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The most cited biological Institute in Russia *

Department of biokinetics

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Biokinetics Dept. was established in 1965 by famous physicochemist Ilya Berezin based on soviet school of enzyme kinetics founded by Nikolay Semenov. Department is engaged in the kinetic study of biological phenomena at the molecular level and exploration of enzymatic mechanisms defining the rate of biological processes. Department has more than 30 years of experience in biocatalysis and design of biocatalytic processes. Latest research topics include search for new applications of enzymes in organic synthesis, optimization of biocatalytic conversions, molecular modelling and rational design of enzymes using methods of theoretical chemistry, bioinformatics, steered and regular molecular dynamics as well as hybrid computational approaches. Laboratory is dealing with kinetics and thermodynamics of enzymatic hydrolysis and synthesis of lactam antibiotics, N-acylated amino acids and their analogues as well as with specificity and stereospecificity of different amidohydrolases. A new thread in department's research activity is associated with in silico methodologies - bioinformatics and molecular modeling - to explore molecular basis of enzymatic transformations, structure-function relationship and promiscuous properties of natural biocatalysts.


Recent papers
  1. Shalaeva D.N., Galperin M.Y., Mulkidjanian A.Y. (2015) Eukaryotic G protein-coupled receptors as descendants of prokaryotic sodium-translocating rhodopsins. Biol. Direct, 10: . >>

  2. Mkrtchyan G., Aleshin V., Parkhomenko Y., Kaehne T., Di Salvo M.L., Parroni A., Contestabile R., Vovk A., Bettendorff L., Bunik V. (2015) Molecular mechanisms of the non-coenzyme action of thiamin in brain: biochemical, structural and pathway analysis. Sci Rep, 5: . >>

  3. Shalaeva D.N., Dibrova D.V., Galperin M.Y., Mulkidjanian A.Y. (2015) Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly. Biol. Direct, 10: . >>

  4. Galkina S.I., Fedorova N.V., Serebryakova M.V., Arifulin E.A., Stadnichuk V.I., Gaponova T.V., Baratova L.A., Sud'ina G.F. (2015) Inhibition of the GTPase dynamin or actin depolymerisation initiates outward plasma membrane tubulation/vesiculation (cytoneme formation) in neutrophils. Biol. Cell, 107 (5): 144-158. >>

  5. Akparov V.K., Timofeev V.I., Khaliullin I.G., Svedas V., Chestukhina G.G., Kuranova I.P. (2015) Structural insights into the broad substrate specificity of carboxypeptidase T from Thermoactinomyces vulgaris. FEBS J., 282 (7): 1214-1224. >>

  6. Diaz-Munoz M.D., Bell S.E., Fairfax K., Monzon-Casanova E., Cunningham A.F., Gonzalez-Porta M., Andrews S.R., Bunik V.I., Zarnack K., Curk T., Heggermont W.A., Heymans S., Gibson G.E., Kontoyiannis D.L., Ule J., Turner M. (2015) The RNA-binding protein HuR is essential for the B cell antibody response. Nat. Immunol., 16 (4): 415-425. >>

  7. Shcherbakova T.A., Panin N.V., Suplatov D.A., Shapovalova I.V., Svedas V.K. (2015) The beta D484N mutant of penicillin acylase from Escherichia coli is more resistant to inactivation by substrates and can effectively perform peptide synthesis in aqueous medium. J. Mol. Catal. B-Enzym., 112: 66-68. >>

  8. Grigorenko B.L., Khrenova M.G., Nilov D.K., Nemukhin A.V., Svedas V.K. (2014) Catalytic Cycle of Penicillin Acylase from Escherichia coli: QM/MM Modeling of Chemical Transformations in the Enzyme Active Site upon Penicillin G Hydrolysis. ACS Catal., 4 (8): 2521-2529. >>

  9. Quinlan C.L., Goncalves R.L.S, Hey-Mogensen M., Yadava N., Bunik V.I., Brand M.D. (2014) The 2-Oxoacid Dehydrogenase Complexes in Mitochondria Can Produce Superoxide/Hydrogen Peroxide at Much Higher Rates Than Complex I. J. Biol. Chem., 289 (12): 8312-8325. >>

  10. Bunik V.I., Tylicki A., Lukashev N.V. (2013) Thiamin diphosphate-dependent enzymes: from enzymology to metabolic regulation, drug design and disease models. FEBS J., 280 (24): 6412-6442. >>

  11. Bunik V.I. (2013) Thiamin-dependent enzymes: new perspectives from the interface between chemistry and biology. FEBS J., 280 (24): 6373-6373. >>

  12. Galkina S.I., Fedorova N.V., Stadnichuk V.I., Sud'ina G.F. (2013) Membrane tubulovesicular extensions (cytonemes) Secretory and adhesive cellular organelles. Celll Adhes. Migr., 7 (2): 174-186. >>

  13. Araujo W.L., Trofimova L., Mkrtchyan G., Steinhauser D., Krall L., Graf A., Fernie A.R., Bunik V.I. (2013) On the role of the mitochondrial 2-oxoglutarate dehydrogenase complex in amino acid metabolism. Amino Acids, 44 (2): 683-700. >>

