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Makarov VA, Popov VO. PDSTP Is the First Drug in Class to Treat Coronavirus Infection. Her Russ Acad Sci 2022; 92:488-490. [PMID: 36091851 PMCID: PMC9447965 DOI: 10.1134/s1019331622040190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/25/2022] [Accepted: 03/12/2022] [Indexed: 06/15/2023]
Abstract
The results of a comprehensive study are presented on the development and creation of an original small PDSTP molecule, able to prevent the SARS-CoV-2 coronavirus infection from binding to the host cell. The PDSTP molecule was designed to electrostatically interact with heparan sulfate proteoglycans on the cell surface, and coronaviruses, particularly SARS-CoV-2, use this mechanism as the first stage of interaction with the cell. By blocking this process, it is possible to stop the life cycle of the virus, thus leading to its death. The drug candidate PDSTP, with its unique mechanism of action, is characterized by a very low toxicity and a high safety profile and demonstrates good efficacy in animal experiments.
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Affiliation(s)
- V. A. Makarov
- Federal Research Center, Fundamentals of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - V. O. Popov
- Federal Research Center, Fundamentals of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Popov VO. Prospects for the Formulation Development of Fast-Burning Low-Gas Pyrotechnic Compositions. RUSS J APPL CHEM+ 2022. [DOI: 10.1134/s1070427222090026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Komov VN, Popov VO. Computational and Theoretical Estimation of the Energy Potential of Highly Filled Propellant Formulations. RUSS J APPL CHEM+ 2022. [DOI: 10.1134/s1070427222080134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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Boyko KM, Nikolaeva AY, Bakunova AK, Stekhanova TN, Rakitina TV, Popov VO, Bezsudnova EY. Three-Dimensional Structure of Thermostable D-Amino Acid Transaminase from the Archaeon Methanocaldococcus jannaschii DSM 2661. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Oshkin IY, Belova SE, Khokhlachev NS, Semenova VA, Chervyakova OP, Chernushkin DV, Tikhonova EN, Mardanov AV, Ravin NV, Popov VO, Pimenov NV, Dedysh SN. Molecular Analysis of the Microbial Community Developing in Continuous Culture of Methylococcus sp. Concept-8 on Natural Gas. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720050173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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But SY, Dedysh SN, Popov VO, Pimenov NV, Khmelenina VN. Construction of a Type-I Metanotroph with Reduced Capacity for Glycogen and Sucrose Accumulation. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820050063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Boyko KM, Nikolaeva AY, Timofeev VI, Popov VO, Bezsudnova EY. Three-Dimensional Structure of Branched-Chain Amino Acid Transaminase from Thermoproteus uzoniensis in Complex with L-Norvaline. CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s1063774520040045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Boyko KM, Nikolaeva AY, Bonchuk AN, Georgiev PG, Popov VO. Crystallization and Preliminary X-Ray Diffraction Analysis of the ZAD Domain of the Serendipity-d Protein from Drosophila melanogaster. CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s1063774520040057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Pometun AA, Boyko KM, Yurchenko TS, Nikolaeva AY, Kargov IS, Atroshenko DL, Savin SS, Popov VO, Tishkov VI. Highly-Active Recombinant Formate Dehydrogenase from Pathogenic Bacterium Staphylococcus aureus: Preparation and Crystallization. Biochemistry (Mosc) 2020; 85:689-696. [PMID: 32586232 DOI: 10.1134/s0006297920060061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
# These authors contributed equally to the work. NAD+-dependent formate dehydrogenase from Staphylococcus aureus (SauFDH) is one of the key enzymes responsible for the survival of this pathogen in the form of biofilms. 3D structure of the enzyme might be helpful in the search for highly specific SauFDH inhibitors that can be used as antibacterial agents exactly against S. aureus biofilms. Here, we prepared a recombinant SauFDH in Escherichia coli cells with a yield of 1 g target protein per liter medium. The developed procedure for the enzyme purification allowed to obtain 400 mg of homogenous enzyme with 61% yield. The specific activity of the purified recombinant SauFDH was 20 U per mg protein, which was 2 times higher than the previously reported activities of formate dehydrogenases. We also found crystallization conditions in the course of two rounds of optimization and obtained 200- and 40-µm crystals for the SauFDH apo- and holoenzymes, respectively. X-ray analysis using synchrotron X-ray sources produced diffraction data sufficient for solving the three-dimensional structures of the apo- and holoenzymes with the resolution of 2.2 and 2.7 Å, respectively. Crystals of the apo- and holoforms of SauFDH had different crystal space groups, which suggest coenzyme binding in the SauFDH holoenzyme.
