Laboratory of Bioorganic Chemistry of Enzymes [Институт химической биологии и фундаментальной медицины]
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Laboratory of Bioorganic Chemistry of Enzymes

Laboratory of Bioorganic Chemistry of Enzymes

Head of the Laboratory



Olga I. Lavrik,
Full Member of RAS, D.Chem.Sci. The Russia State Prize in Science and Technique
Phone: +7(383)363-51-95,


Staff

Name Degree Tel. E-mail Researcher ID
1. Lavrik I. Olga corresponding member 363-51-95 G-4641-2013
2. Moor A. Nina D.Sc. 363-51-96 G-7097-2013
3. Khodyreva N. Svetlana D.Sc. 363-51-96/94 G-4659-2013
4. Petruseva O. Irina Ph.D. 363-51-94
5. Rechkunova I. Nadezda Ph.D. 363-51-96 G-5093-2013
6. Belousova A. Ekaterina Ph.D. 363-51-96 G-4718-2013
7. Vasilyeva A. Inna Ph.D. 363-51-96 G-8450-2013
8. Zakharenko L. Aleksandra Ph.D. 363-51-96 E-4534-2014
9. Lebedeva A. Natalya Ph.D. 363-51-96 G-4758-2013
10.Pestryakov E. Pavel Ph.D. 363-51-96
11.Sukhanova V. Maria Ph.D. 363-51-96 G-5539-2013
12.Anarbayev O. Rashid Ph.D. 363-51-96
13.Ilina S. Ekaterina Ph.D. 363-51-96 G-4224-2013
14.Maltseva A. Ekaterina Ph.D. 363-51-96 G-6953-2013
15.Kutuzov M. Mikhail Ph.D. 363-51-96 G-4239-2013
16.Gaiko D. Natalya 363-51-96
17.Medvedeva I. Lidiya 363-51-94
18.Evdokimov N. Aleksey 363-51-94 G-4325-2013
19.Skosareva V. Lidiya 363-51-96 G-4672-2013

Research focus


  • Study of coordination of base excision repair process in the mammalian system. Investigation of DNA polymerases beta, lambda, apurinic/apyrimidinic endonuclease-1, flap-endonuclease-1, PCNA, XRCC1, poly(ADPribose)polymerase-1 (PARP1) with DNA structures mimicking short- and long-patch base excision repair intermediates. Identification of new participants of base excision repair process in cellular and nuclear extracts by affinity labeling combined with MALDI-MS.
  • Study of the damage recognition process and mechanism of nucleotide excision repair system. Development of methods of NER process modulation for chemotherapy improvement. Study of repair mechanisms of clustered damages.
  • Investigation of translesion synthesis mechanism catalyzed with DNA polymerase beta lambda and iota.
  • Search of new efficient inhibitors and regulators of key enzymes of DNA replication/repair systems as potential drugs in treatment of cancer and other human diseases.
  • X-ray analysis of DNA repair proteins and their complexes with substrates.

