear={2016},\r\nvolume={15},\r\nnumber={2},\r\npages={525-530},\r\ndoi={10.1021/acs.jproteome.5b00871},\r\nnote={cited By 12},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84957643611&doi=10.1021%2facs.jproteome.5b00871&partnerID=40&md5=42435533bb64e48d54488ee3ec24b82b},\r\naffiliation={Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Pogodinskaya 10, Moscow, 119121, Russian Federation; Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute, Leningrad Region, Gatchina, 188300, Russian Federation},\r\nabstract={To obtain more information about human proteome, especially about proteoforms (protein species) coded by 18th chromosome, we separated proteins from human cancer cell line (HepG2) by two-dimensional gel electrophoresis (2DE). Initially, proteins in major spots were identified by MALDI-MS peptide mass fingerprinting. According to parameters (pI/Mw) of identified proteins the gel was calibrated. Using this calibrated gel, a virtual 2D map of proteoforms coded by Chromosome 18 was constructed. Next, the produced gel was divided into 96 sections with determined coordinates. Each section was cut, shredded, and treated by trypsin according to mass-spectrometry protocol. After protein identification by shotgun mass spectrometry using ESI LC-MS/MS, a list of 20 462 proteoforms (product of 3774 genes) was generated. Among them, 165 proteoforms are representing 39 genes of 18th chromosome. The 3D graphs showing the distribution of different proteoforms from the same gene in 2D map were generated. This is a first step in creation of 2DE-based knowledge database of proteins coded by 18th chromosome. © 2015 American Chemical Society.},\r\nauthor_keywords={Chromosome 18;  chromosome-centric;  ESI LC-MS/MS;  inventory;  mass spectrometry;  proteoforms;  proteome;  two-dimensional electrophoresis},\r\ncorrespondence_address1={Naryzhny, S.N.; Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Pogodinskaya 10, Russian Federation; email: snaryzhny@mail.ru},\r\npublisher={American Chemical Society},\r\nissn={15353893},\r\ncoden={JPROB},\r\npubmed_id={26667816},\r\nlanguage={English},\r\nabbrev_source_title={J. Proteome Res.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
\n\n\n
\n To obtain more information about human proteome, especially about proteoforms (protein species) coded by 18th chromosome, we separated proteins from human cancer cell line (HepG2) by two-dimensional gel electrophoresis (2DE). Initially, proteins in major spots were identified by MALDI-MS peptide mass fingerprinting. According to parameters (pI/Mw) of identified proteins the gel was calibrated. Using this calibrated gel, a virtual 2D map of proteoforms coded by Chromosome 18 was constructed. Next, the produced gel was divided into 96 sections with determined coordinates. Each section was cut, shredded, and treated by trypsin according to mass-spectrometry protocol. After protein identification by shotgun mass spectrometry using ESI LC-MS/MS, a list of 20 462 proteoforms (product of 3774 genes) was generated. Among them, 165 proteoforms are representing 39 genes of 18th chromosome. The 3D graphs showing the distribution of different proteoforms from the same gene in 2D map were generated. This is a first step in creation of 2DE-based knowledge database of proteins coded by 18th chromosome. © 2015 American Chemical Society.\n
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\n \n\n \n \n \n \n \n \n Combination of virtual and experimental 2DE together with ESI LC-MS/MS gives a clearer view about proteomes of human cells and plasma.\n \n \n \n \n\n\n \n Naryzhny, S.; Zgoda, V.; Maynskova, M.; Novikova, S.; Ronzhina, N.; Vakhrushev, I.; Khryapova, E.; Lisitsa, A.; Tikhonova, O.; Ponomarenko, E.; and Archakov, A.\n\n\n \n\n\n\n Electrophoresis, 37(2): 302-309. 2016.\n cited By 10\n\n\n\n
\n\n\n\n \n \n \"CombinationPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Naryzhny2016302,\r\nauthor={Naryzhny, S.N. and Zgoda, V.G. and Maynskova, M.A. and Novikova, S.E. and Ronzhina, N.L. and Vakhrushev, I.V. and Khryapova, E.V. and Lisitsa, A.V. and Tikhonova, O.V. and Ponomarenko, E.A. and Archakov, A.I.},\r\ntitle={Combination of virtual and experimental 2DE together with ESI LC-MS/MS gives a clearer view about proteomes of human cells and plasma},\r\njournal={Electrophoresis},\r\nyear={2016},\r\nvolume={37},\r\nnumber={2},\r\npages={302-309},\r\ndoi={10.1002/elps.201500382},\r\nnote={cited By 10},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84953840094&doi=10.1002%2felps.201500382&partnerID=40&md5=afcfe7028803a8a87d12bf8ec59bc5f6},\r\naffiliation={Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russian Federation; B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute, Gatchina, Leningrad district, Russian Federation},\r\nabstract={Virtual and experimental 2DE coupled with ESI LC-MS/MS was introduced to obtain better representation of the information about human proteome. The proteins from HEPG2 cells and human blood plasma were run by 2DE. After staining and protein spot identification by MALDI-TOF MS, the protein maps were generated. The experimental physicochemical parameters (pI/Mw) of the proteoforms further detected by ESI LC-MS/MS in these spots were obtained. Next, the theoretical pI and Mw of identified proteins were calculated using program Compute pI/Mw (http://web.expasy.org/compute_pi/pi_tool-doc.html). Accordingly, the relationship between theoretical and experimental parameters was analyzed, and the correlation plots were built. Additionally, virtual/experimental information about different protein species/proteoforms from the same genes was extracted. As it was revealed from the plots, the major proteoforms detected in HepG2 cell line have pI/Mw parameters similar to theoretical values. In opposite, the minor protein species have mainly very different from theoretical pI and Mw parameters. A similar situation was observed in plasma in much higher degree. It means that minor protein species are heavily modified in cell and even more in plasma proteome. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},\r\nauthor_keywords={2DE;  ESI LC-MS/MS;  Mass spectrometry;  Protein species},\r\ncorrespondence_address1={Naryzhny, S.N.; B.P. Konstantinov Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Orlova Roscha, Russian Federation; email: snaryzhny@mail.ru},\r\npublisher={Wiley-VCH Verlag},\r\nissn={01730835},\r\ncoden={ELCTD},\r\npubmed_id={26454001},\r\nlanguage={English},\r\nabbrev_source_title={Electrophoresis},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
\n\n\n
\n Virtual and experimental 2DE coupled with ESI LC-MS/MS was introduced to obtain better representation of the information about human proteome. The proteins from HEPG2 cells and human blood plasma were run by 2DE. After staining and protein spot identification by MALDI-TOF MS, the protein maps were generated. The experimental physicochemical parameters (pI/Mw) of the proteoforms further detected by ESI LC-MS/MS in these spots were obtained. Next, the theoretical pI and Mw of identified proteins were calculated using program Compute pI/Mw (http://web.expasy.org/compute_pi/pi_tool-doc.html). Accordingly, the relationship between theoretical and experimental parameters was analyzed, and the correlation plots were built. Additionally, virtual/experimental information about different protein species/proteoforms from the same genes was extracted. As it was revealed from the plots, the major proteoforms detected in HepG2 cell line have pI/Mw parameters similar to theoretical values. In opposite, the minor protein species have mainly very different from theoretical pI and Mw parameters. A similar situation was observed in plasma in much higher degree. It means that minor protein species are heavily modified in cell and even more in plasma proteome. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.\n
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\n  \n 2015\n \n \n (3)\n \n \n
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\n \n\n \n \n \n \n \n \n Experimental estimation of proteome size for cells and human plasma.\n \n \n \n \n\n\n \n Naryzhny, S.; Zgoda, V.; Maynskova, M.; Ronzhina, N.; Belyakova, N.; Legina, O.; and Archakov, A.\n\n\n \n\n\n\n Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry, 9(4): 305-311. 2015.\n cited By 1\n\n\n\n
\n\n\n\n \n \n \"ExperimentalPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Naryzhny2015305,\r\nauthor={Naryzhny, S.N. and Zgoda, V.G. and Maynskova, M.A. and Ronzhina, N.L. and Belyakova, N.V. and Legina, O.K. and Archakov, A.I.},\r\ntitle={Experimental estimation of proteome size for cells and human plasma},\r\njournal={Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry},\r\nyear={2015},\r\nvolume={9},\r\nnumber={4},\r\npages={305-311},\r\ndoi={10.1134/S1990750815040034},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84948406580&doi=10.1134%2fS1990750815040034&partnerID=40&md5=88d17be4df459a877d6931120c8d805d},\r\naffiliation={Institute of Biomedical Chemistry, ul. Pogodinskaya 10, Moscow, 119121, Russian Federation; Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Leningrad oblast, 188300, Russian Federation},\r\nabstract={Huge range of concentrations of different proteoforms and insufficient sensitivity of methods for detection of proteins at a single molecule level does not yet allow obtaining the whole image of the human proteome. In our investigations, we tried to evaluate the size of different proteomes (cells and plasma). The approach used is based on detection of protein spots in two-dimensional electrophoresis (2-DE) after protein staining by dyes with different sensitivities. The functional dependence of the number of detected protein spots from sensitivity of protein dyes was generated. Next, by extrapolation of this function curve to theoretical point of the maximum sensitivity (detection of a single smallest polypeptide) it was calculated that a single human cell (HepG2) may contain minimum 70000 proteoforms, human plasma—1.5 million. Utilization of this approach to other, smaller proteomes, showed the competency of this extrapolation. For instance, the size of mycoplasma (Acholeplasma laidlawii) was estimated in 1100 proteoforms, yeast (Saccharomyces cerevisiae)—40000, Escherichia coli—6200, Pyrococcus furiosus—3400. In hepatocytes, the amount of proteoforms was the same as in HepG2–70000. Significance of obtained data is in possibilities to estimating the proteome organization and planning next steps in its study. © 2015, Pleiades Publishing, Ltd.},\r\nauthor_keywords={2-DE;  proteoforms;  proteome},\r\ncorrespondence_address1={Naryzhny, S.N.; Institute of Biomedical Chemistry, ul. Pogodinskaya 10, Russian Federation; email: snaryzhny@mail.ru},\r\npublisher={Maik Nauka-Interperiodica Publishing},\r\nissn={19907508},\r\nlanguage={English},\r\nabbrev_source_title={Biochem. (Moscow) Suppl. Ser. B Biomed. Chem.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
\n\n\n
\n Huge range of concentrations of different proteoforms and insufficient sensitivity of methods for detection of proteins at a single molecule level does not yet allow obtaining the whole image of the human proteome. In our investigations, we tried to evaluate the size of different proteomes (cells and plasma). The approach used is based on detection of protein spots in two-dimensional electrophoresis (2-DE) after protein staining by dyes with different sensitivities. The functional dependence of the number of detected protein spots from sensitivity of protein dyes was generated. Next, by extrapolation of this function curve to theoretical point of the maximum sensitivity (detection of a single smallest polypeptide) it was calculated that a single human cell (HepG2) may contain minimum 70000 proteoforms, human plasma—1.5 million. Utilization of this approach to other, smaller proteomes, showed the competency of this extrapolation. For instance, the size of mycoplasma (Acholeplasma laidlawii) was estimated in 1100 proteoforms, yeast (Saccharomyces cerevisiae)—40000, Escherichia coli—6200, Pyrococcus furiosus—3400. In hepatocytes, the amount of proteoforms was the same as in HepG2–70000. Significance of obtained data is in possibilities to estimating the proteome organization and planning next steps in its study. © 2015, Pleiades Publishing, Ltd.\n
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\n \n\n \n \n \n \n \n \n The novel strain Fusarium proliferatum LE1 (RCAM02409) produces α-L-fucosidase and arylsulfatase during the growth on fucoidan.\n \n \n \n \n\n\n \n Shvetsova, S.; Zhurishkina, E.; Bobrov, K.; Ronzhina, N.; Lapina, I.; Ivanen, D.; Gagkaeva, T.; and Kulminskaya, A.\n\n\n \n\n\n\n Journal of Basic Microbiology, 55(4): 471-479. 2015.\n cited By 10\n\n\n\n
\n\n\n\n \n \n \"ThePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Shvetsova2015471,\r\nauthor={Shvetsova, S.V. and Zhurishkina, E.V. and Bobrov, K.S. and Ronzhina, N.L. and Lapina, I.M. and Ivanen, D.R. and Gagkaeva, T.Y. and Kulminskaya, A.A.},\r\ntitle={The novel strain Fusarium proliferatum LE1 (RCAM02409) produces α-L-fucosidase and arylsulfatase during the growth on fucoidan},\r\njournal={Journal of Basic Microbiology},\r\nyear={2015},\r\nvolume={55},\r\nnumber={4},\r\npages={471-479},\r\ndoi={10.1002/jobm.201400309},\r\nnote={cited By 10},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84964296282&doi=10.1002%2fjobm.201400309&partnerID=40&md5=5abfbe90837307b502556b4393fc9c2e},\r\naffiliation={National Research Center Kurchatov Institute, B.P. Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Russian Federation; St. Petersburg State Polytechnical University, St. Petersburg, Russian Federation; All-Russian Institute of Plant Protection, Russian Academy of Agricultural Sciences, St. Petersburg, Pushkin, Russian Federation},\r\nabstract={Enzymes capable of modifying the sulfated polymeric molecule of fucoidan are mainly produced by different groups of marine organisms: invertebrates, bacteria, and also some fungi. We have discovered and identified a new strain of filamentous fungus Fusarium proliferatum LE1 (deposition number in Russian Collection of Agricultural Microorganisms is RCAM02409), which is a potential producer of fucoidan-degrading enzymes. The strain LE1 (RCAM02409) was identified on the basis of morphological characteristics and analysis of ITS sequences of ribosomal DNA. During submerged cultivation of F. proliferatum LE1 in the nutrient medium containing natural fucoidan sources (the mixture of brown algae Laminaria digitata and Fucus vesiculosus), enzymic activities of α-L-fucosidase and arylsulfatase were inducible. These enzymes hydrolyzed model substrates, para-nitrophenyl α-L-fucopyranoside and para-nitrophenyl sulfate, respectively. However, the α-L-fucosidase is appeared to be a secreted enzyme while the arylsulfatase was an intracellular one. No detectable fucoidanase activity was found during F. proliferatum LE1 growth in submerged culture or in a static one. Comparative screening for fucoidanase/arylsulfatase/α-L-fucosidase activities among several related Fusarium strains showed a uniqueness of F. proliferatum LE1 to produce arylsulfatase and α-L-fucosidase enzymes. Apart them, the strain was shown to produce other glycoside hydrolyses. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},\r\nauthor_keywords={Arylsulfatase;  Fucoidan;  Fusarium proliferatum;  α-L-Fucosidase},\r\ncorrespondence_address1={Kulminskaya, A.A.; Laboratory of Enzymology, Petersburg Nuclear Physics InstituteRussian Federation; email: kulm@omrb.pnpi.spb.ru},\r\npublisher={Wiley-VCH Verlag},\r\nissn={0233111X},\r\ncoden={JBMIE},\r\npubmed_id={25346501},\r\nlanguage={English},\r\nabbrev_source_title={J. Basic Microbiol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
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\n Enzymes capable of modifying the sulfated polymeric molecule of fucoidan are mainly produced by different groups of marine organisms: invertebrates, bacteria, and also some fungi. We have discovered and identified a new strain of filamentous fungus Fusarium proliferatum LE1 (deposition number in Russian Collection of Agricultural Microorganisms is RCAM02409), which is a potential producer of fucoidan-degrading enzymes. The strain LE1 (RCAM02409) was identified on the basis of morphological characteristics and analysis of ITS sequences of ribosomal DNA. During submerged cultivation of F. proliferatum LE1 in the nutrient medium containing natural fucoidan sources (the mixture of brown algae Laminaria digitata and Fucus vesiculosus), enzymic activities of α-L-fucosidase and arylsulfatase were inducible. These enzymes hydrolyzed model substrates, para-nitrophenyl α-L-fucopyranoside and para-nitrophenyl sulfate, respectively. However, the α-L-fucosidase is appeared to be a secreted enzyme while the arylsulfatase was an intracellular one. No detectable fucoidanase activity was found during F. proliferatum LE1 growth in submerged culture or in a static one. Comparative screening for fucoidanase/arylsulfatase/α-L-fucosidase activities among several related Fusarium strains showed a uniqueness of F. proliferatum LE1 to produce arylsulfatase and α-L-fucosidase enzymes. Apart them, the strain was shown to produce other glycoside hydrolyses. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.\n
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\n \n\n \n \n \n \n \n \n Experimental estimation of proteome size for cells and Human plasma.\n \n \n \n \n\n\n \n Naryzhny, S.; Zgoda, V.; Maynskova, M.; Ronzhina, N.; Belyakov, N.; Legina, O.; and Archakov, A.\n\n\n \n\n\n\n Biomeditsinskaya Khimiya, 61(2): 279-285. 2015.\n cited By 4\n\n\n\n
\n\n\n\n \n \n \"ExperimentalPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Naryzhny2015279,\r\nauthor={Naryzhny, S.N. and Zgoda, V.G. and Maynskova, M.A. and Ronzhina, N.L. and Belyakov, N.V. and Legina, O.K. and Archakov, A.I.},\r\ntitle={Experimental estimation of proteome size for cells and Human plasma},\r\njournal={Biomeditsinskaya Khimiya},\r\nyear={2015},\r\nvolume={61},\r\nnumber={2},\r\npages={279-285},\r\ndoi={10.18097/PBMC20156102279},\r\nnote={cited By 4},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84949454275&doi=10.18097%2fPBMC20156102279&partnerID=40&md5=d1eb52ca240c608cb446b827e50aa693},\r\naffiliation={Institute of Biomedical Chemistry, 10 Pogodinskaya Str., Moscow, 119121, Russian Federation; Konstantinov Petersburg Nuclear Physics Institute, Gatchina, Leningrad District, Russian Federation},\r\nabstract={Huge range of concentrations of different protein and insufficient sensitivity of methods for detection of proteins at a single molecule level does not yet allow obtaining the whole image of human proteome. In our investigations, we tried to evaluate the size of different proteomes (cells and plasma). The approach used is based on detection of protein spots in 2-DE after staining by protein dyes with different sensitivities. The function representing the dependence of the number of protein spots on sensitivity of protein dyes was generated. Next, by extrapolation of this function curve to theoretical point of the maximum sensitivity (detection of a single smallest polypeptide) it was calculated that a single human cell (HepG2) may contain minimum 70000 proteoforms, and plasma-1.5 mln. Utilization of this approach to other, smaller proteomes showed the competency of this extrapolation. For instance, the size of mycoplasma (Acholeplasma laidlawii) was estimated in 1100 proteoforms, yeast (Saccharomyces cerevisiae) - 40000, E. coli - 6200, P. furiosus - 3400. In hepatocytes, the amount of proteoforms was the same as in HepG2-70000. Significance of obtained data is in possibilities to estimating the proteome organization and planning next steps in its study.},\r\nauthor_keywords={2DE;  Proteoforms;  Proteome},\r\npublisher={Russian Academy of Medical Sciences},\r\nissn={23106905},\r\npubmed_id={25978394},\r\nlanguage={Russian},\r\nabbrev_source_title={Biomeditsinskaya Khim.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
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\n Huge range of concentrations of different protein and insufficient sensitivity of methods for detection of proteins at a single molecule level does not yet allow obtaining the whole image of human proteome. In our investigations, we tried to evaluate the size of different proteomes (cells and plasma). The approach used is based on detection of protein spots in 2-DE after staining by protein dyes with different sensitivities. The function representing the dependence of the number of protein spots on sensitivity of protein dyes was generated. Next, by extrapolation of this function curve to theoretical point of the maximum sensitivity (detection of a single smallest polypeptide) it was calculated that a single human cell (HepG2) may contain minimum 70000 proteoforms, and plasma-1.5 mln. Utilization of this approach to other, smaller proteomes showed the competency of this extrapolation. For instance, the size of mycoplasma (Acholeplasma laidlawii) was estimated in 1100 proteoforms, yeast (Saccharomyces cerevisiae) - 40000, E. coli - 6200, P. furiosus - 3400. In hepatocytes, the amount of proteoforms was the same as in HepG2-70000. Significance of obtained data is in possibilities to estimating the proteome organization and planning next steps in its study.\n
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\n  \n 2014\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n \n 2DE-based approach for estimation of number of protein species in a cell.\n \n \n \n \n\n\n \n Naryzhny, S.; Lisitsa, A.; Zgoda, V.; Ponomarenko, E.; and Archakov, A.\n\n\n \n\n\n\n Electrophoresis, 35(6): 895-900. 2014.\n cited By 13\n\n\n\n