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Affiliation(s)
- A A Pometun
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia.,Innovations and High Technologies MSU Ltd., Moscow, 109559, Russia
| | - K M Boyko
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - T S Yurchenko
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - A Yu Nikolaeva
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia.,Kurchatov Institute National Research Center, Moscow, 123182, Russia
| | - I S Kargov
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia.,Innovations and High Technologies MSU Ltd., Moscow, 109559, Russia
| | - D L Atroshenko
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia.,Innovations and High Technologies MSU Ltd., Moscow, 109559, Russia
| | - S S Savin
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia.,Innovations and High Technologies MSU Ltd., Moscow, 109559, Russia
| | - V O Popov
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia.,Kurchatov Institute National Research Center, Moscow, 123182, Russia
| | - V I Tishkov
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia. .,Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 119071, Russia.,Innovations and High Technologies MSU Ltd., Moscow, 109559, Russia
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Oshkin IY, Khmelenina VN, But SY, Miroshnikov KK, Belova SE, Khokhlachev NS, Chernushkin DV, Beletsky AV, Mardanov AV, Ravin NV, Popov VO, Dedysh SN, Pimenov NV. Analysis of the Complete Genome Sequence of Strain Concept-8, a Novel Representative of the Genus Methylococcus. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720030121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Bezsudnova EY, Stekhanova TN, Boyko KM, Popov VO. Effect of Ketosubstrate on the Product Yield in the Transamination Reaction Catalyzed by Transaminase from Thermoproteus uzoniensis. DOKL BIOCHEM BIOPHYS 2020; 490:5-8. [PMID: 32342302 DOI: 10.1134/s1607672920010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 09/13/2019] [Accepted: 09/13/2019] [Indexed: 11/23/2022]
Abstract
The study of the equilibrium of reactions catalyzed by thermostable enzymes is in demand for the development of biotechnological enzyme processes. The results of the analysis of equilibrium of transamination reaction catalyzed by thermostable transaminase from the archaeon Thermoproteus uzoniensis are presented below. A comparison of the conversion of substrates was performed for reactions with L-leucine and pyruvate and L-leucine and 2-oxobutyrate at 65°C. The establishment of the equilibrium was controlled by a decrease in the concentration of 2-oxobutyrate or pyruvate and by the accumulation of the keto analog of L-leucine. It was shown that the degree of conversion of L-leucine in the reaction with specific 2-oxobutyrate is higher than in the reaction with nonspecific pyruvate.
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Affiliation(s)
- E Yu Bezsudnova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
| | - T N Stekhanova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - K M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - V O Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.,National Research Centre "Kurchatov Institute", Moscow, Russia
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Filkin SY, Chertova NV, Zenin AA, Lipkin AV, Sichev AA, Bityak DS, Sadykhov EG, Popov VO, Fedorov AN. Expression, purification and biophysical characterization of recombinant Streptomyces violaceoruber phospholipase PLA2 overproduced in Pichia pastoris. Prep Biochem Biotechnol 2020; 50:549-555. [PMID: 31933410 DOI: 10.1080/10826068.2020.1712657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Aim: The main purpose of this work was to develop new protocols for high yield purification of secretory phospholipase A2 (PLA2) and to investigate its biophysical properties.Materials and methods: We have used a Pichia pastoris expression system for PLA2 expression and two-stage chromatography for its purification. The biophysical properties of PLA2 were investigated by circular dichroism.Results: A scalable method for high yield purification of recombinant Streptomyces violaceruber PLA2 was developed. The PLA2 from S. violaceruber was expressed in the methylotrophic yeast P. pastoris. Functional active phospholipase A2 with specific activity 73 U/mg was purified with a concentration of at least 3 mg/mL. The role of different divalent ions in PLA2 thermostability were evaluated. Ca2+ and Ba2+ ions significantly increased thermostability of the enzyme.
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Affiliation(s)
- S Y Filkin
- A.N. Bach Institute of Biochemistry, Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Moscow, Russia
| | - N V Chertova
- A.N. Bach Institute of Biochemistry, Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Moscow, Russia
| | - A A Zenin
- A.N. Bach Institute of Biochemistry, Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Moscow, Russia
| | - A V Lipkin
- A.N. Bach Institute of Biochemistry, Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Moscow, Russia
| | - A A Sichev
- Innovation Center «Birutch», Malobikovo, Russia
| | - D S Bityak
- Innovation Center «Birutch», Malobikovo, Russia
| | - E G Sadykhov
- A.N. Bach Institute of Biochemistry, Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Moscow, Russia
| | - V O Popov
- A.N. Bach Institute of Biochemistry, Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Moscow, Russia
| | - A N Fedorov
- A.N. Bach Institute of Biochemistry, Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Moscow, Russia
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Osipov EM, Hendrickson OD, Tikhonova TV, Zherdev AV, Solopova ON, Sveshnikov PG, Dzantiev BB, Popov VO. Structure of the Anti-C60 Fullerene Antibody Fab Fragment: Structural Determinants of Fullerene Binding. Acta Naturae 2019. [DOI: 10.32607/20758251-2019-11-1-58-65] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The structure of the anti-C60 fullerene antibody Fab fragment (FabC60) was solved by X-ray crystallography. The computer-aided docking of C60 into the antigen-binding pocket of FabC60 showed that binding of C60 to FabC60 is governed by the enthalpy and entropy; namely, by - stacking interactions with aromatic residues of the antigen-binding site and reduction of the solvent-accessible area of the hydrophobic surface of C60. A fragment of the mobile CDR H3 loop located on the surface of FabC60 interferes with C60 binding in the antigen-binding site, thereby resulting in low antibody affinity for C60. The structure of apo-FabC60 has been deposited with pdbid 6H3H.
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Osipov EM, Hendrickson OD, Tikhonova TV, Zherdev AV, Solopova ON, Sveshnikov PG, Dzantiev BB, Popov VO. Structure of the Anti-C60 Fullerene Antibody Fab Fragment: Structural Determinants of Fullerene Binding. Acta Naturae 2019; 11:58-65. [PMID: 31024749 PMCID: PMC6475864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The structure of the anti-C60 fullerene antibody Fab fragment (FabC60) was solved by X-ray crystallography. The computer-aided docking of C60 into the antigen-binding pocket of FabC60 showed that binding of C60 to FabC60 is governed by the enthalpy and entropy; namely, by π-π stacking interactions with aromatic residues of the antigen-binding site and reduction of the solvent-accessible area of the hydrophobic surface of C60. A fragment of the mobile CDR H3 loop located on the surface of FabC60 interferes with C60 binding in the antigen-binding site, thereby resulting in low antibody affinity for C60. The structure of apo-FabC60 has been deposited with pdbid 6H3H.