Main scientific results

  • A novel approach to study in vitro and in vivo of protein complexes of DNA replication and DNA repair using reactive DNA intermediates (synthesized by DNA polymerases using photoreactive dNTP analogs or by chemical methods) has been elaborated. [Khodyreva S.N. & Lavrik O.I., Curr. Med. Chem. 2005. 12, 641; Lavrik O.I. et al., J. Biol. Chem. 2001. 276, 25541].
  • Key role of PARP1 in coordination of the base excision repair pathways has been determined. [Sukhanova M.V. et. al., Nucleic Acids Res. 2005. 33, 1222; Sukhanova M.V. et al., Mutat. Res. 2010. 80, 685].
  • Specific interaction of proteins (HMGB1, Ku70/80, XRCC1, PARP1) with most abundant DNA damages – apurinic/apyrimidinic sites – has been determined. [Prasad R. et al., Mol. Cell. 2007. 27, 829; Nazarkina Z.K. et al., DNA repair. 2007. 6, 254; Ilina E.S. et al., Biochim. Biophys. Acta. 2008. 1784, 1777; Khodyreva S.N. et al. Proc. Natl. Acad. Sci. USA. 2010. 107, 22090].
  • New participants of AP site processing, PARP1 and tyrosyl-DNA phosphodiesterase 1, have been identified. [Khodyreva S.N. et al., Proc. Natl. Acad. Sci. USA, 2010, 107, 22090, Lebedeva N.A. et al., FEBS Lett. 2011. 585, 683].
  • Polar binding of replication protein A – a key factor of eukaryotic DNA replication and repair – with single-stranded DNA has been determined for the first time. The role of p32 and p14 subunits of RPA in the formation of its functional complexes with DNA in DNA replication and DNA repair has been revealed. [Lavrik O.I. et al., Nucleic Acids Res. 1999. 27, 4235; Kolpashchikov D.M. et al., Nucleic Acids Res. 2001. 29, 373].
  • Localization of xeroderma pigmentosum group A and C proteins and replication protein A on damaged DNA in nucleotide excision repair process has been determined. [Krasikova Y.S. et al., Nucleic Acids Res. 2010. 38, 8083; Krasikova Y.S. et al., J. Biol. Chem. 2013. 288, 10936].
  • Structural basis of functional activities of bacterial human mitochondrial and human cytoplasmic phenylalanyl-tRNA synthetases has been explored via X-ray analysis of the enzymes and their complexes with various substrates. [Safro M. et al., In book: The aminoacyl-tRNA synthetases. Georgetown, USA. 2005, 251; Moor N.A. et al., Biochemistry. 2006. 45, 10572; Klipcan L. et al., Structure. 2008. 16, 1095; Finarov I. et al., Structure. 2010. 18, 343].
  • The unique mechanism of productive interaction with tRNA controlled by low-molecular-weight substrates has been discovered. [Moor N.A. et al., Biochemistry. 2003. 42, 10697; Klipcan L. et al., Proc. Natl. Acad. Sci. USA. 2009. 106, 11045; Moor N.A. et al., Chemistry&Biology. 2011. 18, 1221; Klipcan L. et al., J. Mol. Biol. 2012. 415, 52 7].