\n\n\n\n \n \n \"2DE-basedPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Naryzhny2014895,\r\nauthor={Naryzhny, S.N. and Lisitsa, A.V. and Zgoda, V.G. and Ponomarenko, E.A. and Archakov, A.I.},\r\ntitle={2DE-based approach for estimation of number of protein species in a cell},\r\njournal={Electrophoresis},\r\nyear={2014},\r\nvolume={35},\r\nnumber={6},\r\npages={895-900},\r\ndoi={10.1002/elps.201300525},\r\nnote={cited By 13},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84903372428&doi=10.1002%2felps.201300525&partnerID=40&md5=0a917db36bb3ff52bd56028fe044404d},\r\naffiliation={Department of Proteomic Research and Mass Spectrometry, V.N. Orekhovich, Institute of Biomedical Chemistry, Moscow, Russian Federation; Department of Molecular and Radiation Biophysics, B.P. Konstantinov, Petersburg Nuclear Physics Institute, Gatchina, Leningrad District, Russian Federation; Department for Bioinformatics, V.N. Orekhovich, Institute of Biomedical Chemistry, Moscow, Russian Federation; V.N. Orekhovich Institute of Biomedical Chemistry, Moscow, Russian Federation},\r\nabstract={Insufficient sensitivity of methods for detection of proteins at a single molecule level does not yet allow obtaining the whole image of human proteome. But to go further, we need at least to know the proteome size, or how many different protein species compose this proteome. This is the task that could be at least partially realized by the method described in this article. The approach used in our study is based on detection of protein spots in 2DE after staining by protein dyes with various sensitivities. As the different protein spots contain different protein species, counting the spots opens a way for estimation of number of protein species. The function representing the dependence of the number of protein spots on sensitivity or LOD of protein dyes was generated. And extrapolation of this function curve to theoretical point of the maximum sensitivity (detection of a single smallest polypeptide) allowed to counting the number of different molecules (polypeptide species) at the concentration level of a single polypeptide per proteome. Using this approach, it was estimated that the minimal numbers of protein species for model objects, Escherichia coli and Pirococcus furiosus, are 6200 and 3400, respectively. We expect a single human cell (HepG2) to contain minimum 70000 protein species. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.},\r\nauthor_keywords={2DE;  Approach;  Cell;  Number;  Protein species},\r\ncorrespondence_address1={Naryzhny, S.N.; Petersburg Nuclear Physics Institute, Gatchina 188300, Leningrad District, Russian Federation; email: snaryzhny@mail.ru},\r\nissn={01730835},\r\ncoden={ELCTD},\r\npubmed_id={24259369},\r\nlanguage={English},\r\nabbrev_source_title={Electrophoresis},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
\n\n\n
\n Insufficient sensitivity of methods for detection of proteins at a single molecule level does not yet allow obtaining the whole image of human proteome. But to go further, we need at least to know the proteome size, or how many different protein species compose this proteome. This is the task that could be at least partially realized by the method described in this article. The approach used in our study is based on detection of protein spots in 2DE after staining by protein dyes with various sensitivities. As the different protein spots contain different protein species, counting the spots opens a way for estimation of number of protein species. The function representing the dependence of the number of protein spots on sensitivity or LOD of protein dyes was generated. And extrapolation of this function curve to theoretical point of the maximum sensitivity (detection of a single smallest polypeptide) allowed to counting the number of different molecules (polypeptide species) at the concentration level of a single polypeptide per proteome. Using this approach, it was estimated that the minimal numbers of protein species for model objects, Escherichia coli and Pirococcus furiosus, are 6200 and 3400, respectively. We expect a single human cell (HepG2) to contain minimum 70000 protein species. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.\n
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\n \n\n \n \n \n \n \n \n Development of barcode and proteome profiling of glioblastoma.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry, 8(3): 243-251. 2014.\n cited By 7\n\n\n\n
\n\n\n\n \n \n \"DevelopmentPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 High grade glioma (glioblastoma) is the most common brain tumor. Its malignancy makes it the fourth biggest cause of cancer death. In our experiments, we used several glioblastoma cell lines to obtain proteomics information specific for this disease. 2DE separation with following imaging, immunochemistry, spot picking, and mass-spectrometry allowed us to detecting more than 600 protein spots and identifying more than 130 of them. Proteome profiles in normal and glioblastoma cell lines are very similar but levels of several proteins have prominent differences between norm and cancer. Among these proteins are alpha-enolase (ENOA-HUMAN), pyruvate kinase M1/M2 (KPYM-HUMAN), cofilin 1 (COF1-HUMAN), translationally-controlled tumor protein TCTP-HUMAN, annexin 1 (ANXA1-HUMAN), PCNA (PCNA-HUMAN), p53 (TP53-HUMAN) and others. Most interesting results were obtained about protein p53. Its level was dramatically up-regulated and enriched by multiple additional isoforms in all glioblastoma cell lines. An immunological analysis (Western blot) of three hub-proteins (p53, 14-3-3, PCNA) allowed us to creating the minimal barcode of glioblastoma cell lines. These preliminary data point to this barcode as a promising diagnostic tool for testing of the biological fluids from patients. © 2014 Pleiades Publishing, Ltd.\n
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\n  \n 2013\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n \n Chromosomocentric approach to overcoming difficulties in implementation of international project Human Proteome.\n \n \n \n \n\n\n \n Archakov, A.; Zgoda, V.; Kopylov, A.; Naryzhny, S.; Chernobrovkin, A.; Ponomarenko, E.; and Lisitsa, A.\n\n\n \n\n\n\n Ukrain'skyi Biokhimichnyi Zhurnal, 85(6): 8-17. 2013.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"ChromosomocentricPaper\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{Archakov20138,\r\nauthor={Archakov, A.I. and Zgoda, V.G. and Kopylov, A.T. and Naryzhny, S.N. and Chernobrovkin, A.L. and Ponomarenko, E.A. and Lisitsa, A.V.},\r\ntitle={Chromosomocentric approach to overcoming difficulties in implementation of international project Human Proteome},\r\njournal={Ukrain'skyi Biokhimichnyi Zhurnal},\r\nyear={2013},\r\nvolume={85},\r\nnumber={6},\r\npages={8-17},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84890366739&partnerID=40&md5=bcbec90a6d222127b50b7e4336c61146},\r\naffiliation={V. N. Orekhovich Scientific-Research Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Russian Federation; Petersburg Nuclear Physics Institute at National Research Centre, Kurchatov Institute, Russian Federation},\r\nabstract={The international project Human Proteome (PHP), being a logical continuation of the project Human Genome, was started on September 23, 2010. In correspondence with the genocentric approach, the PHP aim is to prepare a catalogue of all human proteins and to decipher a network of their interactions. The PHP implementation difficulties arise because the research subject itself -proteome -is much more complicated than genome. The major problem is the insufficient sensitivity of proteome methods that does not allow detecting low-and ultralow-copy proteins. Bad reproducibility of proteome methods and the lack of so-called gold standard is the second major complicacy in PHP implementation. The third problem is the dynamic character of proteome, its instability in time. The paper deals with possible variants of overcoming these complicacies, preventing from successful implementation of PHP.},\r\nauthor_keywords={Massspectrometric method of monitoring of multiple responses;  Project Human Genome;  Project Human Proteome;  Sensitivity limit},\r\ncorrespondence_address1={V. N. Orekhovich Scientific-Research Institute of Biomedical Chemistry, Russian Academy of Medical SciencesRussian Federation},\r\nissn={02018470},\r\nlanguage={Ukrainian},\r\nabbrev_source_title={Ukr. Biokhim. Zh.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
\n\n\n
\n The international project Human Proteome (PHP), being a logical continuation of the project Human Genome, was started on September 23, 2010. In correspondence with the genocentric approach, the PHP aim is to prepare a catalogue of all human proteins and to decipher a network of their interactions. The PHP implementation difficulties arise because the research subject itself -proteome -is much more complicated than genome. The major problem is the insufficient sensitivity of proteome methods that does not allow detecting low-and ultralow-copy proteins. Bad reproducibility of proteome methods and the lack of so-called gold standard is the second major complicacy in PHP implementation. The third problem is the dynamic character of proteome, its instability in time. The paper deals with possible variants of overcoming these complicacies, preventing from successful implementation of PHP.\n
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\n \n\n \n \n \n \n \n \n Chromosome 18 transcriptome profiling and targeted proteome mapping in depleted plasma, liver tissue and HepG2 cells.\n \n \n \n \n\n\n \n Zgoda, V.; Kopylov, A.; Tikhonova, O.; Moisa, A.; Pyndyk, N.; Farafonova, T.; Novikova, S.; Lisitsa, A.; Ponomarenko, E.; Poverennaya, E.; Radko, S.; Khmeleva, S.; Kurbatov, L.; Filimonov, A.; Bogolyubova, N.; Ilgisonis, E.; Chernobrovkin, A.; Ivanov, A.; Medvedev, A.; Mezentsev, Y.; Moshkovskii, S.; Naryzhny, S.; Ilina, E.; Kostrjukova, E.; Alexeev, D.; Tyakht, A.; Govorun, V.; and Archakov, A.\n\n\n \n\n\n\n Journal of Proteome Research, 12(1): 123-134. 2013.\n cited By 40\n\n\n\n
\n\n\n\n \n \n \"ChromosomePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Zgoda2013123,\r\nauthor={Zgoda, V.G. and Kopylov, A.T. and Tikhonova, O.V. and Moisa, A.A. and Pyndyk, N.V. and Farafonova, T.E. and Novikova, S.E. and Lisitsa, A.V. and Ponomarenko, E.A. and Poverennaya, E.V. and Radko, S.P. and Khmeleva, S.A. and Kurbatov, L.K. and Filimonov, A.D. and Bogolyubova, N.A. and Ilgisonis, E.V. and Chernobrovkin, A.L. and Ivanov, A.S. and Medvedev, A.E. and Mezentsev, Y.V. and Moshkovskii, S.A. and Naryzhny, S.N. and Ilina, E.N. and Kostrjukova, E.S. and Alexeev, D.G. and Tyakht, A.V. and Govorun, V.M. and Archakov, A.I.},\r\ntitle={Chromosome 18 transcriptome profiling and targeted proteome mapping in depleted plasma, liver tissue and HepG2 cells},\r\njournal={Journal of Proteome Research},\r\nyear={2013},\r\nvolume={12},\r\nnumber={1},\r\npages={123-134},\r\ndoi={10.1021/pr300821n},\r\nnote={cited By 40},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84874089699&doi=10.1021%2fpr300821n&partnerID=40&md5=b374b634b3cbbfc434862586bba4d378},\r\naffiliation={Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Russian Federation; Petersburg Nuclear Physics Institute, Gatchina, Leningrad District, Russian Federation; Research Institute of Physical Chemical Medicine, Federal Medical-Biological Agency of the Russian Federation, Russian Federation},\r\nabstract={The final goal of the Russian part of the Chromosome-centric Human Proteome Project (C-HPP) was established as the analysis of the chromosome 18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells with the sensitivity of 10-18 M. Using SRM, we have recently targeted 277 Chr 18 proteins in plasma, liver, and HepG2 cells. On the basis of the results of the survey, the SRM assays were drafted for 250 proteins: 41 proteins were found only in the liver tissue, 82 proteins were specifically detected in depleted plasma, and 127 proteins were mapped in both samples. The targeted analysis of HepG2 cells was carried out for 49 proteins; 41 of them were successfully registered using ordinary SRM and 5 additional proteins were registered using a combination of irreversible binding of proteins on CN-Br Sepharose 4B with SRM. Transcriptome profiling of HepG2 cells performed by RNAseq and RTPCR has shown a significant correlation (r = 0.78) for 42 gene transcripts. A pilot affinity-based interactome analysis was performed for cytochrome b5 using analytical and preparative optical biosensor fishing followed by MS analysis of the fished proteins. All of the data on the proteome complement of the Chr 18 have been integrated into our gene-centric knowledgebase (www.kb18.ru). © 2012 American Chemical Society.},\r\nauthor_keywords={Chromosome 18;  Human proteome project;  Mass spectrometry;  Selected reaction monitoring (SRM);  Targeted proteomics},\r\ncorrespondence_address1={Archakov, A.I.; Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical SciencesRussian Federation; email: alexander.archakov@ibmc.msk.ru},\r\nissn={15353893},\r\ncoden={JPROB},\r\npubmed_id={23256950},\r\nlanguage={English},\r\nabbrev_source_title={J. Proteome Res.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
\n\n\n
\n The final goal of the Russian part of the Chromosome-centric Human Proteome Project (C-HPP) was established as the analysis of the chromosome 18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells with the sensitivity of 10-18 M. Using SRM, we have recently targeted 277 Chr 18 proteins in plasma, liver, and HepG2 cells. On the basis of the results of the survey, the SRM assays were drafted for 250 proteins: 41 proteins were found only in the liver tissue, 82 proteins were specifically detected in depleted plasma, and 127 proteins were mapped in both samples. The targeted analysis of HepG2 cells was carried out for 49 proteins; 41 of them were successfully registered using ordinary SRM and 5 additional proteins were registered using a combination of irreversible binding of proteins on CN-Br Sepharose 4B with SRM. Transcriptome profiling of HepG2 cells performed by RNAseq and RTPCR has shown a significant correlation (r = 0.78) for 42 gene transcripts. A pilot affinity-based interactome analysis was performed for cytochrome b5 using analytical and preparative optical biosensor fishing followed by MS analysis of the fished proteins. All of the data on the proteome complement of the Chr 18 have been integrated into our gene-centric knowledgebase (www.kb18.ru). © 2012 American Chemical Society.\n
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\n  \n 2012\n \n \n (2)\n \n \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 \"PurificationPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{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
\n
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\n 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.\n
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\n \n\n \n \n \n \n \n \n Chromosome-centric approach to overcoming bottlenecks in the Human Proteome Project.\n \n \n \n \n\n\n \n Archakov, A.; Zgoda, V.; Kopylov, A.; Naryzhny, S.; Chernobrovkin, A.; Ponomarenko, E.; and Lisitsa, A.\n\n\n \n\n\n\n Expert review of proteomics, 9(6): 667-676. 2012.\n cited By 31\n\n\n\n
\n\n\n\n \n \n \"Chromosome-centricPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Archakov2012667,\r\nauthor={Archakov, A. and Zgoda, V. and Kopylov, A. and Naryzhny, S. and Chernobrovkin, A. and Ponomarenko, E. and Lisitsa, A.},\r\ntitle={Chromosome-centric approach to overcoming bottlenecks in the Human Proteome Project.},\r\njournal={Expert review of proteomics},\r\nyear={2012},\r\nvolume={9},\r\nnumber={6},\r\npages={667-676},\r\ndoi={10.1586/epr.12.54},\r\nnote={cited By 31},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84874100578&doi=10.1586%2fepr.12.54&partnerID=40&md5=b0d4c62e4fbd379210412f4f1a044470},\r\naffiliation={Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Pogodinskaya Street 10, Moscow, 119121, Russian Federation},\r\nabstract={The international Human Proteome Project (HPP), a logical continuation of the Human Genome Project, was launched on 23 September 2010 in Sydney, Australia. In accordance with the gene-centric approach, the goals of the HPP are to prepare an inventory of all human proteins and decipher the network of cellular protein interactions. The greater complexity of the proteome in comparison to the genome gives rise to three bottlenecks in the implementation of the HPP. The main bottleneck is the insufficient sensitivity of proteomic technologies, hampering the detection of proteins with low- and ultra-low copy numbers. The second bottleneck is related to poor reproducibility of proteomic methods and the lack of a so-called 'gold' standard. The last bottleneck is the dynamic nature of the proteome: its instability over time. The authors here discuss approaches to overcome these bottlenecks in order to improve the success of the HPP.},\r\nfunding_details={Ministry of Education and Science of the Russian Federation16.522.12.2002},\r\n}
\n
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\n The international Human Proteome Project (HPP), a logical continuation of the Human Genome Project, was launched on 23 September 2010 in Sydney, Australia. In accordance with the gene-centric approach, the goals of the HPP are to prepare an inventory of all human proteins and decipher the network of cellular protein interactions. The greater complexity of the proteome in comparison to the genome gives rise to three bottlenecks in the implementation of the HPP. The main bottleneck is the insufficient sensitivity of proteomic technologies, hampering the detection of proteins with low- and ultra-low copy numbers. The second bottleneck is related to poor reproducibility of proteomic methods and the lack of a so-called 'gold' standard. The last bottleneck is the dynamic nature of the proteome: its instability over time. The authors here discuss approaches to overcome these bottlenecks in order to improve the success of the HPP.\n
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\n  \n 2010\n \n \n (6)\n \n \n
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\n \n\n \n \n \n \n \n \n Ratio of 3' → 5'-Exonuclease and DNA-polymerase activities in normal and cancer cells of rodents and humans.\n \n \n \n \n\n\n \n Kravetskaya, T.; Ronzhina, N.; and Krutyakov, V.\n\n\n \n\n\n\n Tsitologiya, 52(8): 634-638. 2010.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"RatioPaper\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{Kravetskaya2010634,\r\nauthor={Kravetskaya, T.P. and Ronzhina, N.L. and Krutyakov, V.M.},\r\ntitle={Ratio of 3' → 5'-Exonuclease and DNA-polymerase activities in normal and cancer cells of rodents and humans},\r\njournal={Tsitologiya},\r\nyear={2010},\r\nvolume={52},\r\nnumber={8},\r\npages={634-638},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-78049293748&partnerID=40&md5=454e4b5a0f4c0e3bb6e4a312f62d95c4},\r\naffiliation={Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute RAS, Gatchina, Russian Federation},\r\nabstract={Mutations in the genes of corrective 3' → 5'-exonucleases as wellas in DNA polymerases lead to decrease in DNA biosynthesis accuracy all over genome. This is accompanied by the increase in mutagenesis and carcinogenesis probabilities. In this work, the activities of 3' → 5'-exonucleases and DNA polymerases were studied in the extracts from normal and cancer cells of rodents and humans, and we are the first to measure their integral ratios. As example, in cultivated dermal fibroblasts of an adult human, the value of the ratio of activities of 3' → 5'-exonucleases to DNA polymerase activity (3'-exo/pol) surpassed several folds the such a value for He- La cells. Similar picture was observed during the comparison of normal fibroblasts of rat embryos and transformed fibroblasts of Chinese hamster A238. Experiments with cell-free extracts of some organs from healthy rats of various ages have shown that normal proliferating cells demonstrate higher 3' → 5'-exonuclease activity and higher values of 3'-exo/pol that quiescent cells. Comparison of these data suggests a violation of the function of corrective 3' → 5'-exonucleases in abnormally growing cancer cells.},\r\nauthor_keywords={3' →5'-exonucleases;  Cancer cells;  Normal cells},\r\ncorrespondence_address1={Krutyakov, V. M.; Division of Molecular and Radiation Biophysics, B.P. Konstantinov Petersburg Nuclear Physics Institute RAS, Gatchina, Russian Federation; email: krut@omrb.pnpi.spb.ru},\r\nissn={00413771},\r\ncoden={TSITA},\r\npubmed_id={20968097},\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 Mutations in the genes of corrective 3' → 5'-exonucleases as wellas in DNA polymerases lead to decrease in DNA biosynthesis accuracy all over genome. This is accompanied by the increase in mutagenesis and carcinogenesis probabilities. In this work, the activities of 3' → 5'-exonucleases and DNA polymerases were studied in the extracts from normal and cancer cells of rodents and humans, and we are the first to measure their integral ratios. As example, in cultivated dermal fibroblasts of an adult human, the value of the ratio of activities of 3' → 5'-exonucleases to DNA polymerase activity (3'-exo/pol) surpassed several folds the such a value for He- La cells. Similar picture was observed during the comparison of normal fibroblasts of rat embryos and transformed fibroblasts of Chinese hamster A238. Experiments with cell-free extracts of some organs from healthy rats of various ages have shown that normal proliferating cells demonstrate higher 3' → 5'-exonuclease activity and higher values of 3'-exo/pol that quiescent cells. Comparison of these data suggests a violation of the function of corrective 3' → 5'-exonucleases in abnormally growing cancer cells.\n
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\n \n\n \n \n \n \n \n \n Investigation of the interaction of repair DNA polymerase β and autonomous 3′ → 5′-exonucleases TREX1 and TREX2.\n \n \n \n \n\n\n \n Belyakova, N.; Legina, O.; Ronzhina, N.; Shevelev, I.; and Krutiakov, V.\n\n\n \n\n\n\n Biology Bulletin, 37(5): 464-470. 2010.\n cited By 1\n\n\n\n
\n\n\n\n \n \n \"InvestigationPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Belyakova2010464,\r\nauthor={Belyakova, N.V. and Legina, O.K. and Ronzhina, N.L. and Shevelev, I.V. and Krutiakov, V.M.},\r\ntitle={Investigation of the interaction of repair DNA polymerase β and autonomous 3′ → 5′-exonucleases TREX1 and TREX2},\r\njournal={Biology Bulletin},\r\nyear={2010},\r\nvolume={37},\r\nnumber={5},\r\npages={464-470},\r\ndoi={10.1134/S1062359010050043},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77957154675&doi=10.1134%2fS1062359010050043&partnerID=40&md5=cd2d467d810c0028191feaff54fbb4e7},\r\naffiliation={Department of Molecular and Radiation Biophysics, Konstantinov Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Orlova Roscha, Leningrad region 188300, Russian Federation},\r\nabstract={The possibility of interaction of recombinant proteins of human repair DNA polymerase β with proofreading 3′ → 5′-exonucleases TREX1 and TREX2 was investigated in vitro for the first time. The results of gel filtration analysis show the formation of a complex between 3′ → 5′-exonucleases mTREX1 and hTREX2 and DNA polymerase β. DNA polymerase activity is shown to increase four-fold in the presence of 3′ → 5′-exonuclease TREX2. The experiments with the use of immunodot and Western blot assays on the binding of DNA-polymerase β with 3′ → 5′-exonucleases TREX1 and TREX2 immobilized on a nitrocellulose membrane provided additional evidence on the direct association of the above proteins in complexes. © 2010 Pleiades Publishing, Ltd.},\r\ncorrespondence_address1={Belyakova, N. V.; Department of Molecular and Radiation Biophysics, Konstantinov Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Orlova Roscha, Leningrad region 188300, Russian Federation; email: bel_tasha@mail.ru},\r\nissn={10623590},\r\ncoden={BRASE},\r\nlanguage={English},\r\nabbrev_source_title={Biol. Bull.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n The possibility of interaction of recombinant proteins of human repair DNA polymerase β with proofreading 3′ → 5′-exonucleases TREX1 and TREX2 was investigated in vitro for the first time. The results of gel filtration analysis show the formation of a complex between 3′ → 5′-exonucleases mTREX1 and hTREX2 and DNA polymerase β. DNA polymerase activity is shown to increase four-fold in the presence of 3′ → 5′-exonuclease TREX2. The experiments with the use of immunodot and Western blot assays on the binding of DNA-polymerase β with 3′ → 5′-exonucleases TREX1 and TREX2 immobilized on a nitrocellulose membrane provided additional evidence on the direct association of the above proteins in complexes. © 2010 Pleiades Publishing, Ltd.\n
