Group of Molecular Modeling

Maria G. Khrenova
Head of the Group
Dr.Sci. (Physics and Mathematics)
INBI, build. 1, room. 267

The interests of Group of Molecular Modeling are mainly focused on the mechanisms of the biochemical processes happening in enzymes, photoreceptor proteins and protein complexes. We apply modern supercomputer molecular modeling tools including combined quantum mechanics/molecular mechanics, quantum chemical methods, molecular dynamics with classic, QM/MM or quantum potentials, bioinformatics analysis and theoretical methods of the electron density analysis.

Selected publications

  1. Meteleshko Yu. I., Nemukhin A., Khrenova M. Novel flavin-based fluorescent proteins with red-shifted emission bands:a computational study  // Photochem. Photobiol. Sci. – 2019. – V. 18. – P. 177-189 ( IF=2.902
  2. Khrenova M. G., Nemukhin A. V., Tsirelson V. G. Origin of the pi-stacking induced shifts in absorption spectral bands of the green fluorescent protein chromophore // Chem. Phys. – 2019. – V. 522. – P. 32-38 ( IF=1.707
  3. Kots E. D., Khrenova M. G., Nemukhin A. V. Allosteric Control of N-Acetyl-Aspartate Hydrolysis by the Y231C and F295S Mutants of Human Aspartoacylase // J. Chem. Inf. Model. 2018 ( IF= 3.760
  4. Grigorenko G. L., Khrenova M. G., Nemukhin A. V. Amide-imide tautomerization in the glutamine side chain in enzymatic and photochemical reactions in proteins // Phys. Chem. Chem. Phys. – 2018. – V. 20. – P. 23827-23836 ( IF=3.906
  5. Khrenova M., Kulakova A., Nemukhin A. Competition between two cysteines in covalent binding of biliverdin to phytochrome domains // Org. Biomol. Chem. – 2018. – V. 16. – P. 7518-7529
  6. Khrenova M.G., Grigorenko B.L., Mironov V.A., Nemukhin A.V. Why does mutation of Gln61 in Ras by the nitro analog NGln maintain activity of Ras-GAP in hydrolysis of guanosine triphosphate? // Proteins – 2015. – V. 83. – P. 2091–2099 ( IF=3.337
  7. Vasilevskaya T., Khrenova M.G., Nemukhin A.V., Thiel W. Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling // J. Comput. Chem. – 2015. – V. 36. – P. 1621–1630 ( IF=3.835
  8. Khrenova M.G., Grigorenko B.L., Kolomeisky A.B., Nemukhin A.V. Hydrolysis of guanosine triphosphate (GTP) by the Ras-GAP protein complex: reaction mechanism and kinetic scheme // J. Phys. Chem. B – 2015. – V. 119. – P. 12838–12845 ( IF=3.607
  9. Khrenova M., Topol I., Collins J., A. Nemukhin A. Estimating orientation factors in the fret theory of fluorescent proteins: The TagRFP-KFP pair and beyond // Biophys J. – 2015. – V. 108. – P. 126-132. ( IF=3.668
  10. Khrenova M. G., Nemukhin A. V., Tatiana D.  Theoretical characterization of the flavin-based fluorescent protein iLOV and its Q489K mutant // J. Phys. Chem. B — 2015. — Vol. 119. — P. 5176–5183. ( IF=3.607
  11. Vasilevskaya T., Khrenova M., Nemukhin A., Thiel W. Methodological aspects of QM/MM calculations: a case study on matrix metalloproteinase-2 // J. Comput. Chem. – 2016. – V. 37. – P. 1801-1809 ( IF=3.835
  12. Kots E.D., Khrenova M.G., Lushchekina S.V., Varfolomeev S.D., Grigorenko B.L., Nemukhin A.V. Modeling the complete catalytic cycle of aspartoacylase // J. Phys. Chem. B – 2016. – V. 120. – P. 4221-4231 ( IF=3.607
  13. Khrenova M.G., Kots E.D., Nemukhin A.V. Reaction mechanism of the guanosine triphosphate hydrolysis by the vision-related protein complex Arl3-RP2 // J. Phys. Chem. B – 2016. – V. 120. – P. 3873-3879 ( IF=3.607
