Study of the Precrystallization Solution of Lysozyme by Accelerated Molecular Dynamics Simulation

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Abstract

The behavior of a dimer isolated from the crystal structure of tetragonal lysozyme has been simulated using the accelerated molecular dynamics method. The simulation time was 240 ns. The simulation data are compared with the data obtained previously using classical molecular dynamics. It is shown that the dimer studied is stable in both experiments, but the accelerated molecular dynamics method made it possible to reveal additional conformational changes in lysozyme molecules.

About the authors

A. S. Ivanovsky

Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia

Email: a.1wanowskiy@gmail.com
Россия, Москва

I. F. Garipov

Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, Moscow, 119333 Russia

Email: ildar.garipov.f@gmail.com
Россия, Москва

Yu. V. Kordonskaya

National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia; Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia

Email: a.1wanowskiy@gmail.com
Россия, Москва; Россия, Москва

V. I. Timofeev

National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia; Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia

Email: a.1wanowskiy@gmail.com
Россия, Москва; Россия, Москва

M. A. Marchenkova

National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia; Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia

Email: a.1wanowskiy@gmail.com
Россия, Москва; Россия, Москва

Yu. V. Pisarevsky

Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia; National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia

Email: a.1wanowskiy@gmail.com
Россия, Москва; Россия, Москва

Yu. A. Dyakova

National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia

Email: a.1wanowskiy@gmail.com
Россия, Москва

M. V. Kovalchuk

National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia; Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, 119333, Moscow, Russia

Author for correspondence.
Email: a.1wanowskiy@gmail.com
Россия, Москва; Россия, Москва

References

  1. Timofeev V., Samygina V. // Crystals. 2023. V. 13 (1). P. 71. https://doi.org/10.3390/cryst13010071
  2. https://www.rcsb.org/stats/summary
  3. Pusey M., Witherow W., Naumann R. // ScienceDirect. 1988. V. 90. P. 105. https://doi.org/10.1016/0022-0248(88)90304-1
  4. Kovalchuk M.V., Blagov A.E., Dyakova Y.A. et al. // Cryst. Growth Des. 2016. V. 16. № 4. P. 1792. https://doi.org/10.1021/acs.cgd.5b01662
  5. Aaron Taudt, Axel Arnold, Jurgen Pleiss // Phys. Rev. E. 2015. V. 91. 033311. https://doi.org/10.1103/PhysRevE.91.033311
  6. Kordonskaya Y.V., Timofeev V.I., Dyakova Y.A. et al. // Crystals. 2021. V. 11 (1). P. 1121. https://doi.org/10.3390/cryst11091121
  7. Antonija Kuzmanic, Bojan Zagrovic // Biophys. J. 2014. V. 106. P. 677. https://doi.org/10.1016/j.bpj.2013.12.022
  8. Cerutti D.S., Trong I., Stenkamp R.E., Lybrand T.P. // Biochemistry. 2008. V. 47–46. P. 12065. https://doi.org/10.1021/bi800894u
  9. Meinhold L., Merzel F., Smith J.C. // Phys. Rev. Lett. 2007. V. 99. 138101. https://doi.org/10.1103/PhysRevLett.99.138101
  10. Cerutti D.S., Trong I., Stenkamp R.E., Lybrand T.P. // J. Phys. Chem. B. 2009. V. 113. № 19. P. 6971. https://doi.org/10.1021/jp9010372
  11. Kordonskaya Y.V., Marchenkova M.A., Timofeev V.I. et al. // J. Biomol. Struct. Dyn. 2020 V. 39 (18). P. 7223. https://doi.org/10.1080/07391102.2020.1803138
  12. Kordonskaya Y.V., Timofeev V.I., Marchenkova M.A., Konarev P.V. // Crystals. 2022. V. 12. P. 484. https://doi.org/10.3390/cryst12040484
  13. Nguyen H., Maier J., Huang H. et al. // J. Am. Chem. Soc. 2014. V. 136 (40). P. 13959. https://doi.org/10.1021/ja5032776
  14. Onufriev A.V., Case D.A. // Annu. Rev. Biophys. 2019. V. 58. P. 275. https://doi.org/10.1146/annurev-biophys-052118-115325
  15. Marrink S.J., Risselada H.J., Yefimov S. et al. // J. Phys. Chem. B. 2007. V. 111. № 27. P. 7812. https://doi.org/10.1021/jp071097f
  16. Sun F., Schroer C.F.E., Palacios C.R. et al. // PLoS Comput. Biol. 2022. V. 16 (4). E. 1007777. https://doi.org/10.1371/journal.pcbi.1007777
  17. Pezeshkian W., Marrink S.J. // Curr. Opin. Cell Biol. 2021. V. 71. P. 103. https://doi.org/10.1016/j.ceb.2021.02.009
  18. Thallmair S., Javanainen M., Fábián B. et al. // J. Phys. Chem. 2021. V. 125. (33). P. 9537. https://doi.org/10.1021/acs.jpcb.1c03665
  19. Frallicciardi J., Melcr J., Siginou P. et al. // Nat. Commun. 2022. V. 13. P. 1605. https://www.nature.com/articles/s41467-022-29272-x
  20. Korotkova P.D., Shumm A.B., Vladimirov Y.A. et al. // Journal of Surface Investigation: X-Ray, Synchrotron and Neutron Techniques. 2021. V. 15. № 4. P. 652.
  21. Hamelberg D., Mongan J., McCammon J.A. // J. Chem. Phys. 2004. V. 120 (24). P. 11919. https://doi.org/10.1063/1.175565
  22. Shaw D.E. et al. // Science. 2010. V. 330. P. 341. https://doi.org/10.1126/science.1187409
  23. Marchenkova M.A. et al. // J. Biomol. Struct. Dyn. 2020. V. 38. № 17. P. 5159. https://doi.org/10.1080/07391102.2019.1696706
  24. Dolinsky T.J. et al. // Nucl. Acids Res. 2004. V. 32. P. W665. https://doi.org/10.1093/nar/gkh381
  25. Case D.A. et al. // J. Comput. Chem. 2005. V. 26. P. 1668. https://doi.org/10.1002/jcc.20290
  26. Tian C. et al. // J. Chem. Theory Comput. 2020. V. 16. P. 528. https://doi.org/10.1021/acs.jctc.9b00591
  27. Jorgensen W.L., Chandrasekhar J., Madura J.D. et al. // J. Chem. Phys. 1983. V. 79 (2). P. 926. https://doi.org/10.1063/1.445869
  28. Allen M.P., Tildesley D.J. // Computer simulation of liquids. New York: Oxford university press, 1991.
  29. Hoover W.G., Ladd A.J.C., Phys B.M. // Phys. Rev. Lett. 1982. V. 48. 1818. https://doi.org/10.1103/PhysRevLett.48.1818
  30. Evans D.J., Chem J. // Chem. Phys. 1983. V. 77 (1). P. 63. https://doi.org/10.1016/0301-0104(83)85065-4
  31. Berendsen H.J.C. et al. // J. Chem. Phys. 1984. V. 81. P. 3684. https://doi.org/10.1063/1.448118
  32. Kordonskaya Y.V., Timofeev V.I., Dyakova Y.A. et al. // Crystals. 2021. V. 11. P. 1534. https://doi.org/10.3390/cryst11121534

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