Laboratory of Biopolymer Modification

Olga S. Fedorova,
prof., D.Chem.Sci.
Phone: +7(383)363-51-75
Email

• Investigation of kinetic and thermodynamic features of enzymatic DNA repair processes and the role of conformational dynamics in the mechanisms of specific sites search on DNA; design of low-molecular-weight inhibitors of enzymes repair as radiosensitizers.
• Human proteomics and metabolomics: mass spectrometry (MS) analysis of serum proteins and metabolites, diagnostics of inborn metabolic disorders (aminoacids errors, organic acid or fatty acid metabolism); MS studies of drugs pharmacokinetics in biological fluids; determination of proteomic markers of diseases associated with human’s 18th chromosome.
• Design of conjugates of nucleic acids with biologically active molecules for magnitoresonance diagnostics of cancer and prolonged inhibition of expression of therapeutically important genes.
• Computational structural genomics and proteomics. Development of advanced computer methods for structural biology. Computational modeling of structure, energy and conformational dynamics of biopolymer complexes for theoretical support of experimental studies.

• A transient kinetics of repair processes catalyzed with 8-oxoguanine DNA glycosylases and AP-endonucleases (E. coli Fpg-protein and Endo VIII, human Ogg1 and Ape1) has been analysed using stopped-flow fluorescence method. The multiple conformational transitions of enzymes were found during catalytic cycles which were responsible for recognition and processing of substrates. These transitions reflected the stages of enzyme binding to DNA and lesion recognition with the mutual adjustment of DNA and enzyme structures to achieve catalytically competent conformations. [Kuznetsov N.A. et al., Nucleic Acids Res. 2005. 33, 3919; Kuznetsov N.A. et al., Biochemistry. 2009. 48, 11335; Timofeyeva N.A. et al., J. Biomol. Struct. Dyn. 2009. 26, 637; Koval V.V. et al., Mutation Res./Fundamental and Molecular Mechanisms of Mutagenesis. 2010. 685, 3; Kanazhevskaya L.Yu. et al., Biochemistry. 2010. 49, 6451].
• The mechanisms of photoinduced and catalyzed oxidative degradation of DNA with oligonucleotides carrying Fe- or Со-phthalocyanine monomer and dimer complexes were studied. It was found that dimer Fe- or Со-phthalocyanine complexes were more efficient catalysts of DNA oxidation in the presence of O2 or H2O2 in comparison with monomer complexes. [Chernonosov A.A. et al., Nucleos. Nucleot. & Nucl. Acids. 2004. 23, 983; Kuznetsova A.A. et al., Bioorg. Med. Chem. Lett. 2009. 19, 4335; Kuznetsova A.A. et al., J. Biomol. Struct. Dyn. 2008. 26, 307].
• It was firstly shown that major protein of blood – human serum albumin – catalyses the cleavage of phosphodiester bonds in RNA. Glycation and N-homocysteinylation of albumin lead to decrease of RNA depolymerization efficiency. [Godovikova T.S. et al, In: Alekseev R.J. and Rebane A.I. (eds.) Serum albumin: structure, functions, and health impacts. 2011. Nova Science Publishers, Inc. New York].
• Multi-functional computer programs for modeling of optimal conformations and conformational dynamics of proteins, RNA and DNA fragments and their complexes in full atomic approximation in aqueous solution were developed. Effective docking method and computer program for docking of molecular ligands and peptides on proteins and RNA are developed. Internet resource with original computational programs for molecular dynamics, blind docking and ligand constructor are designed. [Vorobjev Yu. N., J. Comput. Chem. 2010. 31, 1080; Popov A.V., Vorobjev Yu.N. Molecular Biology (Moscow). 2010. 44, 648; http://bison.niboch.nsc.ru].
• Kinetic bases of chemical modification of single- and double-stranded DNA with reactive derivatives of oligonucleotides, representing conjugates of deoxyribooligonucleotides with 2-chloroethyl alkylating, arylazide photoactive and metal-containing catalytically active groups, have been determined. The approach for evaluation of thermodynamic and structural information from kinetic data was developed. [Fedorova O.S. et al., J. Biomol. Struct. Dyn. 1995. 13, 145; Knorre D.G. et al., Molecular Biology (Moscow). 1998. 32, 123].
• The mechanisms of photoconversion of arylazide reagents used for affinity modification of biopolymers were determined. The methods of synthesis of arylazide derivatives of mono- and oligonucleotides were developed. The approaches for the determination of structures of modification products of protein functional groups were proposed. [Godovikova T.S. et al., Bioconjugate Chem. 1996. 7, 343; Popova T.V. et al., J Photochem Photobiol B. 2001. 61, 68].