  14. Khrenova M. G., Grigorenko B. L., Nemukhin A. V. Theoretical vibrational spectroscopy of intermediates and the reaction mechanism of the guanosine triphosphate hydrolysis by the protein complex ras-gap // Spectrochim. Acta A — 2016. — Vol. 166. — P. 68–72. ( IF=1.977
  15. Khrenova M. G., Tatiana D., Nemukhin A. V. Molecular mechanism of the dark-state recovery in bluf photoreceptors // Chem. Phys. Lett. — 2017. — Vol. 676. — P. 25–31. ( IF=2.145
  16. Popinako A., Antonov M., Dibrova D., Chemeris A., Sokolova O.S. Analysis of the interactions between GMF and Arp2/3 complex in two binding sites by molecular dynamics simulation. Biochemical and Biophysical Research Communications. — 2018 — 496(2) — 529-535. doi: 10.1016/j.bbrc.2018.01.080.
  17. Popinako A., Antonov M., Tikhonov A., Tikhonova T., Popov V. Structural adaptations of octaheme nitrite reductases from haloalkaliphilic Thioalkalivibrio bacteria to alkaline pH and high salinity. PLoS One. 2017 May 16.12(5). IF 3.54
  18. Antonov M. Yu., Popinako A.V., Prokopiev G.A. Molecular dynamics simulation of the structure and dynamics of 5-HT3 serotonin receptor. AIP Conference Proceedings. 2016. 1773.1-6. Article 060001 (2016); ISSN: 0094243X ISBN: 978-073541431-0. DOI: 10.1063/1.4964976
  19. M.Yu. Antonov, A.V.Popinako, G.A. Prokopev, A.O.Vasilyev.  Numerical Modelling of Ion Transport in 5-HT3 Serotonin Receptor using molecular dynamics. Numerical Analysis and Its Applications. NAA 2016. Lecture Notes in Computer Science. 2017. V. 10187. Springer. P. 195-202.
  20. Bezsudnova EY, Petrova TE, Popinako AV, Antonov MY, Stekhanova TN, Popov VO. Intramolecular hydrogen bonding in the polyextremophilic short-chain dehydrogenase from the archaeon Thermococcus sibiricus and its close structural homologs. 2015. Biochimie. P. S0300-9084(15)00257-6. doi: 10.1016/j.biochi.2015.08.010 Epub ahead of print1. IF 3.124. ISSN: 0300-9084
  21. Anastasia Grisel, Anna Popinako, Marina Kasimova, Louisa Stevens, Maria Karlova, Mikhail Moisenovich, Olga Sokolova. Domain Structure and Conformational Changes in rat KV2.1 ion Channel. Journal of Neuroimmune Pharmacology.2014. V.9. №5. P.727-739. IF 4.110
  22. Potapova T.V., Boitzova L.Ju, Golyshev S.A., Popinako A.V. The organization of mitochondria in growing hyphae of Neurospora crassa. Cell and Tissue Biology. Maik Nauka/Interperiodica Publishing (Russian Federation). 2014. V. 8. № 2. P. 166-174
  23. Antonov, M.Yu., Naumenkova, T.V., Popinako A.V., Nikolaev, I.N., Shaitan, K.V. Estimating the profile of the mean force potential for transmembrane transport of a water molecule by the umbrella sampling method. Mathematical Notes of NEFU (Russian Federation). 2014. V.21. N.3. P. 78-86. ISSN 2411-9326
  24. Potapova T.V., Boitzova L.Ju, Golyshev S.A., Popinako A.V. The Organization of Mitochondria during the Neurospora crassa Tip Growth. Cytology (Russian Federation). 2013. V. 55. №11. P. 828-836. IF 0.282
  25. Astakhov A.A., Tsirelson V.G. Spatial localization of electron pairs in molecules using the Fisher information density. Chemical Physics, (2014) 435, 49–56.
  26. Vener M.V., Levina E.O., Astakhov A.A., Tsirelson V.G.. Specific Features of the Extra Strong Intermolecular Hydrogen Bonds in Crystals: Insights from the Theoretical Charge Density Analysis. Chem. Phys. Letters (2015) 638, 233–236.