Database of Intermediates of Enzyme-Catalyzed Chemical Reactions ENIAD

A. A. Moskovsky; Московский А. А.; D. A. Firsov; Фирсов Д. А.; M. G. Khrenova; Хренова М. Г.; V. A. Mironov; Миронов В. А.; T. I. Mulashkina; Мулашкина Т. И.; A. M. Kulakova; Кулакова А. М.; A. V. Nemukhin; Немухин А. В.

doi:10.31857/S0044453723090133

Database of Intermediates of Enzyme-Catalyzed Chemical Reactions ENIAD

Authors: Moskovsky A.A.¹, Firsov D.A.¹, Khrenova M.G.¹^,2, Mironov V.A.¹, Mulashkina T.I.¹, Kulakova A.M.¹, Nemukhin A.V.¹^,3
Affiliations:
1. Moscow State University
2. Federal Research Center of Biotechnology, Russian Academy of Sciences
3. Institute of Biochemical Physics, Russian Academy of Sciences
Issue: Vol 97, No 9 (2023)
Pages: 1324-1328
Section: ХЕМОИНФОРМАТИКА И КОМПЬЮТЕРНОЕ МОДЕЛИРОВАНИЕ
Submitted: 26.02.2025
Published: 01.09.2023
URL: https://innoscience.ru/0044-4537/article/view/668669
DOI: https://doi.org/10.31857/S0044453723090133
EDN: https://elibrary.ru/XKQAYW
ID: 668669

Cite item

Full Text

Open Access
Restricted Access

Access granted
Restricted Access

Subscription Access

Abstract
About the authors
References
Supplementary files
Statistics

Abstract

Enzymatic catalysis is characterized by multistage chemical reactions from enzyme-substrate complexes to products. In a number of cases, in the course of experimental studies, it is possible to characterize the structures and properties of intermediates of complex chemical reactions in proteins. The use of modern computer simulation methods makes it possible to significantly supplement the knowledge of the mechanisms of enzymatic catalysis reactions and provide detailed data on reaction intermediates, including structures with atomic resolution. The materials accumulated to date make it possible to create a unique dat-abase called ENIAD (ENzyme-In-Action-Databank). The article describes the principles of building the ENIAD database, as well as a multiplatform web interface for accessing data (https://lcc.chem.msu.ru/eniad/).

Keywords

enzymatic catalysis, reaction intermediates, molecular modeling, databank

References

Варфоломеев С.Д. Химическая энзимология. М.: Научный мир, 2019. С. 543.
Berman H.M., Henrick K., Nakamura H. // Nature Structural Biology. 2003. V. 10. № 12. P. 980. https://doi.org/10.1038/nsb1203-980
Holliday G.L., Andreini C., Fischer J.D. et al. // Nucleic Acids Res. 2012. V. 40. P. D783.https://doi.org/10.1093/nar/gkr799
Nagano N., Nakayama N., Ikeda K. et al. // Ibid. 2015. V. 43. P. D453.https://doi.org/10.1093/nar/gku946
Ribeiro A.J.M., Holliday J.L., Furnham N. et al. // Ibid. 2018. V. 46. P. D618.https://doi.org/10.1093/nar/gkx1012
Furnham N., Holliday G.L., de Beer T.A.P. et al. // Ibid. 2014. V. 42. P. D485.https://doi.org/10.1093/nar/gkt1243
Warshel A., Levitt M. // J. Mol. Biol. 1976. V. 103. P. 227. https://doi.org/10.1016/0022-2836(76)90311-9
Senn H.M., Thiel W. // Angew. Chemie Int. Ed. 2009. V. 48. P. 1198. https://doi.org/10.1002/anie.200802019
Grigorenko B.L., Kots E.D., Nemukhin A.V. // Org. Biomol. Chem. 2019. V. 17. P. 4879.https://doi.org/10.1039/C9OB00463G
Khrenova M.G., Grigorenko B.L., Kolomeisky A.B. et al. // J. Phys. Chem. B. 2015. V. 119. № 40. P. 12838.https://doi.org/10.1021/acs.jpcb.5b07238
Khrenova M.G., Kots E.D., Nemukhin A.V. // Ibid. 2016. V. 120. № 16. P. 3873.https://doi.org/10.1021/acs.jpcb.6b03363
Docker, Inc. https://www.docker.com, 2019.
The Linux Foundation. https://kubernetes.io, 2019.
Brekhov A.T., Mironov V.A., Moskovsky A.A. et al. // J. Phys.: Conf. Ser. 2019. V. 1392. P. 012049.https://doi.org/10.1088/1742-6596/1392/1/012049
PostgreSQL Global Development Group. https://www.postgresql.org, 2019.
Latino D.A.R.S., Aires-de-Sousa J. // Chemoinf. and Comput. Chem. Biol. 2011. V. 672. P. 325.https://doi.org/10.1007/978-1-60761-839-3_13
O’Boyle N.M., Holliday G.L., Almonacid D.E. et al. // J. Mol. Biol. 2007. V. 368. P. 1484.https://doi.org/10.1016/j.jmb.2007.02.065
Almonacid D.E., Babbitt P.C. // Curr. Opin. Chem. Biol. 2011. V. 15. P. 435.https://doi.org/10.1016/j.cbpa.2011.03.008