- PII
- 10.31857/S0023476124050159-1
- DOI
- 10.31857/S0023476124050159
- Publication type
- Article
- Status
- Published
- Authors
- Volume/ Edition
- Volume 69 / Issue number 5
- Pages
- 885-890
- Abstract
- The molecular dynamics of two types of lysozyme octamers was simulated under crystallization conditions in the MARTINI coarse-grained force field. Comparative analysis of the obtained results with the simulation data for the same octamers modelled in the all-atom field Amber99sb-ildn showed that octamer “A” demonstrates greater stability compared to octamer “B” in both force fields. Thus, the results of molecular dynamics simulations of octamers using both force fields are consistent. Despite several differences in the behavior of the protein in different fields, they do not affect the validity of the data obtained using MARTINI. This confirms the applicability of the MARTINI force field for studying crystallization solutions of proteins.
- Keywords
- Date of publication
- 14.09.2025
- Year of publication
- 2025
- Number of purchasers
- 0
- Views
- 11
References
- 1. 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
- 2. Marchenkova M.A., Volkov V.V., Blagov A.E. et al. // Crystallography Reports. 2016. V. 61. № 1. P. 5. https://doi.org/10.1134/S1063774516010144
- 3. Boikova A.S., D’yakova Y.A., Il’ina K.B. et al. // Crystallography Reports. 2018. V. 63. № 6. P. 865. https://doi.org/10.1134/S1063774518060068
- 4. Kovalchuk M.V., Boikova A.S., Dyakova Y.A. et al. // J. Biomol. Struct. Dyn. 2019. V. 37. № 12. P. 3058. https://doi.org/10.1080/07391102.2018.1507839.
- 5. Marchenkova M.A., Konarev P.V., Rakitina T.V. et al. // J. Biomol Struct. Dyn. V. 38. № 10. P. 2939. https://doi.org/10.1080/07391102.2019.1649195
- 6. Marchenkova M.A., Boikova A.S., Ilina K.B. et al. // Acta Naturae. 2023. V. 15. № 1. P. 58. https://doi.org/10.32607/ACTANATURAE.11815
- 7. Kordonskaya Y.V., Timofeev V.I., Dyakova Y.A. et al. // Crystallography Reports. 2018. V. 63. № 6. P. 947. https://doi.org/10.1134/S1063774518060196
- 8. Kordonskaya Y.V., Timofeev V.I., Marchenkova M.A., Konarev P.V. // Crystals. 2022. V. 12. № 4. P. 484. https://www.mdpi.com/2073-4352/12/4/484
- 9. Kordonskaya Y.V., Timofeev V.I., Dyakova Y.A. et al. // Mend. Commun. 2023. V. 33. № 2. P. 225. https://doi.org/10.1016/J.MENCOM.2023.02.024
- 10. Cerutti D.S., Le Trong I., Stenkamp R.E., Lybrand T.P. // Biochemistry. 2008. V. 47. № 46. P. 12065. https://doi.org/10.1021/bi800894u
- 11. Cerutti D.S., Le Trong I., Stenkamp R.E., Lybrand T.P. // J. Phys. Chem. B. 2009. V. 113. № 19. P. 6971. https://pubs.acs.org/doi/full/10.1021/jp9010372
- 12. Cerutti D.S., Freddolino P.L., Duke R.E., Case D.A. // J. Phys. Chem. B. 2010. V. 114. № 40. P. 12811. https://doi.org/10.1021/jp105813j
- 13. Taudt A., Arnold A., Pleiss J. // Phys. Rev. E. 2015. V. 91. № 3. P. 033311. https://journals.aps.org/pre/abstract/10.1103/PhysRevE.91.033311
- 14. Meinhold L., Merzel F., Smith J.C. // Phys. Rev. Lett. 2007. V. 99. № 13. P. 138101. https://doi.org/10.1103/PhysRevLett.99.138101
- 15. Marrink S.J., Periole X., Tieleman D.P., De Vries A.H. // Phys. Chem. Chem. Phys. 2010. V. 12. № 9. P. 225. https://doi.org/10.1039/B915293H
- 16. Marrink S.J., Risselada H.J., Yefimov S. et al. // J. Phys. Chem. B. 2007. V. 111. № 27. P. 7812. https://pubs.acs.org/doi/full/10.1021/jp071097f
- 17. Monticelli L., Kandasamy S.K., Periole X. et al // J. Chem. Theory Comput. 2008. V. 4. № 5. P. 819. https://pubs.acs.org/doi/abs/10.1021/ct700324x
- 18. Marrink S.J., Monticelli L., Melo M.N. et al. // Wiley Interdiscip Rev. Comput. Mol. Sci. 2022. V. 13. № 1. P. e1620. https://onlinelibrary.wiley.com/doi/full/10.1002/wcms.1620
- 19. Kroon P.C., Grünewald F., Barnoud J. et al. // 2022. https://arxiv.org/abs/2212.01191v3
- 20. Souza P.C.T., Alessandri R., Barnoud J. et al. // Nature Methods. 2021. V. 18. № 4. P. 382. https://www.nature.com/articles/s41592-021-01098-3
- 21. Van Der Spoel D., Lindahl E., Hess B. et al. // J. Comput. Chem. 2005. V. 26. № 16. P. 1701. https://doi.org/10.1002/jcc.20291
- 22. Wassenaar T.A., Ingólfsson H.I., Böckmann R.A. et al. // J. Chem. Theory Comput. 2015. V. 11. № 5. P. 2144. https://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00209
- 23. Bernetti M., Bussi G. // J. Chem. Phys. 2020. V. 153. № 11. Р. 114107. https://doi.org/10.1063/5.0020514
- 24. Berendsen H.J.C., Postma J.P.M., Van Gunsteren W.F. et al. // J. Chem. Phys. 1984. V. 81. № 8. P. 3684. https://doi.org/10.1063/1.448118
- 25. Parrinello M., Rahman A. // J. Chem. Phys. 1982. V. 76. № 5. P. 2662. https://doi.org/10.1063/1.443248
- 26. Van Gunsteren W.F., Berendsen H.J.C. // Mol. Simul. 1988. V. 1. № 3. P. 173. https://doi.org/10.1080/08927028808080941
- 27. Hünenberger P.H., Van Gunsteren W.F. // J. Chem. Phys. 1998. V. 108. № 15. P. 6117. https://doi.org/10.1063/1.476022
- 28. Hess B., Bekker H., Berendsen H.J.C., Fraaije J.G.E.M. // J. Comput. Chem. 1997. V. 18. P. 1463. https://doi.org/10.1002/ (SICI)1096-987X(199709)18:123.0.CO;2-H