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\n \n\n \n \n \n \n \n \n Ratio of 3′ → 5′-exonuclease and DNA polymerase activities in normal and cancer cells of rodents and human.\n \n \n \n \n\n\n \n Kravetskaya, T.; Ronzhina, N.; and Krutyakov, V.\n\n\n \n\n\n\n Cell and Tissue Biology, 4(5): 424-428. 2010.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"RatioPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Kravetskaya2010424,\r\nauthor={Kravetskaya, T.P. and Ronzhina, N.L. and Krutyakov, V.M.},\r\ntitle={Ratio of 3′ → 5′-exonuclease and DNA polymerase activities in normal and cancer cells of rodents and human},\r\njournal={Cell and Tissue Biology},\r\nyear={2010},\r\nvolume={4},\r\nnumber={5},\r\npages={424-428},\r\ndoi={10.1134/S1990519X10050032},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79952075759&doi=10.1134%2fS1990519X10050032&partnerID=40&md5=ba831784399403150043e94b901a7905},\r\naffiliation={Division of Molecular and Radiation Biophysics, Konstantinov St. Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina, Leningrad oblast, Russian Federation},\r\nabstract={Mutations in genes of DNA polymerases or corrective 3′ → 5′-exonucleases lead to a decrease in the fidelity of DNA biosynthesis throughout the genome, which is accompanied by an increase in the probability of mutagenesis and carcinogenesis. In the present work, activities of 3′ → 5′-exonucleases and DNA polymerases are studied in extracts of rodents and human normal and cancer cells and, for the first time, their integral ratios are measured to elucidate the role of correcting exonucleases in carcinogenesis. Thus, in experiments on cells growing in culture, it has been found that in adult human dermal fibroblasts the value of ratio of activity of 3′ → 5′-exonucleases to the DNA polymerase activity (3′-exo/pol) exceeds this ratio for HeLa cells. A similar situation is also observed in a comparison of normal rat embryo fibroblasts and Syrian hamster A238 transformed fibroblasts. Experiments with extracts of the cells some organs of healthy rats of different ages have shown that in norm the proliferating cells are characterized by higher activities of 3′ → 5′-exonucleases and higher 3′-exo/pol values than in quiescent cells. A comparison of these data allows us to conlude that a disturbance in the functions of corrective 3′ → 5′-exonucleases occurs in pathologically growing cancer cells. © 2010 Pleiades Publishing, Ltd.},\r\nauthor_keywords={3′ → 5′-exonucleases;  DNA polymerases;  normal and cancer cells},\r\ncorrespondence_address1={Krutyakov, V. M.; Division of Molecular and Radiation Biophysics, Konstantinov St. Petersburg Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina, Leningrad oblast, Russian Federation; email: krav@omrb.pnpi.spb.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 Mutations in genes of DNA polymerases or corrective 3′ → 5′-exonucleases lead to a decrease in the fidelity of DNA biosynthesis throughout the genome, which is accompanied by an increase in the probability of mutagenesis and carcinogenesis. In the present work, activities of 3′ → 5′-exonucleases and DNA polymerases are studied in extracts of rodents and human normal and cancer cells and, for the first time, their integral ratios are measured to elucidate the role of correcting exonucleases in carcinogenesis. Thus, in experiments on cells growing in culture, it has been found that in adult human dermal fibroblasts the value of ratio of activity of 3′ → 5′-exonucleases to the DNA polymerase activity (3′-exo/pol) exceeds this ratio for HeLa cells. A similar situation is also observed in a comparison of normal rat embryo fibroblasts and Syrian hamster A238 transformed fibroblasts. Experiments with extracts of the cells some organs of healthy rats of different ages have shown that in norm the proliferating cells are characterized by higher activities of 3′ → 5′-exonucleases and higher 3′-exo/pol values than in quiescent cells. A comparison of these data allows us to conlude that a disturbance in the functions of corrective 3′ → 5′-exonucleases occurs in pathologically growing cancer cells. © 2010 Pleiades Publishing, Ltd.\n
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\n \n\n \n \n \n \n \n \n Proliferating cell nuclear antigen in the cytoplasm interacts with components of glycolysis and cancer.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n FEBS Letters, 584(20): 4292-4298. 2010.\n cited By 39\n\n\n\n
\n\n\n\n \n \n \"ProliferatingPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 Proliferating cell nuclear antigen (PCNA) is involved in a wide range of functions in the nucleus. However, a substantial amount of PCNA is also present in the cytoplasm, although their function is unknown. Here we show, through Far-Western blotting and mass spectrometry, that PCNA is associated with several cytoplasmic oncoproteins, including elongation factor, malate dehydrogenase, and peptidyl-prolyl isomerase. Surprisingly, PCNA is also associated with six glycolytic enzymes that are involved in the regulation of steps 4-9 in the glycolysis pathway. Structured summary: MINT-7995351: G3P (uniprotkb:. P04406) and PCNA (uniprotkb:. P12004) colocalize (MI:. 0403) by fluorescence microscopy (MI:. 0416)MINT-7995334: ENOA (uniprotkb:. P06733) and PCNA (uniprotkb:. P12004) colocalize (MI:. 0403) by fluorescence microscopy (MI:. 0416)MINT-7995368: ALDOA (uniprotkb:. P04075) and PCNA (uniprotkb:. P12004) colocalize (MI:. 0403) by fluorescence microscopy (MI:. 0416)MINT-7995141: G3P (uniprotkb:. P04406) binds (MI:. 0407) to PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995182: ENOA (uniprotkb:. P06733) binds (MI:. 0407) to PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995132: G3P (uniprotkb:. P04406) physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995228: PRDX6 (uniprotkb:. P30041) physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995220: CAH2 (uniprotkb:. P00918) physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995114: Triosephosphate isomerase (uniprotkb:. P60174) binds (MI:. 0407) to PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995244: K2C7 (uniprotkb:. P08729) physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995252: ANXA2 (uniprotkb:. P07355) physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995122: Triosephosphate isomerase (uniprotkb:. P60174) physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995093: ALDOA (uniprotkb:. P04075) physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995148: PGK1 (uniprotkb:. P00558) physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995158: PGAM1 (uniprotkb:. P18669)physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995166: PGAM1 (uniprotkb:. P18669) binds (MI:. 0407) to PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995105: ALDOA (uniprotkb:. P04075) binds (MI:. 0407) to PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995260: PPIA (uniprotkb:. P62937) physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995173: ENOA (uniprotkb:. P06733) physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995268: EF1A (uniprotkb:. P68104) physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995236: MDHM (uniprotkb:. P40926) physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995189: RSSA (uniprotkb:. P08865) physically interacts (MI:. 0915) with PCNA (uniprotkb:. P12004) by far western blotting (MI:. 0047)MINT-7995282: PCNA (uniprotkb:. P12004) physically interacts (MI:. 0915) with ALDOA (uniprotkb:. P00883) and G3P (uniprotkb:. P46406) by anti bait coimmunoprecipitation (MI:. 0006). © 2010 Federation of European Biochemical Societies.\n
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\n \n\n \n \n \n \n \n \n [Investigation of the interaction of repair DNA polymerase beta and autonomous 3' –> 5'-exonucleases TREX1 and TREX2].\n \n \n \n \n\n\n \n Beliakova, N.; Legina, O.; Ronzhina, N.; Shevelev, I.; and Krutiakov, V.\n\n\n \n\n\n\n Izvestiia Akademii nauk. Seriia biologicheskaia / Rossiǐskaia akademiia nauk, (5): 547-553. 2010.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"[InvestigationPaper\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{Beliakova2010547,\r\nauthor={Beliakova, N.V. and Legina, O.K. and Ronzhina, N.L. and Shevelev, I.V. and Krutiakov, V.M.},\r\ntitle={[Investigation of the interaction of repair DNA polymerase beta and autonomous 3' --> 5'-exonucleases TREX1 and TREX2].},\r\njournal={Izvestiia Akademii nauk. Seriia biologicheskaia / Rossiǐskaia akademiia nauk},\r\nyear={2010},\r\nnumber={5},\r\npages={547-553},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-79952201662&partnerID=40&md5=899eafb1c03fcc747693b60180f721c6},\r\nabstract={The possibility of interaction of recombinant proteins of human repair DNA polymerase beta with proofreading 3' --> 5'-exonucleases TREX1 and TREX2 was investigated in vitro for the first time. The results of gel filtration analysis show the formation of a complex between 3' --> 5' -exonucleases mTREX1 and hTREX2 and DNA polymerase beta. DNA polymerase activity is shown to increase four-fold in the presence of 3' --> 5'-exonuclease TREX2. The experiments with the use of immunodot and Western blot assays on the binding of DNA-polymerase beta with 3' --> 5'-exonucleases TREX1 and TREX2 immobilized on a nitrocellulose membrane provided additional evidence on the direct association of the above proteins in complexes.},\r\ncorrespondence_address1={Beliakova, N.V.},\r\nissn={10263470},\r\npubmed_id={21077363},\r\nlanguage={Russian},\r\nabbrev_source_title={Izv. Akad. Nauk. Ser. Biol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n The possibility of interaction of recombinant proteins of human repair DNA polymerase beta with proofreading 3' –> 5'-exonucleases TREX1 and TREX2 was investigated in vitro for the first time. The results of gel filtration analysis show the formation of a complex between 3' –> 5' -exonucleases mTREX1 and hTREX2 and DNA polymerase beta. DNA polymerase activity is shown to increase four-fold in the presence of 3' –> 5'-exonuclease TREX2. The experiments with the use of immunodot and Western blot assays on the binding of DNA-polymerase beta with 3' –> 5'-exonucleases TREX1 and TREX2 immobilized on a nitrocellulose membrane provided additional evidence on the direct association of the above proteins in complexes.\n
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\n \n\n \n \n \n \n \n \n The immortalizing and transforming ability of two common human papillomavirus 16 E6 variants with different prevalences in cervical cancer.\n \n \n \n \n\n\n \n Richard, C.; Lanner, C.; Naryzhny, S.; Sherman, L.; Lee, H.; Lambert, P.; and Zehbe, I.\n\n\n \n\n\n\n Oncogene, 29(23): 3435-3445. 2010.\n cited By 44\n\n\n\n
\n\n\n\n \n \n \"ThePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Richard20103435,\r\nauthor={Richard, C. and Lanner, C. and Naryzhny, S.N. and Sherman, L. and Lee, H. and Lambert, P.F. and Zehbe, I.},\r\ntitle={The immortalizing and transforming ability of two common human papillomavirus 16 E6 variants with different prevalences in cervical cancer},\r\njournal={Oncogene},\r\nyear={2010},\r\nvolume={29},\r\nnumber={23},\r\npages={3435-3445},\r\ndoi={10.1038/onc.2010.93},\r\nnote={cited By 44},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-77953479092&doi=10.1038%2fonc.2010.93&partnerID=40&md5=a2b7b7205b3c0b34e3f9617c09aeccaa},\r\naffiliation={Research Laboratory, Thunder Bay Regional Health Sciences Centre, Thunder Bay, ON, Canada; Molecular Genetics, Northern Ontario School of Medicine, Laurentian University, Sudbury, ON, Canada; Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada; Northeastern Ontario Regional Cancer Program, Sudbury Regional Hospital, Sudbury, ON, Canada; Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel; McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, United States; Probe Development and Biomarker Exploration, Thunder Bay Regional Research Institute, 980 Oliver Road, Thunder Bay, ON P7B 6V4, Canada},\r\nabstract={Persistent infection with high-risk human papillomaviruses (HPVs), especially type 16 has been undeniably linked to cervical cancer. The Asian-American (AA) variant of HPV16 is more common in the Americas than the prototype in cervical cancer. The different prevalence is based on three amino acid changes within the E6 protein denoted Q14H/H78Y/L83V. To investigate the mechanism(s) behind this observation, both E6 proteins, in the presence of E7, were evaluated for their ability to extend the life span of and transform primary human foreskin keratinocytes (PHFKs). Long-term cell culture studies resulted in death at passage 9 of vector-transduced PHFKs (negative control), but survival of both E6 PHFKs to passage 65 (and beyond). Compared with E6/E7 PHFKs, AA/E7 PHFKs were significantly faster dividing, developed larger cells in monolayer cultures, showed double the epithelial thickness and expressed cytokeratin 10 when grown as organotypic raft cultures. Telomerase activation and p53 inactivation, two hallmarks of immortalization, were not significantly different between the two populations. Both were resistant to anoikis at later passages, but only AA/E7 PHFKs acquired the capacity for in vitro transformation. Proteomic analysis revealed markedly different protein patterns between E6/E7 and AA/E7, particularly with respect to key cellular metabolic enzymes. Our results provide new insights into the reasons underlying the greater prevalence of the AA variant in cervical cancer as evidenced by characteristics associated with higher oncogenic potential. © 2010 Macmillan Publishers Limited All rights reserved.},\r\nauthor_keywords={Cervical cancer;  Human papillomavirus;  Human primary foreskin keratinocytes;  Immortalization;  Transformation},\r\n}
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\n Persistent infection with high-risk human papillomaviruses (HPVs), especially type 16 has been undeniably linked to cervical cancer. The Asian-American (AA) variant of HPV16 is more common in the Americas than the prototype in cervical cancer. The different prevalence is based on three amino acid changes within the E6 protein denoted Q14H/H78Y/L83V. To investigate the mechanism(s) behind this observation, both E6 proteins, in the presence of E7, were evaluated for their ability to extend the life span of and transform primary human foreskin keratinocytes (PHFKs). Long-term cell culture studies resulted in death at passage 9 of vector-transduced PHFKs (negative control), but survival of both E6 PHFKs to passage 65 (and beyond). Compared with E6/E7 PHFKs, AA/E7 PHFKs were significantly faster dividing, developed larger cells in monolayer cultures, showed double the epithelial thickness and expressed cytokeratin 10 when grown as organotypic raft cultures. Telomerase activation and p53 inactivation, two hallmarks of immortalization, were not significantly different between the two populations. Both were resistant to anoikis at later passages, but only AA/E7 PHFKs acquired the capacity for in vitro transformation. Proteomic analysis revealed markedly different protein patterns between E6/E7 and AA/E7, particularly with respect to key cellular metabolic enzymes. Our results provide new insights into the reasons underlying the greater prevalence of the AA variant in cervical cancer as evidenced by characteristics associated with higher oncogenic potential. © 2010 Macmillan Publishers Limited All rights reserved.\n
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\n \n\n \n \n \n \n \n \n Blue Dry Western: Simple, economic, informative, and fast way of immunodetection.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Analytical Biochemistry, 392(1): 90-95. 2009.\n cited By 22\n\n\n\n
\n\n\n\n \n \n \"BluePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 The analysis by electrophoresis followed by transfer to membranes and immunodetection (Western blot) is probably the most popular technique in protein study. Accordingly, it is a time- and money-consuming procedure. Here a protocol is described where immunodetection can be accomplished in 30 min. This approach also allows permanent staining of proteins by Coomassie Blue R on the membrane before immune staining with clear background and high sensitivity. © 2009 Elsevier Inc. All rights reserved.\n
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\n \n\n \n \n \n \n \n \n Proliferating cell nuclear antigen: A proteomics view.\n \n \n \n \n\n\n \n Naryzhny, S.\n\n\n \n\n\n\n Cellular and Molecular Life Sciences, 65(23): 3789-3808. 2008.\n cited By 153\n\n\n\n
\n\n\n\n \n \n \"ProliferatingPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Naryzhny20083789,\r\nauthor={Naryzhny, S.N.},\r\ntitle={Proliferating cell nuclear antigen: A proteomics view},\r\njournal={Cellular and Molecular Life Sciences},\r\nyear={2008},\r\nvolume={65},\r\nnumber={23},\r\npages={3789-3808},\r\ndoi={10.1007/s00018-008-8305-x},\r\nnote={cited By 153},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-57349184695&doi=10.1007%2fs00018-008-8305-x&partnerID=40&md5=2cb56dc787502f1a625a68665d340e45},\r\naffiliation={Tumour Biology Group, Northeastern Ontario Regional Cancer Program, Sudbury Regional Hospital, 41 Ramsey Lake Road, Sudbury, ON P3E 5J1, Canada},\r\nabstract={Proliferating cell nuclear antigen (PCNA), a cell cycle marker protein, is well known as a DNA sliding clamp for DNA polymerase delta and as an essential component for eukaryotic chromosomal DNA replication and repair. Due to its mobility inside nuclei, PCNA is dynamically presented in a soluble or chromatin-associated form. The heterogeneity and specific modifications of PCNA may reflect its multiple functions and the presence of many binding partners in the cell. The recent proteomics approaches applied to characterizing PCNA interactions revealed multiple PCNA partners with a wide spectrum of activity and unveiled the possible existence of new PCNA functions. Since more than 100 PCNA-interacting proteins and several PCNA modifications have already been reported, a proteomics point of view seems exactly suitable to better understand the role of PCNA in cellular functions. © 2008 Birkhaueser.},\r\nauthor_keywords={Functions;  Interaction;  Proliferating cell nuclear antigen;  Proteomics},\r\ncorrespondence_address1={Naryzhny, S. N.; Tumour Biology Group, Northeastern Ontario Regional Cancer Program, Sudbury Regional Hospital, 41 Ramsey Lake Road, Sudbury, ON P3E 5J1, Canada; email: snaryzhny@hrsrh.on.ca},\r\nissn={1420682X},\r\ncoden={CMLSF},\r\npubmed_id={18726183},\r\nlanguage={English},\r\nabbrev_source_title={Cell. Mol. Life Sci.},\r\ndocument_type={Review},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n Proliferating cell nuclear antigen (PCNA), a cell cycle marker protein, is well known as a DNA sliding clamp for DNA polymerase delta and as an essential component for eukaryotic chromosomal DNA replication and repair. Due to its mobility inside nuclei, PCNA is dynamically presented in a soluble or chromatin-associated form. The heterogeneity and specific modifications of PCNA may reflect its multiple functions and the presence of many binding partners in the cell. The recent proteomics approaches applied to characterizing PCNA interactions revealed multiple PCNA partners with a wide spectrum of activity and unveiled the possible existence of new PCNA functions. Since more than 100 PCNA-interacting proteins and several PCNA modifications have already been reported, a proteomics point of view seems exactly suitable to better understand the role of PCNA in cellular functions. © 2008 Birkhaueser.\n
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\n \n\n \n \n \n \n \n \n Active dissociation of the fluorescent dye hoechst 33342 from DNA in a living cell: Who could do it.\n \n \n \n \n\n\n \n Naryzhny, S.; Levina, V.; Varfolomeeva, E.; Drobchenko, E.; and Filatov, M.\n\n\n \n\n\n\n Wiley Blackwell, 2007.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"ActivePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@BOOK{Naryzhny2007453,\r\nauthor={Naryzhny, S.N. and Levina, V.V. and Varfolomeeva, E.Y. and Drobchenko, E.A. and Filatov, M.V.},\r\ntitle={Active dissociation of the fluorescent dye hoechst 33342 from DNA in a living cell: Who could do it},\r\njournal={From Genome to Proteome: Advances in the Practice & Application of Proteomics},\r\nyear={2007},\r\npages={453-458},\r\ndoi={10.1002/9783527613489.ch59},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84956551553&doi=10.1002%2f9783527613489.ch59&partnerID=40&md5=41038eec12b571fb984fee210e4729d5},\r\naffiliation={Petersburg Nuclear Physics Institute of Russian Academy of Sciences, Gatchina, Leningrad district, Russian Federation},\r\nabstract={It is assumed that DNA in mammalian cells is a dynamic conformationally unstable system. This instability provides the cell with a mechanism for dissociating a large number of substances that bind tightly but not covalently to DNA. Among these is the fluorescent dye Hoechst 33342, which binds to DNA in the minor groove. We have selected cell lines with a high capability for active dissociation of Hoechst 33342. Comparative protein analysis of these lines by means of two-dimensional (2-D) electrophoresis was performed. Cell and nuclear proteins were analyzed from these and normal strains. A few proteins with significantly changed quantities have been found. The preliminary search of the 2-D database allowed us to identity some known and unknown cellular proteins that could participate in active dissociation of the dye from DNA. © 2000 WILEY-VCH Verlag GmbH. All rights reserved.},\r\nauthor_keywords={DNA clearing;  Hoechst 33342;  Mammalian cells;  Two-dimensional Polyacrylamide gel electrophoresis},\r\ncorrespondence_address1={Naryzhny, S.N.; Petersburg Nuclear Physics Institute of Russian Academy of SciencesRussian Federation; email: naryzhny@omrb.pnpi.spb.ru},\r\npublisher={Wiley Blackwell},\r\nisbn={9783527613489; 9783527301546},\r\nlanguage={English},\r\nabbrev_source_title={From Genome to Proteome: Adv. in the Pract. & Appl. of Proteomics},\r\ndocument_type={Book Chapter},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n\n\n