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Affiliation(s)
- E. M. Osipov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, 119071, Moscow, Russia
| | - O. D. Hendrickson
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, 119071, Moscow, Russia
| | - T. V. Tikhonova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, 119071, Moscow, Russia
| | - A. V. Zherdev
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, 119071, Moscow, Russia
| | - O. N. Solopova
- Russian Research Center of Molecular Diagnostics and Therapy, Simpheropolsky Blvd. 8, 113149, Moscow, Russia
| | - P. G. Sveshnikov
- Russian Research Center of Molecular Diagnostics and Therapy, Simpheropolsky Blvd. 8, 113149, Moscow, Russia
| | - B. B. Dzantiev
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, 119071, Moscow, Russia
| | - V. O. Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, 119071, Moscow, Russia
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Baymukhametov TN, Chesnokov YM, Pichkur EB, Boyko KM, Tikhonova TV, Myasnikov AG, Vasiliev AL, Lipkin AV, Popov VO, Kovalchuk MV. Three-Dimensional Structure of Cytochrome c Nitrite Reductase As Determined by Cryo-Electron Microscopy. Acta Naturae 2018. [DOI: 10.32607/20758251-2018-10-3-48-56] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The structure of cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens was determined by cryo-electron microscopy (cryo-EM) at a 2.56 resolution. Possible structural heterogeneity of the enzyme was assessed. The backbone and side-chain orientations in the cryo-EM-based model are, in general, similar to those in the high-resolution X-ray diffraction structure of this enzyme.
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Krupyanskii YF, Loiko NG, Sinitsyn DO, Tereshkina KB, Tereshkin EV, Frolov IA, Chulichkov AL, Bokareva DA, Mysyakina IS, Nikolaev YA, El’-Registan GI, Popov VO, Sokolova OS, Shaitan KV, Popov AN. Biocrystallization in Bacterial and Fungal Cells and Spores. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518040144] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Baymukhametov TN, Chesnokov YM, Pichkur EB, Boyko KM, Tikhonova TV, Myasnikov AG, Vasiliev AL, Lipkin AV, Popov VO, Kovalchuk MV. Three-Dimensional Structure of Cytochrome c Nitrite Reductase As Determined by Cryo-Electron Microscopy. Acta Naturae 2018; 10:48-56. [PMID: 30397526 PMCID: PMC6209398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 12/02/2022] Open
Abstract
The structure of cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens was determined by cryo-electron microscopy (cryo-EM) at a 2.56 Å resolution. Possible structural heterogeneity of the enzyme was assessed. The backbone and side-chain orientations in the cryo-EM-based model are, in general, similar to those in the high-resolution X-ray diffraction structure of this enzyme.
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Affiliation(s)
- T. N. Baymukhametov
- National Research Center «Kurchatov Institute», Akademika Kurchatova Sqr., 1, Moscow, 123182 , Russia
| | - Y. M. Chesnokov
- National Research Center «Kurchatov Institute», Akademika Kurchatova Sqr., 1, Moscow, 123182 , Russia
| | - E. B. Pichkur
- National Research Center «Kurchatov Institute», Akademika Kurchatova Sqr., 1, Moscow, 123182 , Russia
| | - K. M. Boyko
- National Research Center «Kurchatov Institute», Akademika Kurchatova Sqr., 1, Moscow, 123182 , Russia
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bldg. 2, Moscow, 119071, Russia
| | - T. V. Tikhonova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bldg. 2, Moscow, 119071, Russia
| | - A. G. Myasnikov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC «Kurchatov Institute», 188300 , Leningradskaya Oblast, Gatchina, mkr. Orlova roshcha, 1, Russia
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, 67404, 1 rue Laurent Fries, Illkirch, France
- University of California San Francisco Mission Bay, Genentech Hall, San Francisco, CA, 94158- 2517 , USA
| | - A. L. Vasiliev
- National Research Center «Kurchatov Institute», Akademika Kurchatova Sqr., 1, Moscow, 123182 , Russia
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre «Crystallography and Photonics» Russian Academy of Sciences, Leninsky Ave., 59, Moscow, 119333, Russia
| | - A. V. Lipkin
- National Research Center «Kurchatov Institute», Akademika Kurchatova Sqr., 1, Moscow, 123182 , Russia
| | - V. O. Popov
- National Research Center «Kurchatov Institute», Akademika Kurchatova Sqr., 1, Moscow, 123182 , Russia
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bldg. 2, Moscow, 119071, Russia
| | - M. V. Kovalchuk
- National Research Center «Kurchatov Institute», Akademika Kurchatova Sqr., 1, Moscow, 123182 , Russia
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre «Crystallography and Photonics» Russian Academy of Sciences, Leninsky Ave., 59, Moscow, 119333, Russia
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Kravchenko IV, Furalev VA, Popov VO. The Influence of Myofibrils on the Proliferation and Differentiation of Myoblasts Cocultured with Macrophages. DOKL BIOCHEM BIOPHYS 2018; 479:72-76. [PMID: 29779100 DOI: 10.1134/s1607672918020060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Indexed: 11/23/2022]
Abstract
We studied the effect of myofibrils on proliferation and differentiation of myoblasts cocultured with macrophages as well as the effect of incubation of macrophages with myofibrils on the expression by macrophages of the compounds that are cytokines for muscle cells. In the cocultures, macrophages stimulated the proliferation of myoblasts. Myofibrils greatly enhanced the stimulating effect of macrophages, whereas lipopolysaccharide (LPS) completely abolished it. The culture medium conditioned by macrophages activated the proliferation of myoblasts that were incubated with myofibrils but inhibited it when myoblasts were incubated with LPS. Possibly, myofibrils and their constituent proteins activate macrophages in an alternative pathway, enriching the population with M2-type macrophages.Z.