1. Ponomarenko N., Chatziefthimiou S.D., Kurkova I., Mokrushina Y., Stepanova A., Smirnov I., Avakyan M., Bobik T., Mamedov A., Mitkevich V., Belogurov A., Fedorova O.S., Dubina M., Golovin A., Lamzin V., Friboulet A., Makarov A., Wilmanns M., Gabibov A. Role of kappa-lambda light chain constant domain switch in catalytic functionality of A17 reactibody. Acta Crystallographica. Section D: Biological Crystallography. 2014. 70(3), 708-719.
2. Kuznetsova A.A., Kuznetsov N.A., Ishchenko A.A., Saparbaev M.K., Fedorova O.S. Step-by-step mechanism of DNA damage recognition by human 8-oxoguanine DNA glycosylase. Biochim. Biophys. Acta - General Subjects. 2014. 1840(1), 387-395.
3. Lukina M.V., Popov A.V., Koval V.V., Vorobjev Y.N., Fedorova O.S., Zharkov D.O. DNA damage processing by human 8-oxoguanine-DNA glycosylase mutants with the occluded active site. J. Biol. Chem. 2013. 288(40), 28936-28947.
4. Godovikova T.S., Lisitsky V.A., Antonova N.M., Popova T.V., Zakharova O.D., Chubarov A.S., Koptyug I.V., Sagdeev R.Z., Kaptein R., Akulov A.E., Kaledin V., Nikolin V.P., Baiborodin S.I., Koroleva L.S., Silnikov V.N. Ligand-directed Acid-sensitive Amidophosphate 5-Trifluoromethil-2'-deoxyuridine Conjugate as a Potential Theranostic Agent. Bioconjugate Chem. 2013. 15(24-5), 780-795.
5. Fedorova O. S., Tsvetkov Yu. D. Pulsed Electron Double Resonance in Structural Studies of Spin-Labeled Nucleic Acids. Acta Naturae. 2013. 5(1), 9–32.
6. Popov A.V., Vorobjev Y.N., Zharkov D.O. MDTRA: A molecular dynamics trajectory analyzer with a graphical user interface. J. Comput. Chem. 2013. 34(4), 319-325.
7. Kanazhevskaya L.Y., Koval V.V., Fedorova O.S. Conformational dynamics of abasic DNA upon interactions with AP endonuclease 1 revealed by stopped-flow fluorescence analysis. Biochemistry. 2012. 51(6), 1306-1321.
8. Kuznetsov N.A., Vorobjev Y.N., Krasnoperov L.N., Fedorova O.S. Thermodynamics of the Multi-Stage DNA Lesion Recognition and Repair by Formamidopyrimidine-DNA Glycosylase Using Pyrrolocytosine Fluorescence - Stopped-Flow Pre-Steady-State Kinetics. Nucleic Acids Res. 2012. 40(15), 7384–7392.
9. Vorobjev Y.N. Potential of Mean Force of Water–Proton Bath and Molecular Dynamic Simulation of Proteins at Constant pH. J. Comput. Chem. 2012. 33(8), 832-842.
10. Kuznetsov N.A., Koval V.V., Zharkov D.O., Fedorova O.S. Conformational dynamics of interaction of Escherichia coli endonuclease VIII with DNA substrates. DNA Repair. 2012. 11(11), 884-891.
11. Dyakonova E. S., Koval V. V., Ishchenko A. A., Saparbaev M. K., Kaptein R., Fedorova O. S. Kinetics and Mechanism of the Interaction of Saccharomyces cerevisiae AP-endonuclease 1 with DNA Substrates. Biochemistry (Moscow). 2012. 77(10), 1162-1171.
12. Vila J.A., Arnautova Y.A., Vorobjev Y.N., Scheraga H.A. Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH. Proc Nat. Acad. Sci. USA. 2011. 108(14), 5602–5607.
13. Kuznetsov N.A., Milov A.D., Isaev N.P., Vorobjev Yu.N., Koval V.V., Dzuba S.A., Fedorova O.S. and Tsvetkov Yu.D. PELDOR analysis of enzyme-induced structural changes in damaged DNA duplexes. Mol. BioSyst. 2011. 7(9), 2670-2680.
14. Vorobjev Y.N. Advances in Implicit Models of Water Solvent to Compute Conformational Free Energy and Molecular Dynamics of Proteins at Constant pH. Advances in Protein Chemistry and Structural Biology. 2011. 85, 282-322.
15. Vorobjev Y.N. Molecular Dynamics Method for Proteins with Ionization–Conformation Coupling and Equilibrium Titration. Molecular Biology. 2011. 45(2), 309–318.
16. Timofeyeva N.A., Koval V.V., Ishchenko A.A., Saparbaev M.K., Fedorova O.S. Lys98 Substitution in Human AP Endonuclease 1 Affects the Kinetic Mechanism of Enzyme Action in Base Excision and Nucleotide Incision Repair Pathways. PLoS ONE. 2011. 6(9): e24063.
17. Chubarov A.V., Shakirov M.M., Koptyug I.V., Sagdeev R.Z., Knorre D.G., Godovikova T.S. Synthesis and characterization of fluorinated homocysteine derivatives as potential molecular probes for 19F magnetic resonance spectroscopy and imaging. Bioorg. Med. Chem. Lett. 2011. 21(13), 4050-4053.
18. Knorre D.G., Godovikova T.S., Мyzina S.D., Fedorova O.S. Textbook “Bioorganic Chemistry” (2nd Edition). Novosibirsk State University. 2013, 480 pages.

1. Chernonosov А.А., Коval V.V., Fedorova О.S. Method of determination of warfarin alcohol in blood serum. Patent RF N.2486521, 2013.

Research is supported by Grants of the Russian Foundation for Basic Research, Siberian Branch of the Russian Academy of Sciences, and Ministry of education and science of the Russian Federation.

• Spectrometers of stopped-flow SX.18MV and SX20 (Applied Photophysics, UK) for the study of fast biochemical reactions;
• equipment for HPLC from Waters and Agilent;
• preparative liquid chromatography system AKTA Explorer 100 (GE Healthcare Lifescience, Sweden);
• spectrophotometers “Shimadzu” and “Cary 50 Scan”;
• scanning fluorometer Сary Eclipse (Varian).