\n It is assumed that DNA in mammalian cells is a dynamic conformationally unstable system. This instability provides the cell with a mechanism for dissociating a large number of substances that bind tightly but not covalently to DNA. Among these is the fluorescent dye Hoechst 33342, which binds to DNA in the minor groove. We have selected cell lines with a high capability for active dissociation of Hoechst 33342. Comparative protein analysis of these lines by means of two-dimensional (2-D) electrophoresis was performed. Cell and nuclear proteins were analyzed from these and normal strains. A few proteins with significantly changed quantities have been found. The preliminary search of the 2-D database allowed us to identity some known and unknown cellular proteins that could participate in active dissociation of the dye from DNA. © 2000 WILEY-VCH Verlag GmbH. All rights reserved.\n
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\n \n\n \n \n \n \n \n \n Characterization of proliferating cell nuclear antigen (PCNA) isoforms in normal and cancer cells: There is no cancer-associated form of PCNA.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n FEBS Letters, 581(25): 4917-4920. 2007.\n cited By 32\n\n\n\n
\n\n\n\n \n \n \"CharacterizationPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 In order to clarify the status of PCNA in normal and transformed cells, we performed analysis of this protein by 2D-PAGE, Western blot and mass spectrometry. All the cell lines examined contained the major PCNA form (pI 4.57/30 kDa), that is not post-translationally modified. In addition to the major form, two minor isoforms (pI 4.52/30 kDa and pI 4.62/30 kDa) were also detected in all the cell lines examined. However, the level of PCNA in cancer cells is 5-6 folds higher than those in primary and most of the immortalized cells. Taken together, the significant difference in PCNA status between cancer and normal cells is not at the post-translational modifications but in the overall levels of PCNA. Crown Copyright © 2007.\n
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\n \n\n \n \n \n \n \n \n Complex of repair DNA polymerase β with autonomous 3′→5′ exonuclease shows increased accuracy of DNA synthesis.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Biology Bulletin, 34(5): 427-433. 2007.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"ComplexPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 The complexes of repair DNA polymerase β with 3′-exonuclease and some other proteins were isolated from the chromatin of hepatocytes of normal rats for the first time. Biopolymers were extracted from the chromatin by the solution of NaCl and Triton X-100. The extract was fractionated by gel-filtration on Sephacryl S-300 columns successively in low and high ionic strength solutions, on hydroxyapatite, and on Sephadex G-100 columns. The complexes have molecular weights of 100 and 300 kDa. They dissociate to DNA polymerase and exonuclease in the course of chromatography on a DNA-cellulose column or after gel-filtration in the presence of 1 M NaCl. The co-purification of the polymerase and exonuclease is reconstituted in 0.1 M NaCl. The fidelity of monomeric and composite DNA polymerase β was measured using phage φX174 amber 3 as a primer/template. The products of the synthesis were transfected into Escherichia coli spheroplasts, and the frequency of reverse mutations was determined. The complex of DNA polymerase β with 3′-exonuclease was shown to be 30 times more accurate than the monomeric polymerase, which can decrease the probability of repair mutagenesis and carcinogenesis. © 2007 Pleiades Publishing, Inc.\n
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\n \n\n \n \n \n \n \n \n Complex of repair DNA polymerase beta with autonomous 3'–>5'-exonuclease shows increased accuracy of DNA synthesis.\n \n \n \n \n\n\n \n Beliakova, N.; Kravetskaia, T.; Legina, O.; Ronzhina, N.; Shevelev, I.; and Krutiakov, V.\n\n\n \n\n\n\n Izvestiia Akademii nauk. Seriia biologicheskaia / Rossiǐskaia akademiia nauk, (5): 517-523. 2007.\n cited By 4\n\n\n\n
\n\n\n\n \n \n \"ComplexPaper\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{Beliakova2007517,\r\nauthor={Beliakova, N.V. and Kravetskaia, T.P. and Legina, O.K. and Ronzhina, N.L. and Shevelev, I.V. and Krutiakov, V.M.},\r\ntitle={Complex of repair DNA polymerase beta with autonomous 3'-->5'-exonuclease shows increased accuracy of DNA synthesis},\r\njournal={Izvestiia Akademii nauk. Seriia biologicheskaia / Rossiǐskaia akademiia nauk},\r\nyear={2007},\r\nnumber={5},\r\npages={517-523},\r\nnote={cited By 4},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-38449084836&partnerID=40&md5=1e4dd098071654181e2f5b6864c94f6e},\r\nabstract={The complexes of repair DNA polymerase beta with 3'-exonuclease and some other proteins were isolated from the chromatin of hepatocytes of normal rats for the first time. Biopolymers were extracted from the chromatin by the solution of NaCl and Triton X-100. The extract was fractionated by gel-filtration on Sephacryl S-300 columns successively in low and high ionic strength solutions, on hydroxyapatite, and on Sephadex G-100 columns. The complexes have molecular weights of 100 and 300 kDa. They dissociate to DNA polymerase and exonuclease in the course of chromatography on a DNA-cellulose column or after gel-filtration in the presence of 1 M NaCl. The co-purification of the polymerase and exonuclease is reconstituted in 0.1 M NaCl. The fidelity of monomeric and composite DNA polymerase beta was measured using phage phiX174 amber 3 as a primer/template. The products of the synthesis were transfected into Escherichia coli spheroplasts, and the frequency of reverse mutations was determined. The complex of DNA polymerase beta with 3'-exonuclease was shown to be 30 times more accurate than the monomeric polymerase, which can decrease the probability of repair mutagenesis and carcinogenesis.},\r\ncorrespondence_address1={Beliakova, N.V.},\r\nissn={10263470},\r\npubmed_id={18041131},\r\nlanguage={Russian},\r\nabbrev_source_title={Izv. Akad. Nauk. Ser. Biol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
\n\n\n
\n The complexes of repair DNA polymerase beta with 3'-exonuclease and some other proteins were isolated from the chromatin of hepatocytes of normal rats for the first time. Biopolymers were extracted from the chromatin by the solution of NaCl and Triton X-100. The extract was fractionated by gel-filtration on Sephacryl S-300 columns successively in low and high ionic strength solutions, on hydroxyapatite, and on Sephadex G-100 columns. The complexes have molecular weights of 100 and 300 kDa. They dissociate to DNA polymerase and exonuclease in the course of chromatography on a DNA-cellulose column or after gel-filtration in the presence of 1 M NaCl. The co-purification of the polymerase and exonuclease is reconstituted in 0.1 M NaCl. The fidelity of monomeric and composite DNA polymerase beta was measured using phage phiX174 amber 3 as a primer/template. The products of the synthesis were transfected into Escherichia coli spheroplasts, and the frequency of reverse mutations was determined. The complex of DNA polymerase beta with 3'-exonuclease was shown to be 30 times more accurate than the monomeric polymerase, which can decrease the probability of repair mutagenesis and carcinogenesis.\n
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\n  \n 2006\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n Characterization of the human proliferating cell nuclear antigen physico-chemical properties: Aspects of double trimer stability.\n \n \n \n \n\n\n \n Naryzhny, S.; DeSouza, L.; Siu, K.; and Lee, H.\n\n\n \n\n\n\n Biochemistry and Cell Biology, 84(5): 669-676. 2006.\n cited By 19\n\n\n\n
\n\n\n\n \n \n \"CharacterizationPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Naryzhny2006669,\r\nauthor={Naryzhny, S.N. and DeSouza, L.V. and Siu, K.W.M. and Lee, H.},\r\ntitle={Characterization of the human proliferating cell nuclear antigen physico-chemical properties: Aspects of double trimer stability},\r\njournal={Biochemistry and Cell Biology},\r\nyear={2006},\r\nvolume={84},\r\nnumber={5},\r\npages={669-676},\r\ndoi={10.1139/O06-037},\r\nnote={cited By 19},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-33846278748&doi=10.1139%2fO06-037&partnerID=40&md5=1f7e3a72141994867743ed354572f7f7},\r\naffiliation={Department of Research, Northeastern Ontario Regional Cancer Program, Sudbury Regional Hospital, 41 Ramsey Lake Road, Sudbury, Ont. P3E 5J1, Canada; Department of Chemistry, Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ont. M3J 1P3, Canada},\r\nabstract={Its toroidal structure allows the proliferating cell nuclear antigen (PCNA) to wrap around and move along the DNA fiber, thereby dramatically increasing the processivity of DNA polymerization. PCNA is also involved in the regulation of a wide spectrum of other biological functions, including epigenetic inheritance. We have recently reported that mammalian PCNA forms a double trimer complex, which may be critically important in coordinating DNA replication and other cellular functions. To gain a better understanding of the stability of PCNA complexes, we characterized the physico-chemical properties of the PCNA structure by in vivo and in vitro approaches. The data obtained by gel filtration and nondenaturing gel electrophoresis of native PCNA molecules confirm our previous observations, obtained using formaldehyde crosslinking, in which PCNA exists in the cell as a double trimer. We have also found that optimal pH (pH 6.5-7.5) is critical for the stability of the PCNA structure. The presence or absence of ATP, dithiothreitol, and Mg2+ does not affect the stability of the PCNA trimer or double trimer. However, 0.02% SDS can effectively inhibit PCNA double trimer, but not single trimer, formation. Interestingly, glycerol and ammonium sulfate significantly destabilize both PCNA trimer and double trimer structures. © 2006 NRC Canada.},\r\nauthor_keywords={Conditions for protein complex stability;  DNA replication;  Proliferating cell nuclear antigen (PCNA);  Protein structure;  Trimer and double trimer},\r\ncorrespondence_address1={Lee, H.; Department of Research, Northeastern Ontario Regional Cancer Program, Sudbury Regional Hospital, 41 Ramsey Lake Road, Sudbury, Ont. P3E 5J1, Canada; email: hlee@hrsrh.on.ca},\r\nissn={08298211},\r\ncoden={BCBIE},\r\npubmed_id={17167529},\r\nlanguage={English},\r\nabbrev_source_title={Biochem. Cell Biol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
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\n Its toroidal structure allows the proliferating cell nuclear antigen (PCNA) to wrap around and move along the DNA fiber, thereby dramatically increasing the processivity of DNA polymerization. PCNA is also involved in the regulation of a wide spectrum of other biological functions, including epigenetic inheritance. We have recently reported that mammalian PCNA forms a double trimer complex, which may be critically important in coordinating DNA replication and other cellular functions. To gain a better understanding of the stability of PCNA complexes, we characterized the physico-chemical properties of the PCNA structure by in vivo and in vitro approaches. The data obtained by gel filtration and nondenaturing gel electrophoresis of native PCNA molecules confirm our previous observations, obtained using formaldehyde crosslinking, in which PCNA exists in the cell as a double trimer. We have also found that optimal pH (pH 6.5-7.5) is critical for the stability of the PCNA structure. The presence or absence of ATP, dithiothreitol, and Mg2+ does not affect the stability of the PCNA trimer or double trimer. However, 0.02% SDS can effectively inhibit PCNA double trimer, but not single trimer, formation. Interestingly, glycerol and ammonium sulfate significantly destabilize both PCNA trimer and double trimer structures. © 2006 NRC Canada.\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 Proliferating cell nuclear antigen (PCNA) may function as a double homotrimer complex in the mammalian cell.\n \n \n \n \n\n\n \n Naryzhny, S.; Zhao, H.; and Lee, H.\n\n\n \n\n\n\n Journal of Biological Chemistry, 280(14): 13888-13894. 2005.\n cited By 42\n\n\n\n
\n\n\n\n \n \n \"ProliferatingPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Naryzhny200513888,\r\nauthor={Naryzhny, S.N. and Zhao, H. and Lee, H.},\r\ntitle={Proliferating cell nuclear antigen (PCNA) may function as a double homotrimer complex in the mammalian cell},\r\njournal={Journal of Biological Chemistry},\r\nyear={2005},\r\nvolume={280},\r\nnumber={14},\r\npages={13888-13894},\r\ndoi={10.1074/jbc.M500304200},\r\nnote={cited By 42},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-17144365007&doi=10.1074%2fjbc.M500304200&partnerID=40&md5=971337febe9ffc34c27ef1171f8bc74a},\r\naffiliation={Department of Research, NE Ontario Regional Cancer Centre, Sudbury, Ont. P3E 5J1, Canada; Dept. of Research, NE Ontario Regional Cancer Centre, 41 Ramsey Lake Rd., Sudbury, Ont. P3E 5J1, Canada},\r\nabstract={The diverse function of proliferating cell nuclear antigen (PCNA) may be regulated by interactions with different protein partners. Interestingly, the binding sites for all known PCNA-associating proteins are on the outer surface or the C termini ("front") sides of the PCNA trimer. Using cell extracts and purified human PCNA protein, we show here that two PCNA homotrimers form a back-to-back doublet. Mutation analysis suggests that the Arg-5 and Lys-110 residues on the PCNA back side are the contact points of the two homotrimers in the doublet. Furthermore, short synthetic peptides encompassing either Arg-5 or Lys-110 inhibit double trimer formation. We also found that a PCNA double trimer, but not a homotrimer alone, can simultaneously accommodate chromatin assembly factor-1 and polymerase δ. Together, our data supports a model that chromatin remodeling by chromatin assembly factor-1 (and, possibly, many other cellular activities) are tightly coupled with DNA replication (and repair) through a PCNA double trimer complex. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.},\r\ncorrespondence_address1={Lee, H.; Dept. of Research, NE Ontario Regional Cancer Centre, 41 Ramsey Lake Rd., Sudbury, Ont. P3E 5J1, Canada; email: hlee@hrsrh.on.ca},\r\nissn={00219258},\r\ncoden={JBCHA},\r\npubmed_id={15805117},\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 The diverse function of proliferating cell nuclear antigen (PCNA) may be regulated by interactions with different protein partners. Interestingly, the binding sites for all known PCNA-associating proteins are on the outer surface or the C termini (\"front\") sides of the PCNA trimer. Using cell extracts and purified human PCNA protein, we show here that two PCNA homotrimers form a back-to-back doublet. Mutation analysis suggests that the Arg-5 and Lys-110 residues on the PCNA back side are the contact points of the two homotrimers in the doublet. Furthermore, short synthetic peptides encompassing either Arg-5 or Lys-110 inhibit double trimer formation. We also found that a PCNA double trimer, but not a homotrimer alone, can simultaneously accommodate chromatin assembly factor-1 and polymerase δ. Together, our data supports a model that chromatin remodeling by chromatin assembly factor-1 (and, possibly, many other cellular activities) are tightly coupled with DNA replication (and repair) through a PCNA double trimer complex. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.\n
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\n  \n 2004\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n The post-translational modifications of proliferating cell nuclear antigen: Acetylation, not phosphorylation, plays an important role in the regulation of its function.\n \n \n \n \n\n\n \n Naryzhny, S.; and Lee, H.\n\n\n \n\n\n\n Journal of Biological Chemistry, 279(19): 20194-20199. 2004.\n cited By 96\n\n\n\n
\n\n\n\n \n \n \"ThePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Naryzhny200420194,\r\nauthor={Naryzhny, S.N. and Lee, H.},\r\ntitle={The post-translational modifications of proliferating cell nuclear antigen: Acetylation, not phosphorylation, plays an important role in the regulation of its function},\r\njournal={Journal of Biological Chemistry},\r\nyear={2004},\r\nvolume={279},\r\nnumber={19},\r\npages={20194-20199},\r\ndoi={10.1074/jbc.M312850200},\r\nnote={cited By 96},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-2442431498&doi=10.1074%2fjbc.M312850200&partnerID=40&md5=d0cfdc00240bfcab5b5dee68c873bcfc},\r\naffiliation={Department of Research, NE Ontario Regional Cancer Centre, Sudbury, Ont. P3E 5J1, Canada; Dept. of Research, NE Ontario Regional Cancer Centre, 41 Ramsey Lake Rd., Sudbury, Ont. P3E 5J1, Canada},\r\nabstract={The diverse function of proliferating cell nuclear antigen (PCNA) is thought to be due, in large part, to post-translational modifications. Here we show by high resolution two-dimensional PAGE analysis that there are three distinct PCNA isoforms that differ in their acetylation status. The moderately acetylated main (M) form was found in all of the subcellular compartments of cycling cells, whereas the highly acetylated acidic form was primarily found in the nucleoplasm, nuclear matrix, and chromatin. Interestingly, the deacetylated basic form was most pronounced in the nucleoplasm of cycling cells. The cells in G0 and the cytoplasm of cycling cells contained primarily the M form only. Because p300 and histone deacetylase (HDAC1) were co-immunoprecipitated with PCNA, they are likely responsible for the acetylation and deacetylation of PCNA, respectively. We also found that deacetylation reduced the ability of PCNA to bind to DNA polymerases β and δ. Taken together, our data support a model where the acidic and M forms participate in DNA replication, whereas the basic form is associated with the termination of DNA replication.},\r\ncorrespondence_address1={Lee, H.; Dept. of Research, NE Ontario Regional Cancer Centre, 41 Ramsey Lake Rd., Sudbury, Ont. P3E 5J1, Canada; email: hlee@hrsrh.on.ca},\r\nissn={00219258},\r\ncoden={JBCHA},\r\npubmed_id={14988403},\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 The diverse function of proliferating cell nuclear antigen (PCNA) is thought to be due, in large part, to post-translational modifications. Here we show by high resolution two-dimensional PAGE analysis that there are three distinct PCNA isoforms that differ in their acetylation status. The moderately acetylated main (M) form was found in all of the subcellular compartments of cycling cells, whereas the highly acetylated acidic form was primarily found in the nucleoplasm, nuclear matrix, and chromatin. Interestingly, the deacetylated basic form was most pronounced in the nucleoplasm of cycling cells. The cells in G0 and the cytoplasm of cycling cells contained primarily the M form only. Because p300 and histone deacetylase (HDAC1) were co-immunoprecipitated with PCNA, they are likely responsible for the acetylation and deacetylation of PCNA, respectively. We also found that deacetylation reduced the ability of PCNA to bind to DNA polymerases β and δ. Taken together, our data support a model where the acidic and M forms participate in DNA replication, whereas the basic form is associated with the termination of DNA replication.\n
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\n  \n 2003\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n Observation of multiple isoforms and specific proteolysis patterns of proliferating cell nuclear antigen in the context of cell cycle compartments and sample preparations.\n \n \n \n \n\n\n \n Naryzhny, S.; and Lee, H.\n\n\n \n\n\n\n Proteomics, 3(6): 930-936. 2003.\n cited By 25\n\n\n\n
\n\n\n\n \n \n \"ObservationPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Naryzhny2003930,\r\nauthor={Naryzhny, S.N. and Lee, H.},\r\ntitle={Observation of multiple isoforms and specific proteolysis patterns of proliferating cell nuclear antigen in the context of cell cycle compartments and sample preparations},\r\njournal={Proteomics},\r\nyear={2003},\r\nvolume={3},\r\nnumber={6},\r\npages={930-936},\r\ndoi={10.1002/pmic.200300400},\r\nnote={cited By 25},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0038385487&doi=10.1002%2fpmic.200300400&partnerID=40&md5=9e49102abeddd95bb825895ada33ebf8},\r\naffiliation={NE. Ontario Regional Cancer Centre, Sudbury, Ont., Canada; Department of Research, NE. Ontario Regional Cancer Centre, 41 Ramsey Lake Road, Sudbury, Ont. P3E 5J1, Canada},\r\nabstract={The proliferating cell nuclear antigen (PCNA) is an essential component for eukaryotic chromosomal DNA replication and repair. PCNA forms a homotrimer ring, which may function as a DNA sliding clamp for DNA polymerases and, possibly, a docking station for other replication- and repair-related proteins. Several reports have suggested the existence of different PCNA isoforms. Here we confirm, using high resolution two-dimensional electrophoresis with narrow pH ranges, the existence of three PCNA isoforms in both Chinese hamster and human breast cancer cells. Among the three isoforms, M or main form is the dominant one throughout the cell cycle while the relative amounts of the minor components A (acidic) and B (basic) forms appear to vary during the cell cycle. We also observed that a specific pattern of PCNA proteolysis occurred during isoelectric focusing in spite of high urea (8 M) and detergent (2% 3-[(3-cholamidopropyl)dimethylamino]-1-propane sulfonate), which was largely inhibited by the proteosome inhibitor MG132 or boiling. Interestingly, the proteolysis pattern was mainly observed with samples isolated from cells in S and G2 phases. A similar but much lower level of PCNA proteolysis also occurred in vivo within the nuclei of the cells in S phase. Taken together, our data are consistent with the idea that the existence of the different isoforms and specific proteolysis of PCNA are relevant to its functions in vivo.},\r\nauthor_keywords={Cell cycle;  Isoforms;  Proliferating cell nuclear antigen;  Proteolysis;  Two-dimensional gel electrophoresis},\r\ncorrespondence_address1={Lee, H.; Department of Research, NE. Ontario Regional Cancer Centre, 41 Ramsey Lake Road, Sudbury, Ont. P3E 5J1, Canada; email: hlee@neorcc.on.ca},\r\nissn={16159853},\r\ncoden={PROTC},\r\npubmed_id={12833516},\r\nlanguage={English},\r\nabbrev_source_title={Proteomics},\r\ndocument_type={Conference Paper},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n The proliferating cell nuclear antigen (PCNA) is an essential component for eukaryotic chromosomal DNA replication and repair. PCNA forms a homotrimer ring, which may function as a DNA sliding clamp for DNA polymerases and, possibly, a docking station for other replication- and repair-related proteins. Several reports have suggested the existence of different PCNA isoforms. Here we confirm, using high resolution two-dimensional electrophoresis with narrow pH ranges, the existence of three PCNA isoforms in both Chinese hamster and human breast cancer cells. Among the three isoforms, M or main form is the dominant one throughout the cell cycle while the relative amounts of the minor components A (acidic) and B (basic) forms appear to vary during the cell cycle. We also observed that a specific pattern of PCNA proteolysis occurred during isoelectric focusing in spite of high urea (8 M) and detergent (2% 3-[(3-cholamidopropyl)dimethylamino]-1-propane sulfonate), which was largely inhibited by the proteosome inhibitor MG132 or boiling. Interestingly, the proteolysis pattern was mainly observed with samples isolated from cells in S and G2 phases. A similar but much lower level of PCNA proteolysis also occurred in vivo within the nuclei of the cells in S phase. Taken together, our data are consistent with the idea that the existence of the different isoforms and specific proteolysis of PCNA are relevant to its functions in vivo.\n