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Affiliation(s)
- I V Kravchenko
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
| | - V A Furalev
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - V O Popov
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
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Abstract
Branched-chain amino acid aminotransferases (BCATs) catalyze reversible stereoselective transamination of branched-chain amino acids (BCAAs) L-leucine, L-isoleucine, and L-valine. BCATs are the key enzymes of BCAA metabolism in all organisms. The catalysis proceeds through the ping-pong mechanism with the assistance of the cofactor pyridoxal 5'-phosphate (PLP). BCATs differ from other (S)-selective transaminases (TAs) in 3D-structure and organization of the PLP-binding domain. Unlike other (S)-selective TAs, BCATs belong to the PLP fold type IV and are characterized by the proton transfer on the re-face of PLP, in contrast to the si-specificity of proton transfer in fold type I (S)-selective TAs. Moreover, BCATs are the only (S)-selective enzymes within fold type IV TAs. Dual substrate recognition in BCATs is implemented via the "lock and key" mechanism without side-chain rearrangements of the active site residues. Another feature of the active site organization in BCATs is the binding of the substrate α-COOH group on the P-side of the active site near the PLP phosphate group. Close localization of two charged groups seems to increase the effectiveness of external aldimine formation in BCAT catalysis. In this review, the structure-function features and the substrate specificity of bacterial and archaeal BCATs are analyzed. These BCATs differ from eukaryotic ones in the wide substrate specificity, optimal temperature, and reactivity toward pyruvate as the second substrate. The prospects of biotechnological application of BCATs in stereoselective synthesis are discussed.
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Affiliation(s)
- E Yu Bezsudnova
- Bach Institute of Biochemistry, The Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
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Maksimov IV, Maksimova TI, Sarvarova ER, Blagova DK, Popov VO. Endophytic Bacteria as Effective Agents of New-Generation Biopesticides (Review). APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818020072] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kritsky MS, Popov VO. Aleksei Nikolaevich Bach. A Biographical Portrait of the Scientist on the Background of Historical Changes. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818020047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sinitsyn DO, Loiko NG, Gularyan SK, Stepanov AS, Tereshkina KB, Chulichkov AL, Nikolaev AA, El-Registan GI, Popov VO, Sokolova OS, Shaitan KV, Popov AN, Krupyanskii YF. Biocrystallization of bacterial nucleoid under stress. Russ J Phys Chem B 2017. [DOI: 10.1134/s1990793117050128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Boyko KM, Nikolaeva AY, Kachalova GS, Bonchuk AN, Popov VO. Purification, isolation, crystallization, and preliminary X-ray diffraction study of the BTB domain of the centrosomal protein 190 from Drosophila melanogaster. CRYSTALLOGR REP+ 2017. [DOI: 10.1134/s1063774517060050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Boyko KM, Nikolaeva AY, Kachalova GS, Bonchuk AN, Dorovatovskii PV, Popov VO. Preliminary small-angle X-ray scattering and X-ray diffraction studies of the BTB domain of lola protein from Drosophila melanogaster. CRYSTALLOGR REP+ 2017. [DOI: 10.1134/s1063774517060062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Popinako AV, Tikhonova TV, Antonov MY, Shaitan KV, Popov VO. Structural adaptation of active center channels of octaheme nitrite reductases from the haloalkaliphilic bacteria Thioalkalivibrio nitratireducens to a proton deficit. Biophysics (Nagoya-shi) 2017. [DOI: 10.1134/s0006350917020191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Tikhonova TV, Slutskaya ES, Popov VO. Peroxidase activity of octaheme nitrite reductases from bacteria of the Thioalkalivibrio genus. APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817020168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Tikhonova TV, Slutskaya ES, Popov VO. [Peroxidase activity of octaheme nitrite reductases from bacteria of the Thioalkalivibrio genus]. Prikl Biokhim Mikrobiol 2017; 53:155-163. [PMID: 29508973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Closely related penta- and octaheme nitrite reductases catalyze the reduction of nitrite, nitric oxide, and hydroxylamine to ammonium and of sulfite to sulfide. NrfA pentaheme nitrite reductase plays the key role in anaerobic nitrate respiration and the protection of bacterial cells from stresses caused by nitrogen oxides and hydrogen peroxide. Octaheme nitrite reductases from bacteria of the Thioalkalivibrio genus are less studied, and their function in the cell is unknown. In order to estimate the possible role of octaheme nitrite reductases in the cell resistance to oxidative stress, the peroxidase activity of the enzyme from T. nitratireducens (TvNiR) has been studied in detail. Comparative analysis of the active site structure of TvNiR and cytochrome c peroxidases has shown some common features, such as a five-coordinated catalytic heme and identical catalytic residues in active sites. A model of the possible productive binding of peroxide at the active site of TvNiR has been proposed. The peroxidase activity has been measured for TvNiR hexamers and trimers under different conditions (pH, buffers, the addition of CaCl2 and EDTA). The maximum peroxidase activity of TvNiR with ABTS as a substrate (k cat = 17 s–1; k cat/K m = 855 mM–1 s–1) has been 100–300 times lower than the activity of natural peroxidases. The different activities of TvNiR trimers and hexamers indicate that the rate-limiting stage of the reaction is not the catalytic event at the active site but the electron transfer along the heme c electron-transport chain.