Main publications 2011-2014

  1. Kosova A.A., Khodyreva S.N., Lavrik O.I. Ku80 interaction with apurinic/apyrimidinic sites depends on the structure of DNA ends. Biopolymers & Cell. 2014. 30(1), 42-46.
  2. Safa L, Delagoutte E, Petruseva I, Alberti P, Lavrik O, Riou JF, Saintomé C. Binding polarity of RPA to telomeric sequences and influence of G-quadruplex stability. Biochimie. 2014. S0300-9084(14)00115-1.
  3. Lebedeva N.A., Rechkunova N.I., Lavrik O.I. Repair of apurinic/apyrimidinic sites in single-stranded DNA initiated by tyrosyl-DNA phosphodiesterase 1. Dokl Biochem Biophys. 2014. 455(1):68-71.
  4. Petruseva IO, Evdokimov AN, Lavrik OI. Molecular mechanism of global genome nucleotide excision repair. Acta Naturae. 2014. 6(1), 23-34.
  5. Lebedeva N.A., Rechkunova N.I., Ishchenko A.A., Saparbaev M.K., Lavrik O.I. The mechanism of human tyrosyl-DNA phosphodiesterase 1 in the clevage of AP site and its synthetic analogs. DNA Repair. 2013, 12, 1037-1042.
  6. Krasikova Y.S., Rechkunova N.I., Maltseva E.A., Anarbayev R.O., Pestryakov P.E., Sugasawa K., Min J.H., Lavrik O.I. Human and yeast DNA damage recognition complexes bind with high affinity DNA structures mimicking in size transkription bubble. J. Mol. Recognit. 2013. 26, 653-661.
  7. Anarbayev R.O., Vasilyeva I.A., Lavrik O.I. Synthesis of the conjugates of DNA polymerase β with cadmium sulfide nanoparticles and their activity in reverse micelles. J. Mol. Catal. B-Enzym., 2013, 98, 46-54.
  8. Belousova E.A., Vasilyeva I.A., Moor N.A., Zatsepin T.S, Oretskaya T.S., Lavrik O.I. Clustered DNA lesions containing 5-formyluracil and AP site: repair via the BER system. PloS ONE, 2013, 8, e68576.
  9. Efremova A.S., Zakharenko A.L., Shram S.I., Kulikova I.V., Drenichev M.S., Sukhanova M.V., Khodyreva S.N., Myasoedov N.F., Lavrik O.I., Mikhailov S.N. Disaccharide Pyrimidine Nucleosides and Their Derivatives: A Novel Group of Cell-Penetrating Inhibitors of Poly(ADP-Ribose) Polymerase 1. Nucleosides Nucleotides Nucleic Acids, 2013, 32, 510-528.
  10. Evdokimov A.N., Petruseva I.O., Tsidulko А.Yu., Koroleva L.S., Serpokrylova I.Y., Silnikov V.N., Lavrik O.I. New synthetic substrates of mammalian nucleotide excision repair system. Nucleic Acids Res., 2013, 41, e123.
  11. Skosareva L.V., Lebedeva N.A., Lavrik O.I., Rechkunova N.I. Reparation of bulk DNA damages – polycyclic aromatic hydrocarbons derivatives. Molecular Biology (Moscow), 2013, 47, 1-12.
  12. Krasikova Y.S., Rechkunova N.I., Maltseva E.A., Pestryakov P.P., Petruseva I.O., Sugasawa K., Chen X., Min J.H., Lavrik O.I. Comparative analysis of interaction of human and yeast DNA damage recognition complexes with damaged DNA in nucleotide excision repair. J. Biol. Chem., 2013, 288, 10936-10947.
  13. Kutuzov M.M., Khodyreva S.N., Amé J.C., Ilina E.S., Sukhanova M.V., Schreiber V., Lavrik O.I. Interaction of PARP-2 with DNA structures mimicking DNA repair intermediates and consequences on activity of base excision repair proteins. Biochimie, 2013, 95, 1208-1215.
  14. Skosareva L.V., Lebedeva N.A., Rechkunova N.I., Kolbanovskiy A., Geacintov N.E., Lavrik O.I. Human DNA polymerase λ catalyzes lesion bypass across benzo[a]pyrene-derived DNA adduct during base excision repair. DNA Repair, 2012, 11, 367-373.
  15. Klipcan L., Moor N.A., Finarov I., Kessler N., Sukhanova M.V., M.G. Safro. Crystal Structure of Human Mitochondrial PheRS Complexed with tRNAPhe in the Active “Open” State. J. Mol. Biol., 2012. 415, 527-537.
  16. Lebedeva N.A., Rechkunova N.I., El-Khamisy SF, Lavrik O.I. Tyrosyl-DNA phosphodiesterase 1 initiates repair of apurinic/apyrimidinic sites. Biochimie, 2012, 94, 1749-1753.
  17. Pestryakov P.E., Zharkov D.O., Grin I.R., Fomina E.E., Kim E.R., Hamon L., Eliseeva I.A., Petruseva I.O., Curmi P.A., Ovchinnikov L.P., Lavrik O.I. Effect of the multifunctional proteins RPA, YB-1, and XPC repair factor on AP site cleavage by DNA glycosylase NEIL1. J. Mol. Recognit., 2012, 25, 224-233.
  18. Zakharenko A.L., Sokolov D, Luzina O, Sukhanova M.V., Khodyreva S.N., Zakharova O.D., Salakhutdinov N.F., Lavrik O.I. Influence of Usnic Acid and its Derivatives on the Activity of Mammalian Poly(ADP-ribose)polymerase 1 and DNA Polymerase β. Med. Chem., 2012, 8, 883-893.
  19. Sukhanova M., D'Herin C., van Der Kemp P.A., Koval V., Boiteux S., Lavrik O. Ddc1 checkpoint protein and DNA polymerase ε interact with nick-containing DNA repair intermediate in cell extracts of Saccharomyces cerevisiae. DNA Repair, 2011, 10, 815-825.
  20. Lebedeva N.A., Rechkunova N.I., Lavrik O.I. AP-site cleavage activity of tyrosyl-DNA phosphodiesterase 1. FEBS Lett., 2011, 585, 683-686.
  21. Moor N., Klipcan L., Safro M.G. Bacterial and eukaryotic phenylalanyl-tRNA synthetases catalyze misaminoacylation of tRNAPhe with 3,4-dihydroxy-L-phenylalanine. Chemistry&Biology. 2011. 18, 1221-1229.