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\n  \n 2002\n \n \n (3)\n \n \n
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\n \n\n \n \n \n \n \n \n The correcting role of autonomous 3′ → 5′ exonucleases contained in mammalian multienzyme DNA polymerase complexes.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Molecular Biology, 36(6): 857-863. 2002.\n cited By 2\n\n\n\n
\n\n\n\n \n \n \"ThePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 A study was made of the correcting role of autonomous 3′ → 5′ exonucleases (AE) contained in multienzyme DNA polymerase complexes of rat hepatocytes or calf thymocytes. DNA was synthesized on phage φX174 amber3 or M13mp2 primer-templates, and used to transfect Escherichia coli spheroplasts. Frequencies were estimated for direct and reverse mutations resulting from mistakes made in the course of in vitro DNA synthesis. The error rate of the hepatocyte complex was estimated at 3.10-6 with equimolar dNTP, and increased tenfold when proteins accounting for 70% of the total 3′ → 5′ exonuclease activity of the complex were removed. The fidelity of DNA synthesis was completely restored in the presence of exogenous AE (ε subunit of E. coli DNA polymerase III). Nuclear (Pol δn) and cytosolic (Pol δc) forms of DNA polymerase δ were isolated from calf thymocytes. The former was shown to contain an AE (TREX2) absent from the latter. As compared with Pol δ c, Pol δn had a 20-fold higher exo/pol ratio and allowed 4-5 times higher fidelity of DNA synthesis. The error rate of DNA polymerase complexes changed when dNTP were used in nonequimolar amounts.\n
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\n \n\n \n \n \n \n \n \n DNA polymerase-associated and autonomous 3′→5′ exonucleases in invertebrates, unicellulars, and bacteria.\n \n \n \n \n\n\n \n Ronzhina, N.; Belyakova, N.; Kravetskaya, T.; and Krutyakov, V.\n\n\n \n\n\n\n Journal of Evolutionary Biochemistry and Physiology, 38(2): 161-168. 2002.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"DNAPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Ronzhina2002161,\r\nauthor={Ronzhina, N.L. and Belyakova, N.V. and Kravetskaya, T.P. and Krutyakov, V.M.},\r\ntitle={DNA polymerase-associated and autonomous 3′→5′ exonucleases in invertebrates, unicellulars, and bacteria},\r\njournal={Journal of Evolutionary Biochemistry and Physiology},\r\nyear={2002},\r\nvolume={38},\r\nnumber={2},\r\npages={161-168},\r\ndoi={10.1023/A:1016502303352},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-9644274328&doi=10.1023%2fA%3a1016502303352&partnerID=40&md5=f8c1eb010fc4d101bb3e022d11d36d01},\r\naffiliation={Konstantinov St. Petersburg Inst. N., Russian Academy of Science, Gatchina, Russia, Russian Federation},\r\nabstract={Recently we have revealed a high content of autonomous 3′→ 5′ exonucleases (AE), i.e., those not bound covalently with DNA polymerases, in cells of vertebrates, from fish to human [1]. In the present work, using gel filtration method, cell-free extracts were studied from 15 objects located at different positions on the phylogenetic tree, such as archaebacteria, eubacteria, fungi, infusorians, coelenterates, annelids, and arthropods. It is shown that enzymatic activity of AE accounts for from 30 to 88% of the total 3′→5′ exonuclease activity of the extracts. A part of AE is revealed in zone of high-molecular DNA polymerases and can be separated by change of the chromatography conditions. It indicates a probable formation of complexes of AE with DNA polymerases. The high AE activity in cells of different organisms, from archae- and eubacteria to human, allows suggesting these enzymes to play a significant role in correction of polymerase errors in the processes of DNA replication and reparation, as well as in postreplicative correction of heteroduplexes in DNA.},\r\ncorrespondence_address1={Konstantinov St. Petersburg Inst. N., Russian Academy of Science, Gatchina, RussiaRussian Federation},\r\nissn={00220930},\r\ncoden={JEBPA},\r\nlanguage={English},\r\nabbrev_source_title={J. Evol. Biochem. Physiol.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
\n\n\n
\n Recently we have revealed a high content of autonomous 3′→ 5′ exonucleases (AE), i.e., those not bound covalently with DNA polymerases, in cells of vertebrates, from fish to human [1]. In the present work, using gel filtration method, cell-free extracts were studied from 15 objects located at different positions on the phylogenetic tree, such as archaebacteria, eubacteria, fungi, infusorians, coelenterates, annelids, and arthropods. It is shown that enzymatic activity of AE accounts for from 30 to 88% of the total 3′→5′ exonuclease activity of the extracts. A part of AE is revealed in zone of high-molecular DNA polymerases and can be separated by change of the chromatography conditions. It indicates a probable formation of complexes of AE with DNA polymerases. The high AE activity in cells of different organisms, from archae- and eubacteria to human, allows suggesting these enzymes to play a significant role in correction of polymerase errors in the processes of DNA replication and reparation, as well as in postreplicative correction of heteroduplexes in DNA.\n
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\n \n\n \n \n \n \n \n \n Associated with DNA polymerases and autonomic 3'-5'-exonucleases from invertebrates, protozoa and bacteria [Assotsiirovannye s DNK-polimerazami i avtonomnye 3'-5'-ékzonukleazy bespozvonochnykh zhivotnykh, odnokletochnykh organizmov i bakterii.].\n \n \n \n \n\n\n \n Ronzhina, N.; Beliakova, N.; Kravetskaia, T.; and Krutiakov, V.\n\n\n \n\n\n\n Zhurnal Evolyutsionnoi Biokhimii i Fiziologii, 38(2): 125-130. 2002.\n cited By 4\n\n\n\n
\n\n\n\n \n \n \"AssociatedPaper\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{Ronzhina2002125,\r\nauthor={Ronzhina, N.L. and Beliakova, N.V. and Kravetskaia, T.P. and Krutiakov, V.M.},\r\ntitle={Associated with DNA polymerases and autonomic 3'-5'-exonucleases from invertebrates, protozoa and bacteria [Assotsiirovannye s DNK-polimerazami i avtonomnye 3'-5'-ékzonukleazy bespozvonochnykh zhivotnykh, odnokletochnykh organizmov i bakterii.]},\r\njournal={Zhurnal Evolyutsionnoi Biokhimii i Fiziologii},\r\nyear={2002},\r\nvolume={38},\r\nnumber={2},\r\npages={125-130},\r\nnote={cited By 4},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-2242477401&partnerID=40&md5=7898579fd81796f3f83ba0205b3fb257},\r\ncorrespondence_address1={Ronzhina, N.L.},\r\nissn={00444529},\r\npubmed_id={12070910},\r\nlanguage={Russian},\r\nabbrev_source_title={Zh Evol Biokhim Fiziol},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\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 Protein profiles of the Chinese hamster ovary cells in the resting and proliferating stages.\n \n \n \n \n\n\n \n Naryzhny, S.; and Lee, H.\n\n\n \n\n\n\n Electrophoresis, 22(9): 1764-1775. 2001.\n cited By 39\n\n\n\n
\n\n\n\n \n \n \"ProteinPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Naryzhny20011764,\r\nauthor={Naryzhny, S.N. and Lee, H.},\r\ntitle={Protein profiles of the Chinese hamster ovary cells in the resting and proliferating stages},\r\njournal={Electrophoresis},\r\nyear={2001},\r\nvolume={22},\r\nnumber={9},\r\npages={1764-1775},\r\ndoi={10.1002/1522-2683(200105)22:9<1764::AID-ELPS1764>3.0.CO;2-V},\r\nnote={cited By 39},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-70449624651&doi=10.1002%2f1522-2683%28200105%2922%3a9%3c1764%3a%3aAID-ELPS1764%3e3.0.CO%3b2-V&partnerID=40&md5=6af15afeb09e99e3d258565aff4a1ecf},\r\naffiliation={Department of Research, Northeastern Ontario Regional Cancer Centre, 41 Ramsey Lake Road, Sudbury, ON P3E 5J1, Canada},\r\nabstract={Identification and characterization of the proteins that regulate the transition from the resting stage (G0) through G1 to S phase of the cell cycle are of central importance to understand the control of cell proliferation and chromosome replication. Unlike in lower organisms, where relatively small numbers of key factors are involved in this process, the factors involved in the same control mechanisms in mammalian systems are much more complex. Furthermore, accumulating lines of evidence now suggest that the nuclear matrix and chromatin organization also play an essential role for the cell cycle control in mammalian cells. To gain a better understanding of the overall dynamics and changes of the protein factors in the context of matrix/chromatin organization, we examined the protein profiles of the Chinese hamster ovary (CHO) cells in different cell cycle compartments. The methods used in this study included subcellular fractionations (cytosol, nuclear extraction, chromatin, and nuclear matrix), two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), silver staining, and immunoblotting. As expected, significant changes of protein profiles were observed when cells entered into proliferating stages from G0. Among approximately 1200 protein spots analyzed by 2-D PAGE, at least 12 showed marked increase or decrease at this transitional period. Further cell-cycle progression from G1 to S phase showed less dramatic changes of overall protein protile. However, the profile of certain proteins showed rather dramatic changes of their subcellular localization during this transitional period. In particular, the levels of proliferating cell nuclear antigen (PCNA) in the nuclear matrix and chromatin dramatically increased in mid-G1 and in the beginning of S phase, respectively, while the overall PCNA level was relatively constant throughout the cell cycle. © Wiley-VCH Verlag GmbH, 2001.},\r\nauthor_keywords={Cell proliferation;  Chinese hamster ovary cells;  Proliferating cell nuclear antigen;  Subcellular fractionation;  Two-dimensional polyacrylamide gel electrophoresis},\r\ncorrespondence_address1={Lee, H.; Department of Research, Northeastern Ontario Regional Cancer Centre, 41 Ramsey Lake Road, Sudbury, ON P3E 5J1, Canada; email: hlee@neorcc.on.ca},\r\nissn={01730835},\r\ncoden={ELCTD},\r\nlanguage={English},\r\nabbrev_source_title={Electrophoresis},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
\n\n\n
\n Identification and characterization of the proteins that regulate the transition from the resting stage (G0) through G1 to S phase of the cell cycle are of central importance to understand the control of cell proliferation and chromosome replication. Unlike in lower organisms, where relatively small numbers of key factors are involved in this process, the factors involved in the same control mechanisms in mammalian systems are much more complex. Furthermore, accumulating lines of evidence now suggest that the nuclear matrix and chromatin organization also play an essential role for the cell cycle control in mammalian cells. To gain a better understanding of the overall dynamics and changes of the protein factors in the context of matrix/chromatin organization, we examined the protein profiles of the Chinese hamster ovary (CHO) cells in different cell cycle compartments. The methods used in this study included subcellular fractionations (cytosol, nuclear extraction, chromatin, and nuclear matrix), two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), silver staining, and immunoblotting. As expected, significant changes of protein profiles were observed when cells entered into proliferating stages from G0. Among approximately 1200 protein spots analyzed by 2-D PAGE, at least 12 showed marked increase or decrease at this transitional period. Further cell-cycle progression from G1 to S phase showed less dramatic changes of overall protein protile. However, the profile of certain proteins showed rather dramatic changes of their subcellular localization during this transitional period. In particular, the levels of proliferating cell nuclear antigen (PCNA) in the nuclear matrix and chromatin dramatically increased in mid-G1 and in the beginning of S phase, respectively, while the overall PCNA level was relatively constant throughout the cell cycle. © Wiley-VCH Verlag GmbH, 2001.\n
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\n \n\n \n \n \n \n \n \n High accuracy of the DNA synthesis catalyzed by the complex of α-family DNA polymerases with autonomous 3'→5' exonucleases.\n \n \n \n \n\n\n \n Shevelev, I.; Belyakova, N.; Kravetskaya, T.; Smirnova, E.; and Krutyakov, V.\n\n\n \n\n\n\n Doklady Akademii Nauk, 378(1): 114-118. 2001.\n cited By 1\n\n\n\n
\n\n\n\n \n \n \"HighPaper\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{Shevelev2001114,\r\nauthor={Shevelev, I.V. and Belyakova, N.V. and Kravetskaya, T.P. and Smirnova, E.A. and Krutyakov, V.M.},\r\ntitle={High accuracy of the DNA synthesis catalyzed by the complex of α-family DNA polymerases with autonomous 3'→5' exonucleases},\r\njournal={Doklady Akademii Nauk},\r\nyear={2001},\r\nvolume={378},\r\nnumber={1},\r\npages={114-118},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035770038&partnerID=40&md5=a22c377a7a9138288c26013da96bb813},\r\nissn={08695652},\r\ncoden={DAKNE},\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 High accuracy of DNA synthesis catalyzed by the complex of DNA polymerases of the alpha family in the presence of autonomous 3'–>5' exonucleases.\n \n \n \n \n\n\n \n Shevelev, I.; Belyakova, N.; Kravetskaya, T.; Smirnova, E.; and Krutyakov, V.\n\n\n \n\n\n\n Doklady. Biochemistry and biophysics, 378: 156-159. 2001.\n cited By 1\n\n\n\n
\n\n\n\n \n \n \"HighPaper\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{Shevelev2001156,\r\nauthor={Shevelev, I.V. and Belyakova, N.V. and Kravetskaya, T.P. and Smirnova, E.A. and Krutyakov, V.M.},\r\ntitle={High accuracy of DNA synthesis catalyzed by the complex of DNA polymerases of the alpha family in the presence of autonomous 3'-->5' exonucleases.},\r\njournal={Doklady. Biochemistry and biophysics},\r\nyear={2001},\r\nvolume={378},\r\npages={156-159},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0035347666&partnerID=40&md5=2c9d38effafc999e926b5f5463e06509},\r\naffiliation={Konstantinov Institute of Nuclear Physics, Russian Academy of Sciences, Leningrad Oblast, Russia, 188350, Russian Federation},\r\ncorrespondence_address1={Shevelev, I.V.},\r\nissn={16076729},\r\npubmed_id={11712167},\r\nlanguage={English},\r\nabbrev_source_title={Dokl. Biochem. Biophys.},\r\ndocument_type={Article},\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 Related to DNA polymerases and individual 3'–>5'-exonuceases from vertebrates [Assotsiirovannye s DNK-polimerazami i avtonomnye 3'–>5'-ékzonukleazy pozvonochnykh.].\n \n \n \n \n\n\n \n Ronzhina, N.; Kravetskaia, T.; and Krutiakov, V.\n\n\n \n\n\n\n Zhurnal Evolyutsionnoi Biokhimii i Fiziologii, 36(3): 198-201. 2000.\n cited By 4\n\n\n\n
\n\n\n\n \n \n \"RelatedPaper\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{Ronzhina2000198,\r\nauthor={Ronzhina, N.L. and Kravetskaia, T.P. and Krutiakov, V.M.},\r\ntitle={Related to DNA polymerases and individual 3'-->5'-exonuceases from vertebrates [Assotsiirovannye s DNK-polimerazami i avtonomnye 3'-->5'-ékzonukleazy pozvonochnykh.]},\r\njournal={Zhurnal Evolyutsionnoi Biokhimii i Fiziologii},\r\nyear={2000},\r\nvolume={36},\r\nnumber={3},\r\npages={198-201},\r\nnote={cited By 4},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034188839&partnerID=40&md5=771457426f63f34eed9bdf0c5935d03c},\r\ncorrespondence_address1={Ronzhina, N.L.},\r\nissn={00444529},\r\npubmed_id={11075439},\r\nlanguage={Russian},\r\nabbrev_source_title={Zh Evol Biokhim Fiziol},\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 Autonomous 3'→5' exonucleases can proofread for DNA polymerase β from rat liver.\n \n \n \n \n\n\n \n Shevelev, I.; Belyakova, N.; Kravetskaya, T.; and Krutyakov, V.\n\n\n \n\n\n\n Mutation Research - DNA Repair, 459(3): 237-242. 2000.\n cited By 12\n\n\n\n
\n\n\n\n \n \n \"AutonomousPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Shevelev2000237,\r\nauthor={Shevelev, I.V. and Belyakova, N.V. and Kravetskaya, T.P. and Krutyakov, V.M.},\r\ntitle={Autonomous 3'→5' exonucleases can proofread for DNA polymerase β from rat liver},\r\njournal={Mutation Research - DNA Repair},\r\nyear={2000},\r\nvolume={459},\r\nnumber={3},\r\npages={237-242},\r\ndoi={10.1016/S0921-8777(00)00004-5},\r\nnote={cited By 12},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034724752&doi=10.1016%2fS0921-8777%2800%2900004-5&partnerID=40&md5=59ae7e020ad85d8e146cd4ee49d67ba6},\r\naffiliation={Laboratory of DNA Biosynthesis, Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute of the Russia Academy of Sciences, Leningrad District, Gatchina, 188350, Russian Federation},\r\nabstract={Autonomous 3'→5'exonucleases are not bound covalently to DNA polymerases but are often involved in replicative complexes. Such exonucleases from rat liver, calf thymus and Escherichia coli (molecular masses of 28 ± 2 kDa) are shown to increase more than 10-fold the accuracy of DNA polymerase β (the most inaccurate mammalian polymerase) from rat liver in the course of reduplication of the primed DNA of bacteriophage φX174 amber 3 in vitro. The extent of correction increases together with the rise in 3'→5' exonuclease concentration. Extrapolation of the in vitro DNA replication fidelity to the cellular levels of rat exonuclease and β- polymerase suggests that exonucleolytic proofreading could augment the accuracy of DNA synthesis by two orders of magnitude. These results are not explained by exonucleolytic degradation of the primers ('no synthesis-no errors'), since similar data are obtained with the use of the primers 15 or 150 nucleotides long in the course of a fidelity assay of DNA polymerases, both α and β, in the presence of various concentrations of 3'→5' exonuclease. (C) 2000 Elsevier Science B.V.},\r\nauthor_keywords={3'→5' exonuclease;  DNA polymerase β;  Proofreading},\r\nissn={09218777},\r\npubmed_id={10812336},\r\nlanguage={English},\r\nabbrev_source_title={Mutat. Res. DNA Repair},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n Autonomous 3'→5'exonucleases are not bound covalently to DNA polymerases but are often involved in replicative complexes. Such exonucleases from rat liver, calf thymus and Escherichia coli (molecular masses of 28 ± 2 kDa) are shown to increase more than 10-fold the accuracy of DNA polymerase β (the most inaccurate mammalian polymerase) from rat liver in the course of reduplication of the primed DNA of bacteriophage φX174 amber 3 in vitro. The extent of correction increases together with the rise in 3'→5' exonuclease concentration. Extrapolation of the in vitro DNA replication fidelity to the cellular levels of rat exonuclease and β- polymerase suggests that exonucleolytic proofreading could augment the accuracy of DNA synthesis by two orders of magnitude. These results are not explained by exonucleolytic degradation of the primers ('no synthesis-no errors'), since similar data are obtained with the use of the primers 15 or 150 nucleotides long in the course of a fidelity assay of DNA polymerases, both α and β, in the presence of various concentrations of 3'→5' exonuclease. (C) 2000 Elsevier Science B.V.\n
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\n \n\n \n \n \n \n \n \n DNA polymerase-associated and autonomous vertebrate 3′→5′ exonuleases.\n \n \n \n \n\n\n \n Ronzhina, N.; Kravetskaya, T.; and Krutyakov, V.\n\n\n \n\n\n\n Journal of Evolutionary Biochemistry and Physiology, 36(3): 262-266. 2000.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"DNAPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Ronzhina2000262,\r\nauthor={Ronzhina, N.L. and Kravetskaya, T.P. and Krutyakov, V.M.},\r\ntitle={DNA polymerase-associated and autonomous vertebrate 3′→5′ exonuleases},\r\njournal={Journal of Evolutionary Biochemistry and Physiology},\r\nyear={2000},\r\nvolume={36},\r\nnumber={3},\r\npages={262-266},\r\ndoi={10.1007/BF02737041},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-27544446653&doi=10.1007%2fBF02737041&partnerID=40&md5=32467df022a08a12baa8177914f1180e},\r\naffiliation={Laboratory of DNA Synthesis, Department of Molecular and Radiation Biophysics, St. Petersburg Institute of Nuclear Physics, Gatchina, Russian Federation},\r\nabstract={Using methods of gel filtration and ultracentrifugation, cell-free extracts from 12 objects representing the main vertebrate representatives (bony fish, amphibian, reptiles, birds, mammals, including human) were studied. The enzyme activity of autonomous 3′→5′-exonucleases (AE) has been established to be 25-90% of the total 3′→5′ exonuclease activity of the extracts. A part of the AE is revealed in a zone of the DNA polymerases of the α-family and can be separated by changing chromatographic conditions or by repeated fractionation. The high activity of AE allows suggesting their substantial participation in the replicative correction of the DNA-polymerase errors as well as in the postreplicative correction of the heteroduplexes in the vertebrate DNA. © 2000 MAIK "Nauka/Interperiodica".},\r\ncorrespondence_address1={Ronzhina, N.L.; Laboratory of DNA Synthesis, Department of Molecular and Radiation Biophysics, St. Petersburg Institute of Nuclear Physics, Gatchina, Russian Federation},\r\npublisher={Kluwer Academic/Plenum Publishers},\r\nissn={00220930},\r\ncoden={JEBPA},\r\nlanguage={English},\r\nabbrev_source_title={J. Evol. Biochem. Physiol.},\r\ndocument_type={Review},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n Using methods of gel filtration and ultracentrifugation, cell-free extracts from 12 objects representing the main vertebrate representatives (bony fish, amphibian, reptiles, birds, mammals, including human) were studied. The enzyme activity of autonomous 3′→5′-exonucleases (AE) has been established to be 25-90% of the total 3′→5′ exonuclease activity of the extracts. A part of the AE is revealed in a zone of the DNA polymerases of the α-family and can be separated by changing chromatographic conditions or by repeated fractionation. The high activity of AE allows suggesting their substantial participation in the replicative correction of the DNA-polymerase errors as well as in the postreplicative correction of the heteroduplexes in the vertebrate DNA. © 2000 MAIK \"Nauka/Interperiodica\".\n