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Parunova YM, Bushnev SO, Gonzalez-Arribas E, Falkman P, Lipkin AV, Popov VO, Shleev SV, Pankratov DV. Potentially implantable biocathode with the function of charge accumulation based on nanocomposite of polyaniline/carbon nanotubes. RUSS J ELECTROCHEM+ 2016. [DOI: 10.1134/s1023193516120119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Boyko KM, Timofeev VI, Samygina VR, Kuranova IP, Popov VO, Koval’chuk MV. Protein crystallization under microgravity conditions. Analysis of the results of Russian experiments performed on the International Space Station in 2005−2015. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516050059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Safonova TN, Mordkovich NN, Veiko VP, Okorokova NA, Manuvera VA, Dorovatovskii PV, Popov VO, Polyakov KM. Concerted action of two subunits of the functional dimer of Shewanella oneidensis MR-1 uridine phosphorylase derived from a comparison of the C212S mutant and the wild-type enzyme. Acta Crystallogr D Struct Biol 2016; 72:203-10. [PMID: 26894668 DOI: 10.1107/s2059798315024353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/17/2015] [Indexed: 11/10/2022]
Abstract
Uridine phosphorylase (UP; EC 2.4.2.3), a key enzyme in the pyrimidine-salvage pathway, catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. The structure of the C212S mutant of uridine phosphorylase from the facultatively aerobic Gram-negative γ-proteobacterium Shewanella oneidensis MR-1 (SoUP) was determined at 1.68 Å resolution. A comparison of the structures of the mutant and the wild-type enzyme showed that one dimer in the mutant hexamer differs from all other dimers in the mutant and wild-type SoUP (both in the free form and in complex with uridine). The key difference is the `maximum open' state of one of the subunits comprising this dimer, which has not been observed previously for uridine phosphorylases. Some conformational features of the SoUP dimer that provide access of the substrate into the active site are revealed. The binding of the substrate was shown to require the concerted action of two subunits of the dimer. The changes in the three-dimensional structure induced by the C212S mutation account for the lower affinity of the mutant for inorganic phosphate, while the affinity for uridine remains unchanged.
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Affiliation(s)
- T N Safonova
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - N N Mordkovich
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - V P Veiko
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - N A Okorokova
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - V A Manuvera
- Scientific Research Institute of Physical-Chemical Medicine, Federal Medical-Biological Agency, 1a Malaya Pirogovskaya St., Moscow 119435, Russian Federation
| | - P V Dorovatovskii
- National Research Centre `Kurchatov Institute', 1 Pl. Akademika Kurchatova, Moscow 123182, Russian Federation
| | - V O Popov
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - K M Polyakov
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
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Osipov EM, Polyakov KM, Tikhonova TV, Kittl R, Dorovatovskii P, Shleev SV, Popov VO, Ludwig R. Incorporation of copper ions into crystals of T2 copper-depleted laccase from Botrytis aclada. Acta Crystallogr F Struct Biol Commun 2015; 71:1465-9. [PMID: 26625287 PMCID: PMC4666473 DOI: 10.1107/s2053230x1502052x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/29/2015] [Indexed: 11/10/2022] Open
Abstract
Laccases belong to the class of multicopper oxidases catalyzing the oxidation of phenols accompanied by the reduction of molecular oxygen to water without the formation of hydrogen peroxide. The activity of laccases depends on the number of Cu atoms per enzyme molecule. The structure of type 2 copper-depleted laccase from Botrytis aclada has been solved previously. With the aim of obtaining the structure of the native form of the enzyme, crystals of the depleted laccase were soaked in Cu(+)- and Cu(2+)-containing solutions. Copper ions were found to be incorporated into the active site only when Cu(+) was used. A comparative analysis of the native and depleted forms of the enzymes was performed.