Patents

  1. Evdokimov A.N., Petruseva I.O., Tsidulko A.Ju., Koroleva L.S., Serpokrylova I.Ju., Sil’nikov V.N., Lavrik O.I. Evaluation method of activity of nucleotide excision repair system in mammals. Patent RF N.2492242, 2013.
  2. Zakharenko A.L., Sokolov D.N., Luzina O.A., Sukhanova M.V., Khodyreva S.N., Zakharova O.D., Salakhutdinov N.F., Lavrik O.I. Medication for inhibiting human enzyme poly(ADP-ribose)polymerase-1. Patent RF N.2500675, 2013.

Current grants

RFBR (Grants of the Russian Foundation for Basic Research)
  • N.12-04-00337 «Tyrosyl DNA-phosphodiesterase (Tdp1): role in base excision repair» (2012-2014)
  • N.12-04-00178 «Participation of proteins of translesion synthesis in repair of clustered damages» (2012-2014)
  • N.13-04-00538 «A role of protein-protein and DNA-protein interactions in the complex assembly and regulation of nucleotide excision repair» (2013-2015)
  • N.13-04-00555 «Structural assembly of multi-protein complexes and their coordination role in the DNA base excision repair» (2013-2015)
  • N.13-04-01426 «Analysis of processing of apurinic/apyrimidinic sites in mammalian cells of lymphoid and non-lymphoid origin» (2013-2015)
  • N.13-04-93107 «The role of poly(ADP-ribose) polymerases in base excision and nucleotide excision repair» (2013-2015)
  • N.13-04-40197-H «Analysis of DNA repair systems and their regulation in eukaryotes» (2013-2015)
  • N.14-04-00268 «Mechanism and regulation of the processes of DNA multiple damage repair» (2014-2016)
  • N.14-04-31363 «Influence of PARP1 and PARP2 on the interaction of nucleotide excision repair factors XPC-hHR23B and XPA with damaged DNA» (2014-2015)
  • N.14-04-31392 «PARP1 and PARP2 in repair of DNA cluster damages containing nicks and AP sites» (2014-2015)
Programs of the Presidium of RAS

N.6 «Molecular and Cell Biology»

  • N.4 “Human DNA repair systems: functioning and regulation” (2013-2017)
  • N.24 «Fundamental basis for the technology of nanostructures and nanomaterials»
  • N.61 “Quantum dots as the fluorescent labels for the study of DNA repair mechanisms” (2013-2014)
Russian President’ grant for national support of leading scientific schools
  • Grant of the Russian President on the state support of leading Schools of sciences

• SS-420.2014.4 «Structure-functional proteomics of supramolecular complexes of human DNA repair» (2014-2015) (coordinator – corr.-member of RAS Lavrik O.I.)

Scientific equipment:

Laboratory is equipped by sets that are necessary to perform protein expression and purification, affinity labeling and other biochemical experiments. MALDI-MS analyses of DNA-protein complexes are performed with the equipment for general use of the Core Facility of Mass Spectrometric Analysis of ICBFM SB RAS.


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