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\n  \n 1999\n \n \n (3)\n \n \n
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\n \n \n
\n \n\n \n \n \n \n \n \n Proofreading function of autonomous 3′ → 5′ exonucleases in DNA synthesis catalyzed by DNA polymerase ß from rat liver.\n \n \n \n \n\n\n \n Shevelev, J.; Belyakova, N.; Kravetskaya, T.; Ronzhina, N.; Smirnova, E.; Yu Tutaev, K.; Sheveleva, I.; and Krutyakov, V.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 33(5): 758-763. 1999.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"ProofreadingPaper\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{Shevelev1999758,\r\nauthor={Shevelev, J.V. and Belyakova, N.V. and Kravetskaya, T.P. and Ronzhina, N.L. and Smirnova, E.A. and Yu Tutaev, K. and Sheveleva, I. and Krutyakov, V.M.},\r\ntitle={Proofreading function of autonomous 3′ → 5′ exonucleases in DNA synthesis catalyzed by DNA polymerase ß from rat liver},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1999},\r\nvolume={33},\r\nnumber={5},\r\npages={758-763},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033183428&partnerID=40&md5=de6b51ca6842ad0eeb565cb6d67f58aa},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={10579179},\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 Proofreading function of autonomous 3′→5′ exonucleases in DNA synthesis catalyzed by DNA polymerase β from rat liver.\n \n \n \n \n\n\n \n Shevelev, I.; Belyakova, N.; Kravetskaya, T.; Ronzhina, N.; Smirnova, E.; Tutaev, K.; Sheveleva, I.; and Krutyakov, V.\n\n\n \n\n\n\n Molecular Biology, 33(5): 666-671. 1999.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"ProofreadingPaper\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{Shevelev1999666,\r\nauthor={Shevelev, I.V. and Belyakova, N.V. and Kravetskaya, T.P. and Ronzhina, N.L. and Smirnova, E.A. and Tutaev, K.Yu. and Sheveleva, I.I. and Krutyakov, V.M.},\r\ntitle={Proofreading function of autonomous 3′→5′ exonucleases in DNA synthesis catalyzed by DNA polymerase β from rat liver},\r\njournal={Molecular Biology},\r\nyear={1999},\r\nvolume={33},\r\nnumber={5},\r\npages={666-671},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0033196122&partnerID=40&md5=dba74eae740c8f96371e4521826841d3},\r\naffiliation={Konstantinov Inst. for Nucl. Physics, Russian Academy of Sciences, Gatchina, 188350, Russian Federation},\r\nabstract={Autonomous 3′→5′-exonucleases (i.e., those not covalently attached to DNA polymerases but often constituting part of replicative complexes) from rat liver, calf thymus, or Escherichia coli can increase more than ten times the fidelity of DNA polymerase β from rat liver in reduplication of the primed φX174am3 DNA. The degree of correction rises with an increase in the concentration of the 3′→5′-exonuclease and reaches two orders of magnitude upon extrapolation to the values of the cell activity of the enzymes of interest. These data cannot be accounted for by the exonuclease degradation of primers, as virtually equal results were obtained using 15-nt and 150-nt primers upon measuring the fidelity of DNA polymerases α and β in the presence of various concentrations of 3′→5′-exonuclease. An intermolecular mechanism is discussed for correcting mistakes in DNA replication with participation of autonomous 3′→5′-exonucleases capable of splitting single-stranded DNA, and moderately processive or distributive DNA polymerases.},\r\nauthor_keywords={3′→5′-exonucleases;  DNA polymerases α and β;  DNA synthesis fidelity;  Exonuclease correction;  Rat liver},\r\ncorrespondence_address1={Shevelev, I.V.; Konstantinov Inst. for Nucl. Physics, Russian Academy of Sciences, Gatchina, 188350, Russian Federation; email: igor@omrb.pnpi.spb.su},\r\nissn={00268933},\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 Autonomous 3′→5′-exonucleases (i.e., those not covalently attached to DNA polymerases but often constituting part of replicative complexes) from rat liver, calf thymus, or Escherichia coli can increase more than ten times the fidelity of DNA polymerase β from rat liver in reduplication of the primed φX174am3 DNA. The degree of correction rises with an increase in the concentration of the 3′→5′-exonuclease and reaches two orders of magnitude upon extrapolation to the values of the cell activity of the enzymes of interest. These data cannot be accounted for by the exonuclease degradation of primers, as virtually equal results were obtained using 15-nt and 150-nt primers upon measuring the fidelity of DNA polymerases α and β in the presence of various concentrations of 3′→5′-exonuclease. An intermolecular mechanism is discussed for correcting mistakes in DNA replication with participation of autonomous 3′→5′-exonucleases capable of splitting single-stranded DNA, and moderately processive or distributive DNA polymerases.\n
\n\n\n
\n\n\n
\n \n\n \n \n \n \n \n \n Active dissociation of the fluorescent dye Hoechst 33342 from DNA in a living cell: Who could do it?.\n \n \n \n \n\n\n \n Naryzhny, S.; Levina, V.; Varfolomeeva, E.; Drobchenko, E.; and Filatov, M.\n\n\n \n\n\n\n Electrophoresis, 20(4-5): 1033-1038. 1999.\n cited By 3\n\n\n\n
\n\n\n\n \n \n \"ActivePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Naryzhny19991033,\r\nauthor={Naryzhny, S.N. and Levina, V.V. and Varfolomeeva, E.Y. and Drobchenko, E.A. and Filatov, M.V.},\r\ntitle={Active dissociation of the fluorescent dye Hoechst 33342 from DNA in a living cell: Who could do it?},\r\njournal={Electrophoresis},\r\nyear={1999},\r\nvolume={20},\r\nnumber={4-5},\r\npages={1033-1038},\r\ndoi={10.1002/(SICI)1522-2683(19990101)20:4/5<1033::AID-ELPS1033>3.0.CO;2-3},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032957473&doi=10.1002%2f%28SICI%291522-2683%2819990101%2920%3a4%2f5%3c1033%3a%3aAID-ELPS1033%3e3.0.CO%3b2-3&partnerID=40&md5=3f6b63ef15d5a83f4e04cddb3b81eaeb},\r\naffiliation={Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Leningrad district, Russian Federation; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Leningrad district, 188350, Russian Federation},\r\nabstract={It is assumed that DNA in mammalian cells is a dynamic conformationally unstable system. This instability provides the cell with a mechanism for dissociating a large number of substances that bind tightly but not covalently to DNA. Among these is the fluorescent dye Hoechst 33342, which binds to DNA in the minor groove. We have selected cell lines with a high capability for active dissociation of Hoechst 33342. Comparative protein analysis of these lines by means of two-dimensional (2-D) electrophoresis was performed. Cell and nuclear proteins were analyzed from these and normal strains. A few proteins with significantly changed quantities have been found. The preliminary search of the 2-D database allowed us to identity some known and unknown cellular proteins that could participate in active dissociation of the dye from DNA.},\r\nauthor_keywords={DNA clearing;  Hoechst 33342;  Mammalian cells;  Two-dimensional polyacrylamide gel electrophoresis},\r\ncorrespondence_address1={Naryzhny, S.N.; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Leningrad District 188350, Russian Federation; email: naryzhny@omrb.pnpi.spb.ru},\r\nissn={01730835},\r\ncoden={ELCTD},\r\npubmed_id={10344282},\r\nlanguage={English},\r\nabbrev_source_title={Electrophoresis},\r\ndocument_type={Conference Paper},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
\n\n\n
\n It is assumed that DNA in mammalian cells is a dynamic conformationally unstable system. This instability provides the cell with a mechanism for dissociating a large number of substances that bind tightly but not covalently to DNA. Among these is the fluorescent dye Hoechst 33342, which binds to DNA in the minor groove. We have selected cell lines with a high capability for active dissociation of Hoechst 33342. Comparative protein analysis of these lines by means of two-dimensional (2-D) electrophoresis was performed. Cell and nuclear proteins were analyzed from these and normal strains. A few proteins with significantly changed quantities have been found. The preliminary search of the 2-D database allowed us to identity some known and unknown cellular proteins that could participate in active dissociation of the dye from DNA.\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 \n \n \n Strong inhibition of endodeoxyribonucleases at physiological ionic strength.\n \n \n \n \n\n\n \n Shevelev, J.; Legina, O.; Tutaev, K.; and Krutyakov, M.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 32(4): 741-744. 1998.\n cited By 5\n\n\n\n
\n\n\n\n \n \n \"StrongPaper\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{Shevelev1998741,\r\nauthor={Shevelev, J. and Legina, O.K. and Tutaev, K.Y. and Krutyakov, M.},\r\ntitle={Strong inhibition of endodeoxyribonucleases at physiological ionic strength},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1998},\r\nvolume={32},\r\nnumber={4},\r\npages={741-744},\r\nnote={cited By 5},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032112471&partnerID=40&md5=adbdd72531e8037a02de01619ce440f3},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={9785581},\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 Strong inhibition of endodeoxyribonucleases at physiological ionic strength.\n \n \n \n \n\n\n \n Shevelev, I.; Legina, O.; Tutaev, K.; and Krutyakov, V.\n\n\n \n\n\n\n Molecular Biology, 32(4): 617-620. 1998.\n cited By 2\n\n\n\n
\n\n\n\n \n \n \"StrongPaper\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{Shevelev1998617,\r\nauthor={Shevelev, I.V. and Legina, O.K. and Tutaev, K.Yu. and Krutyakov, V.M.},\r\ntitle={Strong inhibition of endodeoxyribonucleases at physiological ionic strength},\r\njournal={Molecular Biology},\r\nyear={1998},\r\nvolume={32},\r\nnumber={4},\r\npages={617-620},\r\nnote={cited By 2},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0032338570&partnerID=40&md5=009a39ba9d3ad1e3457b14fb608ba88c},\r\naffiliation={Konstantinov Inst. of Nucl. Physics, Russian Academy of Sciences, Gatchina, 188350, Russian Federation},\r\nabstract={Endonucleases were inhibited more than 100 times in the presence of 50 mM ammonium sulfate or other salts (NaCl, KCl, NH4Cl, KH2PO4, Na2SO4) at the same ionic strength at pH 7-9, while 3′→5′ exonuclease and DNA polymerase α were inhibited less than two times. The effect was similar with bovine pancreatic DNase I and various endonuclease preparations (cell extracts and purified enzymes from Drosophila melanogaster embryos, rat liver, rat spleen, rat brain gray substance, calf spleen, and calf thymus), regardless of the substrate (Escherichia coli native or denatured DNA, phage λ DNA, phage φX174 single-stranded circular DNA and its replicative forms). In vitro inhibition at nearly physiological salt concentrations (150-200 mM) explains the relatively low endonuclease activity in vivo and in cell extracts. DNA degradation during apoptosis can be due to a local decrease in ionic strength and, therefore, activation of cell endonucleases. Ionic strength inhibition of endonucleases allows exact estimation of the activity of various DNA enzymes (polymerases, helicases, topoisomerases, exonucleases, etc.) during their isolation and purification, and can be used to protect phage DNA in various experiments.},\r\nauthor_keywords={Endodeoxyribonucleases;  Inhibition;  Ionic strength;  Physiological conditions},\r\ncorrespondence_address1={Shevelev, I.V.; Konstantinov Inst. of Nucl. Physics, Russian Academy of Sciences, Gatchina, 188350, Russian Federation; email: igor@omrb.pnpi.spb.ru},\r\nissn={00268933},\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 Endonucleases were inhibited more than 100 times in the presence of 50 mM ammonium sulfate or other salts (NaCl, KCl, NH4Cl, KH2PO4, Na2SO4) at the same ionic strength at pH 7-9, while 3′→5′ exonuclease and DNA polymerase α were inhibited less than two times. The effect was similar with bovine pancreatic DNase I and various endonuclease preparations (cell extracts and purified enzymes from Drosophila melanogaster embryos, rat liver, rat spleen, rat brain gray substance, calf spleen, and calf thymus), regardless of the substrate (Escherichia coli native or denatured DNA, phage λ DNA, phage φX174 single-stranded circular DNA and its replicative forms). In vitro inhibition at nearly physiological salt concentrations (150-200 mM) explains the relatively low endonuclease activity in vivo and in cell extracts. DNA degradation during apoptosis can be due to a local decrease in ionic strength and, therefore, activation of cell endonucleases. Ionic strength inhibition of endonucleases allows exact estimation of the activity of various DNA enzymes (polymerases, helicases, topoisomerases, exonucleases, etc.) during their isolation and purification, and can be used to protect phage DNA in various experiments.\n
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\n  \n 1997\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n 'Active' two-dimensional electrophoresis of rat liver DNA-polymerase.\n \n \n \n \n\n\n \n Naryzhny, S.\n\n\n \n\n\n\n Electrophoresis, 18(3-4): 553-556. 1997.\n cited By 4\n\n\n\n
\n\n\n\n \n \n \"'Active'Paper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Naryzhny1997553,\r\nauthor={Naryzhny, S.N.},\r\ntitle={'Active' two-dimensional electrophoresis of rat liver DNA-polymerase},\r\njournal={Electrophoresis},\r\nyear={1997},\r\nvolume={18},\r\nnumber={3-4},\r\npages={553-556},\r\ndoi={10.1002/elps.1150180336},\r\nnote={cited By 4},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030948280&doi=10.1002%2felps.1150180336&partnerID=40&md5=fadbd9a8d2fd234ae5e75af70ad34ebe},\r\naffiliation={Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Leningrad district, Russian Federation; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Leningrad district, 188350, Russian Federation},\r\nabstract={The approach of so-called active gel analysis was used to determine the position and appearance of the catalytic subunit of rat liver DNA polymerase a on a two-dimensional (2-D) electrophoretic map. In this case a polyacrylamide gel containing DNA was used for the second dimension. DNA presence does not change the 2-D protein pattern but makes it possible to conduct a polymerase reaction directly in the gel after separation. A crude extract of rat liver nuclei was used for analysis. The extract is quickly isolated and contains mainly DNA polymerase a activity. It was shown that this enzyme restores its activity after 2-D electrophoresis and sodium dodecyl sulfate (SDS) elution. After polymerase reaction with labeled dNTPs and autoradiography, the catalytic polypeptide or, rather, polypeptide cluster is revealed as chains of spots (possibly because of the presence of different hydrolyzed and phosphorylated forms). These spots are located on the 2-D electrophoretic map in the region corresponding to molecular masses of 160, 140, and 130 kDa and pI 5.5-6.2.},\r\nauthor_keywords={'Active' gel;  DNA Polymerase;  Two-dimensiional polyacrylamide gel electrophoresis},\r\ncorrespondence_address1={Naryzhny, S.N.; Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina, Leningrad district 188350, Russian Federation; email: naryzhny@omrb.pnpi.spb.ru},\r\npublisher={Wiley-VCH Verlag},\r\nissn={01730835},\r\ncoden={ELCTD},\r\npubmed_id={9150940},\r\nlanguage={English},\r\nabbrev_source_title={ELECTROPHORESIS},\r\ndocument_type={Conference Paper},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
\n\n\n
\n The approach of so-called active gel analysis was used to determine the position and appearance of the catalytic subunit of rat liver DNA polymerase a on a two-dimensional (2-D) electrophoretic map. In this case a polyacrylamide gel containing DNA was used for the second dimension. DNA presence does not change the 2-D protein pattern but makes it possible to conduct a polymerase reaction directly in the gel after separation. A crude extract of rat liver nuclei was used for analysis. The extract is quickly isolated and contains mainly DNA polymerase a activity. It was shown that this enzyme restores its activity after 2-D electrophoresis and sodium dodecyl sulfate (SDS) elution. After polymerase reaction with labeled dNTPs and autoradiography, the catalytic polypeptide or, rather, polypeptide cluster is revealed as chains of spots (possibly because of the presence of different hydrolyzed and phosphorylated forms). These spots are located on the 2-D electrophoretic map in the region corresponding to molecular masses of 160, 140, and 130 kDa and pI 5.5-6.2.\n
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\n  \n 1996\n \n \n (5)\n \n \n
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\n \n\n \n \n \n \n \n \n External proofreading of DNA replication errors in rat cells.\n \n \n \n \n\n\n \n Shevelev, I.; Kravetskaya, T.; Legina, O.; and Krutikov, V.\n\n\n \n\n\n\n Doklady Akademii Nauk, 346(2): 263-265. 1996.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"ExternalPaper\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{Shevelev1996263,\r\nauthor={Shevelev, I.V. and Kravetskaya, T.P. and Legina, O.K. and Krutikov, V.M.},\r\ntitle={External proofreading of DNA replication errors in rat cells},\r\njournal={Doklady Akademii Nauk},\r\nyear={1996},\r\nvolume={346},\r\nnumber={2},\r\npages={263-265},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0029686744&partnerID=40&md5=dcdfe0177591b1a17934f5d0d74a418e},\r\nissn={08695652},\r\ncoden={DAKNE},\r\npubmed_id={8640126},\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 Purification of protein kinase catalytic subunit from the complex form of rat liver DNA polymerase α by denaturing electrofractionation.\n \n \n \n \n\n\n \n Naryzhnyi, S.\n\n\n \n\n\n\n Molecular Biology, 30(6 SUPPL. 2): 845-849. 1996.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"PurificationPaper\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{Naryzhnyi1996845,\r\nauthor={Naryzhnyi, S.N.},\r\ntitle={Purification of protein kinase catalytic subunit from the complex form of rat liver DNA polymerase α by denaturing electrofractionation},\r\njournal={Molecular Biology},\r\nyear={1996},\r\nvolume={30},\r\nnumber={6 SUPPL. 2},\r\npages={845-849},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030336225&partnerID=40&md5=d3a11625100e354d5de924f154f2d0ce},\r\naffiliation={Konstantinov Inst. of Nucl. Physics, Russian Academy of Sciences, Gatchina, 188350, Russian Federation},\r\nabstract={Homogeneous protein kinase [EC 2.7.1.37] from the complex form of rat liver DNA polymerase α was purified by denaturing electrophoresis. The polypeptide had a molecular mass of 60 kDa and pI = 6.8. The new simple method of electrofractionation takes full advantage of the high resolution of SDS electrophoresis, and makes it possible to obtain concentrated virtually homogeneous proteins in preparative quantities with an almost 100% yield. Using mild denaturation, the target enzyme could be detected by activity and isolated after electrofractionation. The method was also successfully used to purify the proofreading 3′-5′ exonuclease.},\r\nauthor_keywords={DNA-polymerase;  Electrofractionation;  Protein kinase},\r\ncorrespondence_address1={Naryzhnyi, S.N.; Konstantinov Inst. of Nucl. Physics, Russian Academy of Sciences, Gatchina, 188350, Russian Federation},\r\nissn={00268933},\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 Homogeneous protein kinase [EC 2.7.1.37] from the complex form of rat liver DNA polymerase α was purified by denaturing electrophoresis. The polypeptide had a molecular mass of 60 kDa and pI = 6.8. The new simple method of electrofractionation takes full advantage of the high resolution of SDS electrophoresis, and makes it possible to obtain concentrated virtually homogeneous proteins in preparative quantities with an almost 100% yield. Using mild denaturation, the target enzyme could be detected by activity and isolated after electrofractionation. The method was also successfully used to purify the proofreading 3′-5′ exonuclease.\n
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\n \n\n \n \n \n \n \n \n Isolation of catalytically active subunit of protein kinase from a complex form of DNA-polymerase alpha in the rat liver using electrofractionation in denaturing conditions [Vydelenie kataliticheski aktivnoi sub''edinitsy proteinkinazy iz kompleksnoi formy DNK-polimerazy alpha pecheni krysy metodom élektrofraktsionirovaniia v denaturiruiushchikh usloviiakh.].\n \n \n \n \n\n\n \n Naryzhnyi, S.\n\n\n \n\n\n\n Molekuliarnaia biologiia, 30(6): 1402-1408. 1996.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"IsolationPaper\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{Naryzhnyi19961402,\r\nauthor={Naryzhnyi, S.N.},\r\ntitle={Isolation of catalytically active subunit of protein kinase from a complex form of DNA-polymerase alpha in the rat liver using electrofractionation in denaturing conditions [Vydelenie kataliticheski aktivnoi sub''edinitsy proteinkinazy iz kompleksnoi formy DNK-polimerazy alpha pecheni krysy metodom élektrofraktsionirovaniia v denaturiruiushchikh usloviiakh.]},\r\njournal={Molekuliarnaia biologiia},\r\nyear={1996},\r\nvolume={30},\r\nnumber={6},\r\npages={1402-1408},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0030277730&partnerID=40&md5=c64a5da1b3d57b0edd4f60cc79c49b61},\r\ncorrespondence_address1={Naryzhnyi, S.N.},\r\nissn={00268984},\r\npubmed_id={9026730},\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 Upside-down stopped-flow electrofractionation of complex protein mixtures.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Analytical Biochemistry, 238(1): 50-53. 1996.\n cited By 17\n\n\n\n
\n\n\n\n \n \n \"Upside-downPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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 The excellent resolution of SDS-PAGE in protein analysis stimulated the creation of various preparative devices. The main approach used in these devices is the construction of a elution chamber in the lower end of the polyacrylamide gel cylinder or plate. Although this continuous lower buffer flow electrofractionation system serves as an acceptable preparative electrophoresis, some limitations to this approach exist. There is strong dilution of protein zones by the eluting buffer, which drastically restricts the sensitivity of the determination of minor proteins, and the restricted current flow caused by electric resistance arising from the column holder prevents application to purification of complex protein mixtures. To overcome these problems, the upside-down stopped-flow electrofractionation system (UDSFE) was designed. The necessary quantity of fraction is drawn with a pipet in a small volume from just above the gel cylinder. This invention improves the possibility of electrofractionation of deluted complex protein mixtures. The efficiency of this technique is demonstrated by purification a protein kinase from rat liver. The method has also been successfully used for purification of error-correcting 3'-5' exonuclease.\n