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Affiliation(s)
- E. M. Osipov
- Laboratory of Enzyme Engineering, A. N. Bach Institute of Biochemistry, Leninsky pr. 33, Moscow 119071, Russian Federation
| | - K. M. Polyakov
- Laboratory of Enzyme Engineering, A. N. Bach Institute of Biochemistry, Leninsky pr. 33, Moscow 119071, Russian Federation
- Engelhardt Institute of Molecular Biology, Vavilova str. 32, Moscow 119991, Russian Federation
| | - T. V. Tikhonova
- Laboratory of Enzyme Engineering, A. N. Bach Institute of Biochemistry, Leninsky pr. 33, Moscow 119071, Russian Federation
| | - R. Kittl
- Department of Food Science and Technology, BOKU – University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Wien, Austria
| | - P.V. Dorovatovskii
- RSC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
| | - S. V. Shleev
- Laboratory of Enzyme Engineering, A. N. Bach Institute of Biochemistry, Leninsky pr. 33, Moscow 119071, Russian Federation
- RSC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
| | - V. O. Popov
- Laboratory of Enzyme Engineering, A. N. Bach Institute of Biochemistry, Leninsky pr. 33, Moscow 119071, Russian Federation
- RSC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
| | - R. Ludwig
- Department of Food Science and Technology, BOKU – University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Wien, Austria
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Boyko KM, Popov VO, Kovalchuk MV. Promising approaches to crystallization of macromolecules suppressing the convective mass transport to the growing crystal. Russ Chem Rev 2015. [DOI: 10.1070/rcr4557] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Trofimov AA, Polyakov KM, Lazarenko VA, Popov AN, Tikhonova TV, Tikhonov AV, Popov VO. Structural study of the X-ray-induced enzymatic reaction of octahaem cytochromecnitrite reductase. ACTA ACUST UNITED AC 2015; 71:1087-94. [DOI: 10.1107/s1399004715003053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 02/12/2015] [Indexed: 11/10/2022]
Abstract
Octahaem cytochromecnitrite reductase from the bacteriumThioalkalivibrio nitratireducenscatalyzes the reduction of nitrite to ammonium and of sulfite to sulfide. The reducing properties of X-ray radiation and the high quality of the enzyme crystals allow study of the catalytic reaction of cytochromecnitrite reductase directly in a crystal of the enzyme, with the reaction being induced by X-rays. Series of diffraction data sets with increasing absorbed dose were collected from crystals of the free form of the enzyme and its complexes with nitrite and sulfite. The corresponding structures revealed gradual changes associated with the reduction of the catalytic haems by X-rays. In the case of the nitrite complex the conversion of the nitrite ions bound in the active sites to NO species was observed, which is the beginning of the catalytic reaction. For the free form, an increase in the distance between the oxygen ligand bound to the catalytic haem and the iron ion of the haem took place. In the case of the sulfite complex no enzymatic reaction was detected, but there were changes in the arrangement of the active-site water molecules that were presumably associated with a change in the protonation state of the sulfite ions.
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Petrova TE, Slutskaya ES, Boyko KM, Sokolova OS, Rakitina TV, Korzhenevskiy DA, Gorbacheva MA, Bezsudnova EY, Popov VO. Structure of the dodecamer of the aminopeptidase APDkam598 from the archaeon Desulfurococcus kamchatkensis. Acta Crystallogr F Struct Biol Commun 2015; 71:277-85. [PMID: 25760701 PMCID: PMC4356302 DOI: 10.1107/s2053230x15000783] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 01/14/2015] [Indexed: 11/10/2022] Open
Abstract
The crystal structure of the aminopeptidase APDkam589 from the thermophilic crenarchaeon Desulfurococcus kamchatkensis was determined at a resolution of 3.0 Å. In the crystal, the monomer of APDkam589 and its symmetry-related monomers are densely packed to form a 12-subunit complex. Single-particle electron-microscopy analysis confirms that APDkam589 is present as a compact dodecamer in solution. The APDkam589 molecule is built similarly to the molecules of the PhTET peptidases, which have the highest sequence identity to APDkam589 among known structures and were isolated from the more thermostable archaeon Pyrococcus horikoshii. A comparison of the interactions of the subunits in APDkam589 with those in PhTET1, PhTET2 and PhTET3 reveals that APDkam589 has a much lower total number of salt bridges, which correlates with the lower thermostability of APDkam589. The monomer of APDkam589 has six Trp residues, five of which are on the external surface of the dodecamer. A superposition of the structure of APDkam589 with those having a high sequence similarity to APDkam589 reveals that, although the positions of Trp45, Trp252 and Trp358 are not conserved in the sequences, the spatial locations of the Trp residues in these models are similar.
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Affiliation(s)
- T. E. Petrova
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
- Institute of Mathematical Problems of Biology, RAS, Institutskaja str. 4, Pushchino 142290, Russian Federation
| | - E. S. Slutskaya
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
| | - K. M. Boyko
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
| | - O. S. Sokolova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/73, Moscow 119991, Russian Federation
| | - T. V. Rakitina
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
- Institute of Bioorganic Chemistry, RAS, Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - D. A. Korzhenevskiy
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
| | - M. A. Gorbacheva
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
| | - E. Y. Bezsudnova
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
| | - V. O. Popov
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
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Tikhonova TV, Popov VO. Structural and functional studies of multiheme cytochromes c involved in extracellular electron transport in bacterial dissimilatory metal reduction. Biochemistry Moscow 2015; 79:1584-601. [DOI: 10.1134/s0006297914130094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Stekhanova TN, Bezsudnova EY, Mardanov AV, Osipov EM, Ravin NV, Skryabin KG, Popov VO. Nicotinamidase from the thermophilic archaeon Acidilobus saccharovorans: structural and functional characteristics. Biochemistry (Mosc) 2014; 79:54-61. [PMID: 24512664 DOI: 10.1134/s0006297914010088] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Nicotinamidase is involved in the maintenance of NAD+ homeostasis and in the NAD+ salvage pathway of most prokaryotes, and it is considered as a possible drug target. The gene (ASAC_0847) encoding a hypothetical nicotinamidase has been found in the genome of the thermophilic archaeon Acidilobus saccharovorans. The product of this gene, NA_As0847, has been expressed in Escherichia coli, isolated, and characterized as a Fe(2+)-containing nicotinamidase (k(cat)/K(m) = 427 mM(-1)·sec(-1))/pyrazinamidase (k(cat)/K(m) = 331 mM(-1)·sec(-1)). NA_As0847 is a homodimer with molecular mass 46.4 kDa. The enzyme has high thermostability (T(1/2) (60°C) = 180 min, T(1/2) (80°C) = 35 min) and thermophilicity (T(opt) = 90°C, E(a) = 30.2 ± 1.0 kJ/mol) and broad pH interval of activity, with the optimum at pH 7.5. Special features of NA_As0847 are the presence of Fe2+ instead of Zn2+ in the active site of the enzyme and inhibition of the enzyme activity by Zn2+ at micromolar concentrations. Analysis of the amino acid sequence revealed a new motif of the metal-binding site (DXHXXXDXXEXXXWXXH) for homological archaeal nicotinamidases.