  14. Graf A., Trofimova L., Loshinskaja A., Mkrtchyan G., Strokina A., Lovat M., Tylicky A., Strumilo S., Bettendorff L., Bunik V.I. (2013) Up-regulation of 2-oxoglutarate dehydrogenase as a stress response. Int. J. Biochem. Cell Biol., 45 (1): 175-189. >>

  15. Novikov F.N., Stroganov O.V., Khaliullin I.G., Panin N.V., Shapovalova I.V., Chilov G.G., Svedas V.K. (2013) Molecular modeling of different substrate-binding modes and their role in penicillin acylase catalysis. FEBS J., 280 (1): 115-126. >>

  16. Suplatov D.A., Besenmatter W., Svedas V.K., Svendsen A. (2012) Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities. Protein Eng. Des. Sel., 25 (11): 689-697. >>

  17. Galkina S.I., Fedorova N.V., Serebryakova M.V., Romanova J.M., Golyshev S.A., Stadnichuk V.I., Baratova L.A., Sud'ina G.F., Klein T. (2012) Proteome analysis identified human neutrophil membrane tubulovesicular extensions (cytonemes, membrane tethers) as bactericide trafficking. Biochim. Biophys. Acta-Gen. Subj., 1820 (11): 1705-1714. >>

  18. Romanova N.N., Rybalko I.I., Tallo T.G., Zyk N.V., Svedas V.K. (2012) Synthesis of Schiff bases from 3-amino-3-arylpropionic acid esters in aqueous medium. Russ. J. Organ. Chem., 48 (6): 860-863. >>

  19. Guranda D.T., Ushakov G.A., Yolkin P.G., Svedas V.K. (2012) Thermodynamics of phenylacetamides synthesis: Linear free energy relationship with the pK of amine. J. Mol. Catal. B-Enzym., 74 (1): 48-53. >>

  20. Golenkina E.A., Galkina S.I., Romanova J.M., Lazarenko M.I., Sud'ina G.F. (2011) Involvement of red blood cells in the regulation of leukotriene synthesis in polymorphonuclear leucocytes upon interaction with Salmonella Typhimurium. Apmis, 119 (9): 635-642.

  21. Parkhomenko Y.M., Kudryavtsev P.A., Pylypchuk S.Y., Chekhivska L.I., Stepanenko S.P., Sergiichuk A.A., Bunik V.I. (2011) Chronic alcoholism in rats induces a compensatory response, preserving brain thiamine diphosphate, but the brain 2-oxo acid dehydrogenases are inactivated despite unchanged coenzyme levels. Journal of Neurochemistry, 117 (6): 1055-1065.

  22. Zakharenko A.L., Sukhanova M.V., Khodyreva S.N., Novikov F.N., Stroylov V.S., Nilov D.K., Chilov G.G., Svedas V.K., Lavrik O.I. (2011) Improved procedure of the search for poly(ADP-Ribose) polymerase-1 potential inhibitors with the use of the molecular docking approach. Molecular Biology, 45 (3): 517-521.

  23. Nilov D.K., Shabalin I.G., Popov V.O., Svedas V.K. (2011) Investigation of Formate Transport through the Substrate Channel of Formate Dehydrogenase by Steered Molecular Dynamics Simulations. Biochemistry-Moscow, 76 (2): 172-174.

  24. Bunik V.I. (2011) Metabolic Networking through Enzymatic Sensing, Signaling and Response to Homeostatic Fluctuations. Cellular Networks - Positioning, Performance Analysis, Reliability, Agassi Melikov (Ed.), : 377-405. >>

  25. Bunik V.I., Schloss J.V., Pinto J.T., Dudareva N., Cooper A.J. (2011) A survey of oxidative paracatalytic reactions catalyzed by enzymes that generate carbanionic intermediates: implications for ROS production, cancer etiology, and neurodegenerative diseases. Adv Enzymol Relat Areas Mol Biol, 77: 307-60.

  26. Tylicki A., Bunik V.I., Strumiеlo S. (2011) 2-Oxoglutarate dehydrogenase complex and its multipoint control. Postepy Biochem, 57 (3): 304-13.

  27. Chernorizov K.A., Elkina J.L., Semenyuk P.I., Svedas V.K., Muronetz V.I. (2010) Novel Inhibitors of Glyceraldehyde-3-phosphate Dehydrogenase: Covalent Modification of NAD-Binding Site by Aromatic Thiols. Biochemistry-Moscow, 75 (12): 1444-1449.

  28. Sokolov A.V., Golenkina E.A., Kostevich V.A., Vasilyev V.B., Sud'ina G.F. (2010) Interaction of Ceruloplasmin and 5-Lipoxygenase. Biochemistry-Moscow, 75 (12): 1464-1469.

  29. Trofimova L., Lovat M., Groznaya A., Efimova E., Dunaeva T., Maslova M., Graf A., Bunik V. (2010) Behavioral impact of the regulation of the brain 2-oxoglutarate dehydrogenase complex by synthetic phosphonate analog of 2-oxoglutarate: implications into the role of the complex in neurodegenerative diseases. Int J Alzheimers Dis, 2010: 749061.

  30. Zagryazhskaya A.N., Lindner S.C., Grishina Z.V., Galkina S.I., Steinhilber D., Sud'ina G.F. (2010) Nitric oxide mediates distinct effects of various LPS chemotypes on phagocytosis and leukotriene synthesis in human neutrophils. Cell Biology, 42 (6): 921-931.

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