\n\n\n
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\n \n\n \n \n \n \n \n \n 'External' proofreading of DNA replication errors and mammalian autonomous 3′ → 5′exonucleases.\n \n \n \n \n\n\n \n \n\n\n \n\n\n\n Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis, 352(1-2): 51-55. 1996.\n cited By 18\n\n\n\n
\n\n\n\n \n \n \"'External'Paper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \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 Mammalian nuclear DNA polymerases α and β are known to be devoid of the editing 3′ → 5′ exonucleolytic activity. The base substitutions misinserted by these polymerases could be eliminated with two kinds of an 'external' proofreading carried out (1) by the 3′ → 5′ exonuclease function intrinsic to DNA polymerases δ and ε or/and (2) by the autonomous 3′ → 5′ exonucleases non-associated covalently with DNA polymerases. DNA polymerases δ and ε can be separated from autonomous 3′ → 5′ exonucleases by means of sedimentation. Ultracentrifugation of the nuclear extracts and cytosols from normal and regenerating rat liver as well as from total embryos has shown the bulk of the cellular 3′ → 5′ exonucleolytic activity is due to autonomous nucleases. Moreover, the level of such a specific activity correlates with the replicative status of the organs from adult animals: spleen > regenerating liver > normal liver > cardiac muscle > brain, maximum difference being an order of magnitude. In addition, autonomous exonucleases were shown to be the constituents of the multienzyme forms of DNA polymerases α and β. Hence, autonomous 3′ → 5′ exonucleases seem to be the principal participants in an 'external' proofreading.\n
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\n  \n 1993\n \n \n (3)\n \n \n
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\n \n\n \n \n \n \n \n \n Proof‐reading 3′→5′ exonucleases isolated from rat liver nuclei.\n \n \n \n \n\n\n \n BELYAKOVA, N.; KLEINER, N.; KRAVETSKAYA, T.; LEGINA, O.; NARYZHNY, S.; PERRINO, F.; SHEVELEV, I.; and KRUTYAKOV, V.\n\n\n \n\n\n\n European Journal of Biochemistry, 217(2): 493-500. 1993.\n cited By 34\n\n\n\n
\n\n\n\n \n \n \"Proof‐readingPaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{BELYAKOVA1993493,\r\nauthor={BELYAKOVA, N.V. and KLEINER, N.E. and KRAVETSKAYA, T.P. and LEGINA, O.K. and NARYZHNY, S.N. and PERRINO, F.W. and SHEVELEV, I.V. and KRUTYAKOV, V.M.},\r\ntitle={Proof‐reading 3′→5′ exonucleases isolated from rat liver nuclei},\r\njournal={European Journal of Biochemistry},\r\nyear={1993},\r\nvolume={217},\r\nnumber={2},\r\npages={493-500},\r\ndoi={10.1111/j.1432-1033.1993.tb18269.x},\r\nnote={cited By 34},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0027445624&doi=10.1111%2fj.1432-1033.1993.tb18269.x&partnerID=40&md5=a80eebe3e584943ab18fbe4c3960052f},\r\naffiliation={Laboratory of DNA Biosynthesis, Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute of the Russia Academy of Sciences, Gatchina, Russian Federation; Bowman Gray School of Medicine, Wake Forest University, Department of Biochemistry, 300 South Hawthorne Road, Winston-Salem, United States},\r\nabstract={Mammalian nuclear DNA polymerases α and β are known to be devoid of the editing 3′→5′ exonucleolytic activity. Presumably this activity could be effected by the exonucleases non‐associated covalently with DNA polymerases. Two 3′→5′ exonucleases of 40 kDa and 50 kDa (exo‐40 and exo‐50) have been isolated from rat liver nuclei and purified to near homogeneity. They are shown to excise mismatched nucleotides from poly[d(A‐T)] template, respectively, 10‐fold and 2‐fold faster than the matched ones. Upon addition of either of these exonucleases to the DNA polymerase α from rat liver or calf thymus, the fidelity of in‐vitro reproduction of the primed DNA from bacteriophage φX174 amber 3 is increased 5–10‐fold, levels of exonuclease and DNA‐polymerase activities being similar. Extrapolation of in‐vitro DNA‐replication fidelity to the cellular levels of activities of the exonucleases and the α‐polymerase suggests that exonucleolytic proofreading augments the accuracy of DNA synthesis by 2–3 orders of magnitude. Copyright © 1993, Wiley Blackwell. All rights reserved},\r\ncorrespondence_address1={KRUTYAKOV, V.M.; Petersburg Nuclear Physics Institute, Russia Academy of Sciences, Leningrad District, Gatchina, 188350, Russian Federation},\r\nissn={00142956},\r\npubmed_id={8223593},\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 Mammalian nuclear DNA polymerases α and β are known to be devoid of the editing 3′→5′ exonucleolytic activity. Presumably this activity could be effected by the exonucleases non‐associated covalently with DNA polymerases. Two 3′→5′ exonucleases of 40 kDa and 50 kDa (exo‐40 and exo‐50) have been isolated from rat liver nuclei and purified to near homogeneity. They are shown to excise mismatched nucleotides from poly[d(A‐T)] template, respectively, 10‐fold and 2‐fold faster than the matched ones. Upon addition of either of these exonucleases to the DNA polymerase α from rat liver or calf thymus, the fidelity of in‐vitro reproduction of the primed DNA from bacteriophage φX174 amber 3 is increased 5–10‐fold, levels of exonuclease and DNA‐polymerase activities being similar. Extrapolation of in‐vitro DNA‐replication fidelity to the cellular levels of activities of the exonucleases and the α‐polymerase suggests that exonucleolytic proofreading augments the accuracy of DNA synthesis by 2–3 orders of magnitude. Copyright © 1993, Wiley Blackwell. All rights reserved\n
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\n \n\n \n \n \n \n \n \n Contribution of 3'→5' exonucleases from rat liver nuclei to fidelity of DNA synthesis catalyzed by mammalian DNA polymerases α.\n \n \n \n \n\n\n \n Shevelev, I.; Kravetskaya, T.; Legina, O.; Naryzhny, S.; Perrino, F.; and Krutyakov, V.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 27(2): 335-341. 1993.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"ContributionPaper\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{Shevelev1993335,\r\nauthor={Shevelev, I.V. and Kravetskaya, T.P. and Legina, O.K. and Naryzhny, S.N. and Perrino, F.W. and Krutyakov, V.M.},\r\ntitle={Contribution of 3'→5' exonucleases from rat liver nuclei to fidelity of DNA synthesis catalyzed by mammalian DNA polymerases α},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1993},\r\nvolume={27},\r\nnumber={2},\r\npages={335-341},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0027567999&partnerID=40&md5=f677d754a24b85c7760473f48283924b},\r\naffiliation={St.-Petersb. Inst. Nuclear Physics, Russian Academy of Sciences, Gatchina 188350, Russian Federation},\r\ncorrespondence_address1={Shevelev, I.V.; St.-Petersb. Inst. Nuclear Physics, Russian Academy of Sciences, Gatchina 188350, Russian Federation},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={8387631},\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 Purification of a protein phosphokinase from a complex form of rat liver DNA polymerase α.\n \n \n \n \n\n\n \n Shevelev, I.; Naryzhnyi, S.; and Krutyakov, V.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 27(3): 531-537. 1993.\n cited By 1\n\n\n\n
\n\n\n\n \n \n \"PurificationPaper\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{Shevelev1993531,\r\nauthor={Shevelev, I.V. and Naryzhnyi, S.N. and Krutyakov, V.M.},\r\ntitle={Purification of a protein phosphokinase from a complex form of rat liver DNA polymerase α},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1993},\r\nvolume={27},\r\nnumber={3},\r\npages={531-537},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0027603367&partnerID=40&md5=f7be1758dc7a00dee2b342ca48176614},\r\naffiliation={St.Petersb. Inst. of Nuclear Physics, Russian Academy of Sciences, Gatchina 188350, Russian Federation},\r\ncorrespondence_address1={Shevelev, I.V.; St.Petersb. Inst. of Nuclear Physics, Russian Academy of Sciences, Gatchina 188350, Russian Federation},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={8316239},\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 1992\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n \n 3'–>5'-exonucleases of the rat liver and the correction of replication errors [3'–>5'-ékzonukleazy pecheny krysy i korrektsiia oshibok replikatsii.].\n \n \n \n \n\n\n \n Beliakova, N.; Kleǐner, N.; Kravetskaia, T.; Legina, O.; Naryzhnyǐ, S.; Perrino, F.; Shevelev, I.; and Krutiakov, V.\n\n\n \n\n\n\n Izevestiya Akademii Nauk SSSR - Seriya Biologicheskaya, (5): 744-752. 1992.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"3'–>5'-exonucleasesPaper\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{Beliakova1992744,\r\nauthor={Beliakova, N.V. and Kleǐner, N.E. and Kravetskaia, T.P. and Legina, O.K. and Naryzhnyǐ, S.N. and Perrino, F.V. and Shevelev, I.V. and Krutiakov, V.M.},\r\ntitle={3'-->5'-exonucleases of the rat liver and the correction of replication errors [3'-->5'-ékzonukleazy pecheny krysy i korrektsiia oshibok replikatsii.]},\r\njournal={Izevestiya Akademii Nauk SSSR - Seriya Biologicheskaya},\r\nyear={1992},\r\nnumber={5},\r\npages={744-752},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0026913065&partnerID=40&md5=8ca9f142a707ad58594872da062096e1},\r\nabstract={Mammalian nuclear DNA polymerases alpha and beta are lack of the proofreading 3'-->5' exonucleolytic activity. 40 and 50 kDa 3'-->5' exonucleases were isolated from rat liver. The exonucleases were shown to excise mismatched nucleotides from poly[d(A--T)] template 10 and 2 fold faster than matched ones. The addition of either exonuclease to DNA polymerase alpha from rat liver or calf thymus 5-10 times increased the accuracy of reproduction of primed DNA from bacteriophage phi X174 amber 3, values of exonuclease and DNA polymerase activities being approximately equal. The exonuclease activity surpasses the DNA polymerase one by an order of magnitude in chromatin and nuclear membrane. These data, taken together, are indicative of potent proofreading into hepatocytes.},\r\ncorrespondence_address1={Beliakova, N.V.},\r\nissn={00023329},\r\npubmed_id={1332991},\r\nlanguage={Russian},\r\nabbrev_source_title={Izv Akad Nauk SSSR Biol},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
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\n Mammalian nuclear DNA polymerases alpha and beta are lack of the proofreading 3'–>5' exonucleolytic activity. 40 and 50 kDa 3'–>5' exonucleases were isolated from rat liver. The exonucleases were shown to excise mismatched nucleotides from poly[d(A–T)] template 10 and 2 fold faster than matched ones. The addition of either exonuclease to DNA polymerase alpha from rat liver or calf thymus 5-10 times increased the accuracy of reproduction of primed DNA from bacteriophage phi X174 amber 3, values of exonuclease and DNA polymerase activities being approximately equal. The exonuclease activity surpasses the DNA polymerase one by an order of magnitude in chromatin and nuclear membrane. These data, taken together, are indicative of potent proofreading into hepatocytes.\n
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\n \n\n \n \n \n \n \n \n Detection of DNA-binding proteins in polyacrylamide gel after denaturing electrophoresis.\n \n \n \n \n\n\n \n Naryzhnyi, S.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 26(2): 307-314. 1992.\n cited By 2\n\n\n\n
\n\n\n\n \n \n \"DetectionPaper\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{Naryzhnyi1992307,\r\nauthor={Naryzhnyi, S.N.},\r\ntitle={Detection of DNA-binding proteins in polyacrylamide gel after denaturing electrophoresis},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1992},\r\nvolume={26},\r\nnumber={2},\r\npages={307-314},\r\nnote={cited By 2},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0026511968&partnerID=40&md5=27801e44d860ab2432085f43e754715f},\r\naffiliation={B.P. Konstantinov Inst. Nucl. Phys., Russian Academy of Sciences, Gatchina 188350, Russia},\r\ncorrespondence_address1={Naryzhnyi, S.N.; B.P. Konstantinov Inst. Nucl. Phys., Russian Academy of Sciences, Gatchina 188350, Russia},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={1339951},\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 1991\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n The 3'—-5'-exonucleases of rat liver enhance the fidelity of DNA synthesis catalyzed by mammalian DNA-polymerase alpha [3'—-5'-ékzonukleazy pecheni krysy povyshaiut tochnost' sinteza DNK, kataliziruemogo DNK-polimerazami al'fa mlekopitaiushchikh.].\n \n \n \n \n\n\n \n Shevelev, I.; Legina, O.; Naryzhnyǐ, S.; Perrino, F.; and Krutiakov, V.\n\n\n \n\n\n\n Doklady Akademii nauk SSSR, 318(2): 477-480. 1991.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"ThePaper\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{Shevelev1991477,\r\nauthor={Shevelev, I.V. and Legina, O.K. and Naryzhnyǐ, S.N. and Perrino, F.P. and Krutiakov, V.M.},\r\ntitle={The 3'----5'-exonucleases of rat liver enhance the fidelity of DNA synthesis catalyzed by mammalian DNA-polymerase alpha [3'----5'-ékzonukleazy pecheni krysy povyshaiut tochnost' sinteza DNK, kataliziruemogo DNK-polimerazami al'fa mlekopitaiushchikh.]},\r\njournal={Doklady Akademii nauk SSSR},\r\nyear={1991},\r\nvolume={318},\r\nnumber={2},\r\npages={477-480},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0026084501&partnerID=40&md5=510d42093b15d90b5ff76e467176ceb7},\r\ncorrespondence_address1={Shevelev, I.V.},\r\nissn={00023264},\r\npubmed_id={1654246},\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 1990\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n Homogeneous 3'→5'-exonucleases and their multienzyme complexes for rat liver.\n \n \n \n \n\n\n \n Legina, O.; Belyakova, N.; Kleiner, N.; Naryzhny, S.; and Krutyakov, V.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 24(1): 156-162. 1990.\n cited By 4\n\n\n\n
\n\n\n\n \n \n \"HomogeneousPaper\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{Legina1990156,\r\nauthor={Legina, O.K. and Belyakova, N.V. and Kleiner, N.E. and Naryzhny, S.N. and Krutyakov, V.M.},\r\ntitle={Homogeneous 3'→5'-exonucleases and their multienzyme complexes for rat liver},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1990},\r\nvolume={24},\r\nnumber={1},\r\npages={156-162},\r\nnote={cited By 4},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0025112448&partnerID=40&md5=2a6c7e45e2c1d3f0806ffbfedca62319},\r\naffiliation={B.P. Konstantinov Institute of Nuclear Physics, Academy of Sciences of the USSR, Gatchina, Leningrad Region 188350, Russia},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={2348819},\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 1989\n \n \n (3)\n \n \n
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\n \n\n \n \n \n \n \n \n An analysis of normal and regenerating rat liver proteins by two-dimensional gel electrophoresis.\n \n \n \n \n\n\n \n Naryzhny, S.; and Krutyakov, V.\n\n\n \n\n\n\n Biokhimiya, 54(12): 2030-2036. 1989.\n cited By 3\n\n\n\n
\n\n\n\n \n \n \"AnPaper\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{Naryzhny19892030,\r\nauthor={Naryzhny, S.N. and Krutyakov, V.M.},\r\ntitle={An analysis of normal and regenerating rat liver proteins by two-dimensional gel electrophoresis},\r\njournal={Biokhimiya},\r\nyear={1989},\r\nvolume={54},\r\nnumber={12},\r\npages={2030-2036},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0024828779&partnerID=40&md5=56cac20b5aeb553b7da0b6dee69c240a},\r\naffiliation={B.P. Konstantinov Leningrad Institute of Nuclear Physics, USSR Academy of Sciences, Gatchina, Russia},\r\nabstract={The major proteins of homogenate, cytosol, nuclei and nuclear membrane extract from normal and regenerating rat liver were studied by two-dimensional electrophoresis with a view of detecting proteins involved in DNA replication regulation. Essential quantitative differences in three out of 200 polypeptides separated as spots and dyed with Cpomassie R-250 on two dimensional maps were revealed. The content of the p38 nuclear protein (M(r)≃38 kD, pI≃4) increases 6 - 8-fold in the S-phase. The level of another nuclear protein, p50 (M(r)≃50 kD, pI≃6.5) decreases 2 - 3-fold. The cytoplasmic protein p35 (M(r)≃35 kD, pI≃8) also decreases 2 - 3-fold. Moreover, the p40 protein (M(r)≃40 kD, pI≃6) whose content in the nuclei sharply rises up to 20 times after sham operation was revealed.},\r\nauthor_keywords={DNA replication;  Proteins;  rat liver regeneration;  Two-dimensional electrophoresis},\r\nissn={03209725},\r\ncoden={BIOHA},\r\npubmed_id={2633804},\r\nlanguage={Russian},\r\nabbrev_source_title={BIOKHIMIYA},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n The major proteins of homogenate, cytosol, nuclei and nuclear membrane extract from normal and regenerating rat liver were studied by two-dimensional electrophoresis with a view of detecting proteins involved in DNA replication regulation. Essential quantitative differences in three out of 200 polypeptides separated as spots and dyed with Cpomassie R-250 on two dimensional maps were revealed. The content of the p38 nuclear protein (M(r)≃38 kD, pI≃4) increases 6 - 8-fold in the S-phase. The level of another nuclear protein, p50 (M(r)≃50 kD, pI≃6.5) decreases 2 - 3-fold. The cytoplasmic protein p35 (M(r)≃35 kD, pI≃8) also decreases 2 - 3-fold. Moreover, the p40 protein (M(r)≃40 kD, pI≃6) whose content in the nuclei sharply rises up to 20 times after sham operation was revealed.\n
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\n \n\n \n \n \n \n \n \n Synthesis of heat-shock proteins in Saccharomyces cerevisiae protoplasts [Sintez belkov teplovogo shoka protoplastami drozhzheǐ Saccharomyces cerevisiae.].\n \n \n \n \n\n\n \n Bekker, M.; Akhmedov, A.; Smolina, V.; and Naryzhnyǐ, S.\n\n\n \n\n\n\n Molekuliarnaia genetika, mikrobiologiia i virusologiia, (5): 15-19. 1989.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"SynthesisPaper\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{Bekker198915,\r\nauthor={Bekker, M.L. and Akhmedov, A.T. and Smolina, V.S. and Naryzhnyǐ, S.N.},\r\ntitle={Synthesis of heat-shock proteins in Saccharomyces cerevisiae protoplasts [Sintez belkov teplovogo shoka protoplastami drozhzheǐ Saccharomyces cerevisiae.]},\r\njournal={Molekuliarnaia genetika, mikrobiologiia i virusologiia},\r\nyear={1989},\r\nnumber={5},\r\npages={15-19},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0024672440&partnerID=40&md5=94439ab56409fb5c3e95bef97414393d},\r\nabstract={The effect of cellular capsule elimination in Saccharomyces cerevisiae yeasts (protoplast formation) on the heat-shock protein synthesis and the synthesis of the proteins in protoplasts were studied. The methods of mono- and dimeric electrophoresis have demonstrated that (1) about 18 heat-shock proteins with the molecular masses 26-98 Kd are synthesized in cells at 41 degrees C; (2) protoplast formation per se does not induce the synthesis of heat-shock proteins, but the induction of these proteins in protoplasts at 41 degrees C is similar to the one in intact cells. The protoplast formation induces the synthesis of specific proteins different from heat-shock proteins and the synthesis is inhibited by the heat-shock. The heat-shock induces modification of 88 and 86 Kd heat-shock proteins. It inhibits the synthesis of a number of peptides (15-50 Kd) in cells and protoplasts.},\r\ncorrespondence_address1={Bekker, M.L.},\r\nissn={02080613},\r\npubmed_id={2664488},\r\nlanguage={Russian},\r\nabbrev_source_title={Mol Gen Mikrobiol Virusol},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n\n\n
\n The effect of cellular capsule elimination in Saccharomyces cerevisiae yeasts (protoplast formation) on the heat-shock protein synthesis and the synthesis of the proteins in protoplasts were studied. The methods of mono- and dimeric electrophoresis have demonstrated that (1) about 18 heat-shock proteins with the molecular masses 26-98 Kd are synthesized in cells at 41 degrees C; (2) protoplast formation per se does not induce the synthesis of heat-shock proteins, but the induction of these proteins in protoplasts at 41 degrees C is similar to the one in intact cells. The protoplast formation induces the synthesis of specific proteins different from heat-shock proteins and the synthesis is inhibited by the heat-shock. The heat-shock induces modification of 88 and 86 Kd heat-shock proteins. It inhibits the synthesis of a number of peptides (15-50 Kd) in cells and protoplasts.\n
\n\n\n
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\n \n\n \n \n \n \n \n \n Characterization of DNA isolated from a complex form of DNA polymerase α from rat liver.\n \n \n \n \n\n\n \n Timchenko, N.; Belyakova, N.; Timchenko, L.; and Krutyakov, V.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 23(4): 1171-1176. 1989.\n cited By 3\n\n\n\n
\n\n\n\n \n \n \"CharacterizationPaper\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{Timchenko19891171,\r\nauthor={Timchenko, N.A. and Belyakova, N.V. and Timchenko, L.T. and Krutyakov, V.M.},\r\ntitle={Characterization of DNA isolated from a complex form of DNA polymerase α from rat liver},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1989},\r\nvolume={23},\r\nnumber={4},\r\npages={1171-1176},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0024319088&partnerID=40&md5=1260d70148c59e486a11c5c198760006},\r\naffiliation={B.P. Konstantinov Leningrad Institute of Nuclear Physics, Academy of Sciences of the USSR, Gatchina 188350, Russian Federation},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={2586509},\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 1988\n \n \n (1)\n \n \n
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\n \n \n
\n \n\n \n \n \n \n \n \n Complexes of nuclear DNA polymerases with 3'→5' exonucleases from rat liver.\n \n \n \n \n\n\n \n Kleiner, N.; Kravetskaya, T.; Legina, O.; Naryzhny, S.; and Krutyakov, V.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 22(2): 498-505. 1988.\n cited By 6\n\n\n\n
\n\n\n\n \n \n \"ComplexesPaper\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{Kleiner1988498,\r\nauthor={Kleiner, N.E. and Kravetskaya, T.P. and Legina, O.K. and Naryzhny, S.N. and Krutyakov, V.M.},\r\ntitle={Complexes of nuclear DNA polymerases with 3'→5' exonucleases from rat liver},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1988},\r\nvolume={22},\r\nnumber={2},\r\npages={498-505},\r\nnote={cited By 6},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0023971705&partnerID=40&md5=81812f8daa699b3955852833cbb65847},\r\naffiliation={B.P. Konstantinov Institute of Nuclear Physics, Academy of Sciences of the USSR, Gatchina, Leningrad Region 188350},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={2839767},\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 1985\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n Enzymatic and structural mechanism of DNA repair in isolated mammalian chromatin.\n \n \n \n \n\n\n \n Krutyakov, V.; Belyakova, N.; Kravetskaya, T.; and Naryzhny, S.\n\n\n \n\n\n\n Izevestiya Akademii Nauk SSSR - Seriya Biologicheskaya, NO. 4: 562-571. 1985.\n cited By 3\n\n\n\n