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Affiliation(s)
- T N Stekhanova
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, 119071, Russia.
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Boyko KM, Gorbacheva MA, Rakitina TV, Korzhenevsky DA, Dorovatovsky PV, Lipkin AV, Popov VO. Identification of the ligand in the structure of the protein with unknown function STM4435 from Salmonella typhimurium. DOKL BIOCHEM BIOPHYS 2014; 457:121-4. [PMID: 25172330 DOI: 10.1134/s1607672914040012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Indexed: 01/09/2023]
Abstract
The unidentified ligand, which is present in the crystal of the protein with unknown function STM4435 from Salmonella typhimurium, was identified using a combination of high-resolution X-ray crystallography and accurate-mass time-of-flight mass spectrometry. The identified glycerol was present as a component of the solutions used for the isolation and crystallization of the protein and serves as the ligand mimicking the natural metabolite, presumably, 2-keto-myo-isonitol, which is indicative of the involvement of STM4435 in the myo-isonitol catabolism. The results of the present study show that this approach holds promise in complex studies aimed at determining, refining, or confirming the protein functions.
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Affiliation(s)
- K M Boyko
- Bach Institute of Biochemistry, Russian Academy of Sciences, Leninskii pr. 33, Moscow, 119071, Russia,
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Platonova TA, Pridvorova SM, Zherdev AV, Vasilevskaya LS, Arianova EA, Gmoshinski IV, Khotimchenko SA, Dzantiev BB, Popov VO, Tutelyan VA. Identification of silver nanoparticles in the small intestinal mucosa, liver, and spleen of rats by transmission electron microscopy. Bull Exp Biol Med 2014; 155:236-41. [PMID: 24130999 DOI: 10.1007/s10517-013-2122-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The effects of water-dispersed Ag nanoparticles on the small intestinal mucosa, liver, and spleen of rats were studied by transmission electron microscopy. Acute experiments demonstrated penetration of Ag nanoparticles injected into the isolated intestinal loop into the intestinal mucosa, liver, and splenic tissues. Ultrastructural changes (lobed nucleus, megamitochondria) were found in the studied organs. These data indicated that injection of water-dispersed Ag nanoparticles into the gastrointestinal tract was followed by their penetration through the epithelium of the small intestinal mucosa into other organs, e.g. into the liver and spleen. This fact is essential for evaluation of potential risks of the nanoparticle effects on human health and environment.
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Affiliation(s)
- T A Platonova
- A. N. Bach Institute of Biochemistry, the Russian Academy of Sciences; Institute of Nutrition, the Russian Academy of Medical Sciences, Moscow, Russia.
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Pankratov DV, Zeifman YS, Dudareva АV, Pankratova GK, Khlupova ME, Parunova YM, Zajtsev DN, Bashirova NF, Popov VO, Shleev SV. Impact of Surface Modification with Gold Nanoparticles on the Bioelectrocatalytic Parameters of Immobilized Bilirubin Oxidase. Acta Naturae 2014. [DOI: 10.32607/20758251-2014-6-1-102-106] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We unveil experimental evidence that put into question the widely held notion concerning the impact of nanoparticles on the bioelectrocatalytic parameters of enzymatic electrodes. Comparative studies of the bioelectrocatalytic properties of fungal bilirubin oxidase from Myrothecium verrucaria adsorbed on gold electrodes, modified with gold nanoparticles of different diameters, clearly indicate that neither the direct electron transfer rate (standard heterogeneous electron transfer rate constants were calculated to be 319 s -1) nor the biocatalytic activity of the adsorbed enzyme (bioelectrocatalytic constants were calculated to be 3411 s -1) depends on the size of the nanoparticles, which had diameters close to or larger than those of the enzyme molecules.
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Mordkovich NN, Safonova TN, Manuvera VA, Veiko VP, Polyakov KM, Alekseev KS, Mikhailov SN, Popov VO. Physicochemical characterization of uridine phosphorylase from Shewanella oneidensis MR-1. DOKL BIOCHEM BIOPHYS 2013; 451:187-9. [DOI: 10.1134/s1607672913040054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Indexed: 11/22/2022]
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Boyko KM, Lipkin AV, Popov VO, Kovalchuk MV. From gene to structure: The protein factory of the NBICS Centre of Kurchatov Institute. CRYSTALLOGR REP+ 2013. [DOI: 10.1134/s106377451105004x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Trofimov AA, Polyakov KM, Tikhonov AV, Bezsudnova EY, Dorovatovskii PV, Gumerov VM, Ravin NV, Skryabin KG, Popov VO. Structures of β-glycosidase from Acidilobus saccharovorans in complexes with tris and glycerol. DOKL BIOCHEM BIOPHYS 2013; 449:99-101. [DOI: 10.1134/s1607672913020129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Indexed: 11/23/2022]
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Furalyov VA, Kravchenko IV, Popov VO. Targeted delivery of siRNA to differentiated murine myotubes in culture by a conjugate of cationic oligopeptide with FS2 venom. Biochemistry (Mosc) 2013; 78:418-23. [PMID: 23590445 DOI: 10.1134/s0006297913040111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A conjugate of the ligand of FS2 venom dihydropyridine receptors with a cationic arginine-containing oligopeptide was synthesized. It was found that the conjugate provides siRNA delivery to murine myotubes differentiated in vitro. The effect of RNA interference with the use of siRNA complexes with the conjugate was observed when siRNA concentrations were an order of magnitude lower than those used in the case of siRNA complexes with a non-conjugated oligopeptide.
