Temperature influence on the stability of the precursor cluster of the thermolysin crystal

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Abstract

We used the molecular dynamics method to assess the stability of the precursor-cluster (hexamer) of thermolysin crystal over a wide range of temperatures (10–90°C). The simulation results showed that as the temperature increases, the stability of the hexamer, in general, decreases, however, the hexamer does not dissociate at any of the considered temperatures. At a temperature of 60°C, an increase in the stability of the hexamer was observed. This value is close to the temperature of maximum enzymatic activity of thermolysin (70°C). Based on the analysis of the results, it was assumed that the crystallization of thermolysin could be carried out at 60°C.

Full Text

Restricted Access

About the authors

Y. V. Kordonskaya

National Research Centre “Kurchatov Institute”

Author for correspondence.
Email: yukord@mail.ru
Russian Federation, Moscow

V. I. Timofeev

NRC “Kurchatov Institute”

Email: yukord@mail.ru

Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics

Russian Federation, Moscow

M. А. Marchenkova

NRC “Kurchatov Institute”; Southern Federal University

Email: yukord@mail.ru

Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics; The Smart Materials Research Institute

Russian Federation, Moscow; Rostov-on-Don

Y. V. Pisarevsky

NRC “Kurchatov Institute”

Email: yukord@mail.ru

Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics

Russian Federation, Moscow

S. Y. Silvestrova

The Loginov Moscow Clinical Scientific Center Moscow Health Department

Email: yukord@mail.ru
Russian Federation, Moscow

Y. A. Dyakova

National Research Centre “Kurchatov Institute”

Email: yukord@mail.ru
Russian Federation, Moscow

M. V. Kovalchuk

National Research Centre “Kurchatov Institute”; NRC “Kurchatov Institute”

Email: yukord@mail.ru

Shubnikov Institute of Crystallography of Kurchatov Complex of Crystallography and Photonics

Russian Federation, Moscow; Moscow

References

  1. 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
  2. Du S., Wankowicz S.A., Yabukarski F. et al. // bioRxiv. 2023. https://doi.org/10.1101/2023.05.05.539620
  3. Kordonskaya Y.V., Timofeev V.I., Dyakova Y.A. et al. // Crystals. 2022. V. 12. № 11. P. 1645. https://doi.org/10.3390/CRYST12111645
  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. 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
  6. van den Burg B., Eijsink V. // Handbook of Proteolytic Enzymes. 2013. V. 1. P. 540. https://doi.org/10.1016/B978-0-12-382219-2.00111-3
  7. Lam M.P.Y., Lau E., Liu X. et al. // Comprehensive Sampling and Sample Preparation: Analytical Techniques for Scientists. 2012. P. 307. https://doi.org/10.1016/B978-0-12-381373-2.00085-5
  8. Adekoya O.A., Sylte I. // Chem. Biol. Drug. Des. 2009. V. 73. № 1. P. 7. https://doi.org/10.1111/J.1747-0285.2008.00757.X
  9. DeLano W.L. // The PyMOL Molecular Graphics System, Version 1.8; Schrödinger, LLC: New York, NY, USA, 2015.
  10. Jurrus E., Engel D., Star K. et al. // Protein Sci. 2018. V. 27. № 1. P. 112. https://doi.org/10.1002/PRO.3280
  11. 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
  12. Lindorff-Larsen K., Piana S., Palmo K. et al. // Proteins: Structure, Function and Bioinformatics. 2010. V. 78. № 8. P. 1950. https://doi.org/10.1002/prot.22711
  13. Horn H.W., Swope W.C., Pitera J.W. et al. // J. Chem. Phys. 2004. V. 120. № 20. P. 9665. https://doi.org/10.1063/1.1683075
  14. Dimitropoulos D., Ionides J., Henrick K. // Curr. Protoc. Bioinf. 2006. P. 14.3.1–14.3.3.
  15. Michaud-Agrawal N., Denning E.J., Woolf T.B., Beckstein O. // J. Comput. Chem. 2011. V. 32. № 10. P. 2319. https://doi.org/10.1002/JCC.21787
  16. Gowers R.J., Linke M., Barnoud J. et al. // 15th Python in Science Conference, Los Alamos, NM (United States), Sep 11. 2016. P. 98. https://doi.org/10.25080/Majora629e541a-00e
  17. Sousa Da Silva A.W., Vranken W.F. // BMC Res Notes. 2012. V. 5. № 1. P. 1. https://doi.org/10.1186/1756-0500-5-367/FIGURES/3
  18. Essmann U., Perera L., Berkowitz M.L. et al. // J. Chem. Phys. 1995. V. 103. P. 8577. https://doi.org/10.1063/1.470117
  19. 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
  20. Parrinello M., Rahman A. // J. Chem. Phys. 1982. V. 76. № 5. P. 2662. https://doi.org/10.1063/1.443248
  21. Van Gunsteren W.F., Berendsen H.J.C. // Mol. Simul. 1988. V. 1. № 3. P. 173. https://doi.org/10.1080/08927028808080941
  22. 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)18:12<1463:: AID-JCC4>3.0.CO;2-H

Supplementary files

Supplementary Files
Action
1. JATS XML
Download
2. Fig. 1. RMSF values ​​of the precursor cluster (hexamer) of the thermolysin crystal in the crystallization solution at temperatures in the range from 10–90°C. Each colored curve corresponds to one simulation, the black one to the RMSF values ​​averaged over all independent simulations (three or five) at a certain temperature.

Download (746KB)
Indexing metadata
3. Fig. 2. Precursor cluster (hexamer) of thermolysin crystal in two projections. Letters A–F denote the monomers that make up the hexamer. Green spheres show calcium ions, gray spheres – zinc ions.

Download (480KB)
Indexing metadata
4. Fig. 3. RMSF values ​​averaged over all Cα atoms of the thermolysin crystal precursor cluster in the crystallization solution at different temperatures (from 10 to 90°C). The indicated errors are one standard deviation when averaging RMSF over independent simulations.

Download (73KB)
Indexing metadata
5. Fig. 4. The least stable hexamers at the end of the simulation (100 ns) in two projections at 50 (left) and 70°C (right). Thermolysin molecules do not detach from the hexamer even during MD of the most unstable structures.

Download (201KB)
Indexing metadata

Copyright (c) 2024 Russian Academy of Sciences