\n\n\n\n \n \n \"EnzymaticPaper\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{Krutyakov1985562,\r\nauthor={Krutyakov, V.M. and Belyakova, N.V. and Kravetskaya, T.P. and Naryzhny, S.N.},\r\ntitle={Enzymatic and structural mechanism of DNA repair in isolated mammalian chromatin},\r\njournal={Izevestiya Akademii Nauk SSSR - Seriya Biologicheskaya},\r\nyear={1985},\r\nvolume={NO. 4},\r\npages={562-571},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0021891279&partnerID=40&md5=46018e7915737ecaed2fc7c6303d34d3},\r\naffiliation={B.P. Konstantinov Institute of Nuclear Physics, Academy of Sciences of the USSR, Leningrad, Russian Federation},\r\nissn={00023329},\r\ncoden={IANBA},\r\npubmed_id={4056206},\r\nlanguage={Russian},\r\nabbrev_source_title={IZV. AKAD. NAUK SSSR SER. BIOL.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n  \n 1984\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n 2′,3′-Dideoxy-3′-aminonucleoside 5′-triphosphates inhibit the repair of DNA in rat liver chromatin.\n \n \n \n \n\n\n \n Krayevsky, A.; Kukhanova, M.; Alexandrova, L.; Belyakova, N.; and Krutyakov, V.\n\n\n \n\n\n\n BBA - Gene Structure and Expression, 783(3): 216-220. 1984.\n cited By 3\n\n\n\n
\n\n\n\n \n \n \"2′,3′-Dideoxy-3′-aminonucleosidePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \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{Krayevsky1984216,\r\nauthor={Krayevsky, A. and Kukhanova, M. and Alexandrova, L. and Belyakova, N. and Krutyakov, V.},\r\ntitle={2′,3′-Dideoxy-3′-aminonucleoside 5′-triphosphates inhibit the repair of DNA in rat liver chromatin},\r\njournal={BBA - Gene Structure and Expression},\r\nyear={1984},\r\nvolume={783},\r\nnumber={3},\r\npages={216-220},\r\ndoi={10.1016/0167-4781(84)90031-9},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0021715876&doi=10.1016%2f0167-4781%2884%2990031-9&partnerID=40&md5=66c4aa4a017e09ac19492c0d9df212d6},\r\naffiliation={Institute of Molecular Biology, the USSR Academy of Sciences, Vavilov str. 32, Moscow, B-334 117984, Russian Federation; B.P. Konstantinov Nuclear Physics Institute, the USSR Academy of Sciences, Gatchina, Leningrad District 188350, Russian Federation},\r\nabstract={2′,3′-Dideoxy-3′-aminonucleoside 5′-triphosphates are shown to be strong inhibitors of repair DNA synthesis in γ-irradiated rat liver chromatin. The activity of these compounds is comparable with that of the most effective inhibitor of the DNA polymerase β-catalyzed repair DNA synthesis. © 1984.},\r\nauthor_keywords={(Rat liver);  Dideoxyaminonucleotide;  DNA repair;  DNA synthesis;  Nucleotide derivative;  γ-irradiation},\r\ncorrespondence_address1={Krayevsky, A.; Institute of Molecular Biology, the USSR Academy of Sciences, Vavilov str. 32, Moscow, B-334 117984, Russian Federation},\r\nissn={01674781},\r\ncoden={BBGSD},\r\npubmed_id={6509056},\r\nlanguage={English},\r\nabbrev_source_title={Biochim. Biophys. Acta Gene Struct. Expr.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
\n
\n\n\n
\n 2′,3′-Dideoxy-3′-aminonucleoside 5′-triphosphates are shown to be strong inhibitors of repair DNA synthesis in γ-irradiated rat liver chromatin. The activity of these compounds is comparable with that of the most effective inhibitor of the DNA polymerase β-catalyzed repair DNA synthesis. © 1984.\n
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\n  \n 1983\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n Eukaryotic 3' leads to 5'-exonuclease correcting DNA-polymerase errors [Eukarioticheskaia 3' vedet K 5'-ékzonukleaza, ispravliaiushchaia DNK-polimeraznye oshibki.].\n \n \n \n \n\n\n \n Krutiakov, V.; Beliakova, N.; Kleǐner, N.; Legina, O.; and Shevelev, I.\n\n\n \n\n\n\n Doklady Akademii nauk SSSR, 272(6): 1491-1494. 1983.\n cited By 5\n\n\n\n
\n\n\n\n \n \n \"EukaryoticPaper\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{Krutiakov19831491,\r\nauthor={Krutiakov, V.M. and Beliakova, N.V. and Kleǐner, N.E. and Legina, O.K. and Shevelev, I.V.},\r\ntitle={Eukaryotic 3' leads to 5'-exonuclease correcting DNA-polymerase errors [Eukarioticheskaia 3' vedet K 5'-ékzonukleaza, ispravliaiushchaia DNK-polimeraznye oshibki.]},\r\njournal={Doklady Akademii nauk SSSR},\r\nyear={1983},\r\nvolume={272},\r\nnumber={6},\r\npages={1491-1494},\r\nnote={cited By 5},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0021004330&partnerID=40&md5=f26d2fe1fe72142b7ad3fe3e4933fdec},\r\ncorrespondence_address1={Krutiakov, V.M.},\r\nissn={00023264},\r\npubmed_id={6317317},\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 1982\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n \n Enzymic and structural aspects of repair DNA synthesis activation in mammalian chromatin.\n \n \n \n \n\n\n \n Belyakova, N.; Naryzhnyi, S.; Filatov, M.; and Krutyakov, V.\n\n\n \n\n\n\n Radiobiologiya, 22(5): 593-596. 1982.\n cited By 1\n\n\n\n
\n\n\n\n \n \n \"EnzymicPaper\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{Belyakova1982593,\r\nauthor={Belyakova, N.V. and Naryzhnyi, S.N. and Filatov, M.V. and Krutyakov, V.M.},\r\ntitle={Enzymic and structural aspects of repair DNA synthesis activation in mammalian chromatin},\r\njournal={Radiobiologiya},\r\nyear={1982},\r\nvolume={22},\r\nnumber={5},\r\npages={593-596},\r\nnote={cited By 1},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020448912&partnerID=40&md5=e6f60aadab293185ae5595d6bf4bebdf},\r\naffiliation={B.P. Konstantinov Leningrad Inst. Nucl. Phys., USSR Acad. Sci., Gatchina},\r\nabstract={Analysis was made of the enzymic and structural factors responsible for activation of repair DNA synthesis in γ-irradiated chromatin isolated from rat liver or some human cells. The results obtained prompted us to reduce by 10-12 times the dose of radiation used before. With doses of 30 Gy and 10 Gy, the value of the original repair synthesis was doubled in the chromatin of rat liver and HeLa cells, respectively.},\r\nissn={00338192},\r\ncoden={RADOA},\r\npubmed_id={6294723},\r\nlanguage={Russian},\r\nabbrev_source_title={RADIOBIOLOGIYA},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n Analysis was made of the enzymic and structural factors responsible for activation of repair DNA synthesis in γ-irradiated chromatin isolated from rat liver or some human cells. The results obtained prompted us to reduce by 10-12 times the dose of radiation used before. With doses of 30 Gy and 10 Gy, the value of the original repair synthesis was doubled in the chromatin of rat liver and HeLa cells, respectively.\n
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\n \n\n \n \n \n \n \n \n Effect of antitumour antibiotic bleomycin on DNA polymerase activity.\n \n \n \n \n\n\n \n Naryzhny, S.; Shevelev, I.; and Krutyakov, V.\n\n\n \n\n\n\n Biokhimiya, 47(7): 1212-1215. 1982.\n cited By 3\n\n\n\n
\n\n\n\n \n \n \"EffectPaper\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{Naryzhny19821212,\r\nauthor={Naryzhny, S.N. and Shevelev, I.V. and Krutyakov, V.M.},\r\ntitle={Effect of antitumour antibiotic bleomycin on DNA polymerase activity},\r\njournal={Biokhimiya},\r\nyear={1982},\r\nvolume={47},\r\nnumber={7},\r\npages={1212-1215},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0020002172&partnerID=40&md5=5346810a54285601f7cfcf332982d98a},\r\naffiliation={B.P. Konstantinov Leningrad Inst. Nucl. Phys., USSR Acad. Sci., Gatchina, Leningrad Reg.},\r\nissn={03209725},\r\ncoden={BIOHA},\r\npubmed_id={6180778},\r\nlanguage={Russian},\r\nabbrev_source_title={BIOKHIMIYA},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n  \n 1981\n \n \n (2)\n \n \n
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\n \n\n \n \n \n \n \n \n Effect of radioprotective agents, 2-mercaptoethylamine and 5-methoxytryptamine, on activity of some repair enzymes.\n \n \n \n \n\n\n \n Belyakova, N.; Kravetskaya, T.; and Krutyakov, V.\n\n\n \n\n\n\n Radiobiologiya, 21(2): 198-203. 1981.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"EffectPaper\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{Belyakova1981198,\r\nauthor={Belyakova, N.V. and Kravetskaya, T.P. and Krutyakov, V.M.},\r\ntitle={Effect of radioprotective agents, 2-mercaptoethylamine and 5-methoxytryptamine, on activity of some repair enzymes},\r\njournal={Radiobiologiya},\r\nyear={1981},\r\nvolume={21},\r\nnumber={2},\r\npages={198-203},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0019544474&partnerID=40&md5=6edd8dcd4ebe8cb72193e5fcbd38adb6},\r\naffiliation={B.P. Konstantinov Leningrad Inst. Nucl. Phys., USSR Acad. Sci., Gatchina},\r\nabstract={A study was made of the effect of the radioprotective agents, 2-mercapto-ethylamine and 5-methoxytryptamine, on the activity of DNA-polymerase I and exonuclease III from E. coli, DNA-polymerases α and β, endonuclease I and 3'-exonuclease from rat liver chromatin. The effect of the radioprotective agents on the activity of purified enzymes was compared with their effect on corresponding activities of chromatin, nuclei and cells, as well as with the effect on DNP and chromatin structures. It is assumed that the radioprotective agents increase condensation of the chromatin which is accompanied by the attenuation of postradiation nuclease degradation of DNA and, accordingly, a decrease in the probability of enzymatic production of poorly repaired double-stranded DNA breaks.},\r\nissn={00338192},\r\ncoden={RADOA},\r\npubmed_id={6264539},\r\nlanguage={Russian},\r\nabbrev_source_title={RADIOBIOLOGIYA},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n A study was made of the effect of the radioprotective agents, 2-mercapto-ethylamine and 5-methoxytryptamine, on the activity of DNA-polymerase I and exonuclease III from E. coli, DNA-polymerases α and β, endonuclease I and 3'-exonuclease from rat liver chromatin. The effect of the radioprotective agents on the activity of purified enzymes was compared with their effect on corresponding activities of chromatin, nuclei and cells, as well as with the effect on DNP and chromatin structures. It is assumed that the radioprotective agents increase condensation of the chromatin which is accompanied by the attenuation of postradiation nuclease degradation of DNA and, accordingly, a decrease in the probability of enzymatic production of poorly repaired double-stranded DNA breaks.\n
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\n \n\n \n \n \n \n \n \n Low transfecting efficiency of phage lambda ring chromosomes and their fragments formed by membrane nucleases [Nizkaia éffektivnost' kol'tsevykh khromosom faga lambda i ikh fragmentov, obrazovannykh obolochechnymi nukleazami, pri transfektsii.].\n \n \n \n \n\n\n \n Drabkina, L.; Konevega, L.; Legina, O.; and Mosevitskiǐ, M.\n\n\n \n\n\n\n Genetika, 17(1): 52-59. 1981.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"LowPaper\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{Drabkina198152,\r\nauthor={Drabkina, L.E. and Konevega, L.V. and Legina, O.K. and Mosevitskiǐ, M.I.},\r\ntitle={Low transfecting efficiency of phage lambda ring chromosomes and their fragments formed by membrane nucleases [Nizkaia éffektivnost' kol'tsevykh khromosom faga lambda i ikh fragmentov, obrazovannykh obolochechnymi nukleazami, pri transfektsii.]},\r\njournal={Genetika},\r\nyear={1981},\r\nvolume={17},\r\nnumber={1},\r\npages={52-59},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0019502150&partnerID=40&md5=8f925a8425cb62686866eeff15d7ab8b},\r\nabstract={Transfection efficiency of a number of lambda DNA samples differing in ring to linear molecules ratio was determined. Graphic extrapolation to the zero content of linear molecules showed that efficiency of ring molecules did not exceed 5% of that of linear molecules. Probably, this difference is caused by more fast penetration of linear molecules into the cell and, therefore, by lower probability of their degradation by cell wall nucleases. Fragments of both ring and linear molecules formed by cell wall nucleases proved to be inactive in marker rescue experiments.},\r\ncorrespondence_address1={Drabkina, L.E.},\r\nissn={00166758},\r\npubmed_id={6453042},\r\nlanguage={Russian},\r\nabbrev_source_title={Genetika},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n Transfection efficiency of a number of lambda DNA samples differing in ring to linear molecules ratio was determined. Graphic extrapolation to the zero content of linear molecules showed that efficiency of ring molecules did not exceed 5% of that of linear molecules. Probably, this difference is caused by more fast penetration of linear molecules into the cell and, therefore, by lower probability of their degradation by cell wall nucleases. Fragments of both ring and linear molecules formed by cell wall nucleases proved to be inactive in marker rescue experiments.\n
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\n  \n 1980\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n Mechanism of activating action of ATP on repair synthesis of DNA in chromatin.\n \n \n \n \n\n\n \n Belyakova, N.; Narizhny, S.; and Krutyakov, V.\n\n\n \n\n\n\n Molekulyarnaya Biologiya, 14(3): 586-594. 1980.\n cited By 3\n\n\n\n
\n\n\n\n \n \n \"MechanismPaper\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{Belyakova1980586,\r\nauthor={Belyakova, N.V. and Narizhny, S.N. and Krutyakov, V.M.},\r\ntitle={Mechanism of activating action of ATP on repair synthesis of DNA in chromatin},\r\njournal={Molekulyarnaya Biologiya},\r\nyear={1980},\r\nvolume={14},\r\nnumber={3},\r\npages={586-594},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0018960439&partnerID=40&md5=128c4af591d8445775c9f2cdfda044ff},\r\naffiliation={B.P.Konstantinov Inst. Nucl. Phys., Acad. Sci. USSR, Gatchina},\r\nissn={00268984},\r\ncoden={MOBIB},\r\npubmed_id={6250023},\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 (2)\n \n \n
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\n \n\n \n \n \n \n \n \n Effect of radioprotective agents on endogenous DNA synthesis and degradation in nuclei and chromatin.\n \n \n \n \n\n\n \n Kravetskaya, T.; Bagiyan, G.; Belyakova, N.; and Krutyakov, V.\n\n\n \n\n\n\n Radiobiologiya, 18(6): 836-841. 1978.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"EffectPaper\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{Kravetskaya1978836,\r\nauthor={Kravetskaya, T.P. and Bagiyan, G.A. and Belyakova, N.V. and Krutyakov, V.M.},\r\ntitle={Effect of radioprotective agents on endogenous DNA synthesis and degradation in nuclei and chromatin},\r\njournal={Radiobiologiya},\r\nyear={1978},\r\nvolume={18},\r\nnumber={6},\r\npages={836-841},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0018253241&partnerID=40&md5=dde0c704a78ba2b20d960701773bcc1a},\r\naffiliation={B.P. Konstantinov Inst. Nucl. Phys., USSR Acad. Sci., Leningrad},\r\nissn={00338192},\r\ncoden={RADOA},\r\npubmed_id={740861},\r\nlanguage={Russian},\r\nabbrev_source_title={RADIOBIOLOGIYA},\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 On the mechanism of raising the transfection efficiency of lysogenic or infected with helper phage calcinated Escherichia coli cells with λ DNA.\n \n \n \n \n\n\n \n Drabkina, L.; Konevega, L.; Legina, O.; and Mosevitsky, M.\n\n\n \n\n\n\n Genetika, 14(7): 1153-1163. 1978.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"OnPaper\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{Drabkina19781153,\r\nauthor={Drabkina, L.E. and Konevega, L.V. and Legina, O.K. and Mosevitsky, M.I.},\r\ntitle={On the mechanism of raising the transfection efficiency of lysogenic or infected with helper phage calcinated Escherichia coli cells with λ DNA},\r\njournal={Genetika},\r\nyear={1978},\r\nvolume={14},\r\nnumber={7},\r\npages={1153-1163},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0017833035&partnerID=40&md5=e7b4618ec48d0cca88002fe770910ab6},\r\naffiliation={B.P. Konstantinov Inst. Nucl. Phys., Acad. Scis USSR, Leningrad, Russian Federation},\r\nissn={00166758},\r\ncoden={GNKAA},\r\npubmed_id={352809},\r\nlanguage={Russian},\r\nabbrev_source_title={GENETIKA},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n  \n 1976\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n Dependence of transfection efficiency of calcium treated Escherichia coli cells on bacterial genotype and form of lambda DNA.\n \n \n \n \n\n\n \n Drabkina, L.; Konevega, L.; Legina, O.; and Mosevitsky, M.\n\n\n \n\n\n\n MGG Molecular & General Genetics, 144(1): 83-86. 1976.\n cited By 3\n\n\n\n
\n\n\n\n \n \n \"DependencePaper\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\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{Drabkina197683,\r\nauthor={Drabkina, L.E. and Konevega, L.V. and Legina, O.K. and Mosevitsky, M.I.},\r\ntitle={Dependence of transfection efficiency of calcium treated Escherichia coli cells on bacterial genotype and form of lambda DNA},\r\njournal={MGG Molecular & General Genetics},\r\nyear={1976},\r\nvolume={144},\r\nnumber={1},\r\npages={83-86},\r\ndoi={10.1007/BF00277309},\r\nnote={cited By 3},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0017276873&doi=10.1007%2fBF00277309&partnerID=40&md5=92b1c9e0c5d7cb8ac9517c32c8308b64},\r\naffiliation={Institute of Nuclear Physics, Academy of Sciences of the USSR, Leningrad, Russia},\r\nabstract={The transfecting activity of linear λ DNA is 100 times higher in calcium treated E. coli K 12 (λi434) than in non-lysogenic strains: the levels of transfection are 1-2.107 and 1-2.105 infective centers per 1 μg of λ DNA, respectively. The high efficiency of lysogenic cells transfection is not due to the spontaneously liberated "helper" phage. Evidently, it is called forth by transfecting DNA-prophage recombination or/and by inhibition of nuclease activity in lysogenic cells. Both ring forms λ DNA (supercoiled and open circles) show very low infectivity, if any, in calcinated cells. © 1976 Springer-Verlag.},\r\ncorrespondence_address1={Drabkina, L.E.; Institute of Nuclear Physics, Academy of Sciences of the USSR, Leningrad, Russia},\r\npublisher={Springer-Verlag},\r\nissn={00268925},\r\ncoden={MGGEA},\r\npubmed_id={772416},\r\nlanguage={English},\r\nabbrev_source_title={Molec. Gen. Genet.},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n\r\n
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\n The transfecting activity of linear λ DNA is 100 times higher in calcium treated E. coli K 12 (λi434) than in non-lysogenic strains: the levels of transfection are 1-2.107 and 1-2.105 infective centers per 1 μg of λ DNA, respectively. The high efficiency of lysogenic cells transfection is not due to the spontaneously liberated \"helper\" phage. Evidently, it is called forth by transfecting DNA-prophage recombination or/and by inhibition of nuclease activity in lysogenic cells. Both ring forms λ DNA (supercoiled and open circles) show very low infectivity, if any, in calcinated cells. © 1976 Springer-Verlag.\n
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\n  \n 1975\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n Infectiousness of various forms of phage λ DNA in transfection of calcinated cells of E. coli.\n \n \n \n \n\n\n \n Drabkina, L.; Konevega, L.; Legina, O.; and Mosevitskii, M.\n\n\n \n\n\n\n Molecular Biology, 9(3): 301-307. 1975.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"InfectiousnessPaper\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{Drabkina1975301,\r\nauthor={Drabkina, L.E. and Konevega, L.V. and Legina, O.K. and Mosevitskii, M.I.},\r\ntitle={Infectiousness of various forms of phage λ DNA in transfection of calcinated cells of E. coli},\r\njournal={Molecular Biology},\r\nyear={1975},\r\nvolume={9},\r\nnumber={3},\r\npages={301-307},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0016779758&partnerID=40&md5=aa5b69b394c9e80ebdcd7120e6a6d8c5},\r\naffiliation={B.P. Konstantinov Inst. Nucl. Phys., Acad. Sci. USSR, Leningrad, Russian Federation},\r\nabstract={The infectiousness of linear molecules of λ DNA in transfection of calcinated cells of E. coli K12 (λ(i434)) is 100 times as high as in the transfection of nonlysogenic cells of the same strain: (2 ± 1) x 107 and 1 x 105 infectious centers per μg λ DNA, respectively. The increased effectiveness of the transfection of lysogenic cells is not associated with the presence of a phage promoter spontaneously liberated by them. It can be assumed that it is due to the interaction of DNA with the prophage and (or) to reduced activity of nucleases capable of attacking λ DNA in the lysogenic cells. Ring molecules of λ DNA penetrate into the calcinated cells just as readily as linear molecules but possess substantially lower infectiousness.},\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 The infectiousness of linear molecules of λ DNA in transfection of calcinated cells of E. coli K12 (λ(i434)) is 100 times as high as in the transfection of nonlysogenic cells of the same strain: (2 ± 1) x 107 and 1 x 105 infectious centers per μg λ DNA, respectively. The increased effectiveness of the transfection of lysogenic cells is not associated with the presence of a phage promoter spontaneously liberated by them. It can be assumed that it is due to the interaction of DNA with the prophage and (or) to reduced activity of nucleases capable of attacking λ DNA in the lysogenic cells. Ring molecules of λ DNA penetrate into the calcinated cells just as readily as linear molecules but possess substantially lower infectiousness.\n
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\n  \n 1972\n \n \n (1)\n \n \n
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\n \n\n \n \n \n \n \n \n Influence of proflavine on the cyclization and aggregation of phage lambda DNA.\n \n \n \n \n\n\n \n Drabkina, L.; Konevega, L.; Legina, O.; and Mosevitskii, M.\n\n\n \n\n\n\n Molecular Biology, 6(5): 520-525. 1972.\n cited By 0\n\n\n\n
\n\n\n\n \n \n \"InfluencePaper\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{Drabkina1972520,\r\nauthor={Drabkina, L.E. and Konevega, L.V. and Legina, O.K. and Mosevitskii, M.I.},\r\ntitle={Influence of proflavine on the cyclization and aggregation of phage lambda DNA.},\r\njournal={Molecular Biology},\r\nyear={1972},\r\nvolume={6},\r\nnumber={5},\r\npages={520-525},\r\nnote={cited By 0},\r\nurl={https://www.scopus.com/inward/record.uri?eid=2-s2.0-0015391662&partnerID=40&md5=2f9f4efc819752ac33fc8297cf20884d},\r\ncorrespondence_address1={Drabkina, L.E.},\r\nissn={00268933},\r\npubmed_id={4660954},\r\nlanguage={English},\r\nabbrev_source_title={Mol Biol},\r\ndocument_type={Article},\r\nsource={Scopus},\r\n}\r\n
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