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Affiliation(s)
- V A Furalyov
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, 119071, Russia
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Gmoshinski IV, Khotimchenko SA, Popov VO, Dzantiev BB, Zherdev AV, Demin VF, Buzulukov YP. Nanomaterials and nanotechnologies: methods of analysis and control. Russ Chem Rev 2013. [DOI: 10.1070/rc2013v082n01abeh004329] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Slutskaya ES, Bezsudnova EY, Mardanov AV, Safenkova IV, Kleimenov SY, Chebotareva NA, Gumerov VM, Ravin NV, Skryabin KG, Popov VO. Iron-dependent superoxide dismutase from novel thermoacidophilic crenarchaeon Acidilobus saccharovorans: from gene to active enzyme. Biochemistry (Mosc) 2012; 77:1368-76. [PMID: 23244732 DOI: 10.1134/s0006297912120048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A gene encoding superoxide dismutase was revealed in the genome of the thermoacidophilic crenarchaeon Acidilobus saccharovorans. A recombinant expression vector was constructed and transformed into E. coli cells. The novel recombinant superoxide dismutase was purified and characterized. The enzyme was shown to be an iron-dependent superoxide dismutase able to bind various bivalent metals in the active site. According to differential scanning calorimetric data, the denaturation temperature of the enzyme is 107.3°C. The maximal activity of the Fe(II) reconstituted enzyme defined by xanthine oxidase assay is 1700 U/mg protein. Study of the thermal stability of the superoxide dismutase samples with various metal contents by tryptophan fluorescence indicated that the thermal stability and activity of the enzyme directly depend on the nature of the reconstituted metal and the degree of saturation of binding sites.
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Affiliation(s)
- E S Slutskaya
- Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, 119071 Moscow, Russia.
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Petrova T, Bezsudnova EY, Boyko KM, Mardanov AV, Polyakov KM, Volkov VV, Kozin M, Ravin NV, Shabalin IG, Skryabin KG, Stekhanova TN, Kovalchuk MV, Popov VO. ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1440-7. [PMID: 23192021 PMCID: PMC3509962 DOI: 10.1107/s1744309112043394] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 10/18/2012] [Indexed: 11/10/2022]
Abstract
DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5'-phosphate and 3'-hydroxyl termini. Their function is essential for maintaining genome integrity in the replication, recombination and repair of DNA. High flexibility is important for the function of DNA ligase molecules. Two types of overall conformations of archaeal DNA ligase that depend on the relative position of the OB-fold domain have previously been revealed: closed and open extended conformations. The structure of ATP-dependent DNA ligase from Thermococcus sp. 1519 (LigTh1519) in the crystalline state determined at a resolution of 3.02 Å shows a new relative arrangement of the OB-fold domain which is intermediate between the positions of this domain in the closed and the open extended conformations of previously determined archaeal DNA ligases. However, small-angle X-ray scattering (SAXS) measurements indicate that in solution the LigTh1519 molecule adopts either an open extended conformation or both an intermediate and an open extended conformation with the open extended conformation being dominant.
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Affiliation(s)
- T Petrova
- Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation.
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Lisitskaia KV, Nikolaev IV, Torkova AA, Popov VO, Koroleva OV. [Analysis of functional properties of biologically active substances using eukaryotic cell models (review)]. Prikl Biokhim Mikrobiol 2012; 48:581-599. [PMID: 23330384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This work presents an analysis of current data on the investigation into the functional properties of biologically active substances in model systems based on cultivated human cells. The knowledge regarding the practical application of cell cultures for the analysis of functional properties of bioactive substances is summarized, including antioxidant, immunomodulating, pro- and prebiotics, and chemoprevention properties. The most promising directions in cell culture model development for the investigation of functional properties, including three-dimensional models, are discussed.
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Trofimov AA, Slutskaya EA, Polyakov KM, Dorovatovskii PV, Gumerov VM, Popov VO. Influence of intermolecular contacts on the structure of recombinant prolidase from Thermococcus sibiricus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1275-8. [PMID: 23143231 PMCID: PMC3515363 DOI: 10.1107/s174430911203761x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 08/31/2012] [Indexed: 11/10/2022]
Abstract
Prolidases are peptidases that are specific for dipeptides with proline as the second residue. The structure of recombinant prolidase from the hyperthermophilic archaeon Thermococcus sibiricus (Tsprol) was determined at 2.6 Å resolution. The homodimer of Tsprol is characterized by a complete lack of interactions between the N- and C-terminal domains of the two subunits and hence can be considered to be the most open structure when compared with previously structurally studied prolidases. This structure exists owing to intermolecular coordination bonds between cadmium ions derived from the crystallization solution and histidine residues of a His tag and aspartate and glutamate residues, which link the dimers to each other. This linking leads to the formation of a crystal with a loose packing of protein molecules and low resistance to mechanical influence and temperature increase.
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Affiliation(s)
- A A Trofimov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russian Federation.
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Lisitskaya KV, Nikolaev IV, Torkova AA, Popov VO, Koroleva OV. Analysis of functional properties of biologically active substances using eukaryotic cell models (review). APPL BIOCHEM MICRO+ 2012. [DOI: 10.1134/s0003683812060087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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