Email this article 
STRUCTURAL BIOINFORMATICS STUDY OF THE STRUCTURAL BASIS OF SUBSTRATE SPECIFICITY OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS
- Authors: Garipov I.F.1, Timofeev V.I.1,2, Zayats E.A.3, Abramchikc Y.A.3, Kostromina M.A.3, Konstantinova I.D.3, Esipov R.S.3
-
Affiliations:
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, Moscow, 119333 Russia
- National Research Centre “Kurchatov Institute,” Moscow, 123182 Russia
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
- Issue: Vol 68, No 2 (2023)
- Pages: 268-275
- Section: STRUCTURE OF MACROMOLECULAR COMPOUNDS
- URL: https://rjmseer.com/0023-4761/article/view/673503
- DOI: https://doi.org/10.31857/S0023476123010101
- EDN: https://elibrary.ru/GAXNVC
- ID: 673503
Cite item
Open Access
Access granted
Subscription Access
Abstract
Molecular dynamics simulations were performed for wild-type purine nucleoside phosphorylase in complexes with two substrates (adenosine and guanosine). The MD simulations were also performed for the mutant form of the enzyme with the same substrates. The free energy changes upon the formation of the complexes were evaluated from the molecular dynamics trajectories by the MM-GBSA method.
About the authors
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
V. I. Timofeev
Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics,” Russian Academy of Sciences, Moscow, 119333 Russia; National Research Centre “Kurchatov Institute,” Moscow, 123182 Russia
Email: ildar.garipov.f@gmail.com
Россия, Москва; Россия, Москва
E. A. Zayats
Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
Email: ildar.garipov.f@gmail.com
Россия, Москва
Yu. A. Abramchikc
Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
Email: ildar.garipov.f@gmail.com
Россия, Москва
M. A. Kostromina
Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
Email: ildar.garipov.f@gmail.com
Россия, Москва
I. D. Konstantinova
Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
Email: ildar.garipov.f@gmail.com
Россия, Москва
R. S. Esipov
Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
Author for correspondence.
Email: ildar.garipov.f@gmail.com
Россия, Москва
References
- Timofeev V.I., Fateev I.V., Kostromina M.A. et al. // J. Biomol. Struct. Dyn. 2020. V. 40. P. 1. https://doi.org/10.1080/07391102.2020.1848628
- Tomoike F., Kuramitsu S., Masui R. // Extremophiles. 2013. V. 17. P. 505. https://doi.org/10.1007/s00792-013-0535-7
- Погосян Л.Г., Акопян Ж.И. // Биомедицинская химия. 2013. Т. 59. № 5. С. 483. https://doi.org/10.18097/pbmc20135905483
- Salomon-Ferrer R., Case D.A., Walker R.C. // WIREs Comput. Mol. Sci. 2013. V. 3. P. 198. https://doi.org/10.1002/wcms.1121
- Case D.A., Cheatham T.E., III, Darden T. et al. // J. Comput. Chem. 2005. V. 26. P. 1668. https://doi.org/10.1002/jcc.20290
- Maier J.A., Martinez C., Kasavajhala K. et al. // J. Chem. Theory Comput. 2015. V. 11. P. 3696. https://doi.org/10.1021/acs.jctc.5b00255
- Salomon-Ferrer R., Goetz A.W., Poole D. et al. // J. Chem. Theory Comput. 2013. V. 9. P. 3878. https://doi.org/10.1021/ct400314y
- Jorgensen W. L., Chandrasekhar J., Madura J.D. et al. // J. Chem. Phys. 1983. V. 79. P. 926. https://doi.org/10.1063/1.445869
- Allen M.P., Tildesley D.J. Computer simulation of liquids. New York: Oxford university press, 1991. https://doi.org/10.2307/2938686
- Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F. et al. // J. Chem. Phys. 1984. V. 81. P. 3684. https://doi.org/10.1063/1.448118
- Darden T., York D., Pedersen L. // J. Chem. Phys. 1993. V. 98. P. 10089. https://doi.org/10.1063/1.464397
- Kollman P.A., Massova I., Reyes C. et al. // Acc. Chem. Res. 2000. V. 33. P. 889. https://doi.org/10.1021/ar000033j
- Srinivasan J., Trevathan M.W., Beroza P. et al. // Theor. Chem. Acc. 1999. V. 101. P. 426. https://doi.org/10.1007/s002140050460
- Miller B.R., McGee T.D., Swails J.M. et al. // J. Chemical Theory and Computation. 2012. V. 8. P. 3314. https://doi.org/10.1021/ct300418h
- Onufriev A., Bashford D., Case D.A. // Proteins. 2004. V. 55. P. 383. https://doi.org/10.1002/prot.20033
- Schrödinger L.L.C. The PyMOL Molecular Graphics System, Version 2.0
- Mikhailopulo I.A., Miroshnikov A.I. // Acta Naturae. 2010. V. 2. P. 36. https://doi.org/10.32607/20758251-2017-9-2-47-58
- Fateev I.V., Kostromina M.A., Abramchik Y.A. et al. // Biomolecules. 2021. V. 11. P. 586. https://doi.org/10.3390/biom11040586
- Roy B., Depaix A., Périgaud C. et al. // Chem. Rev. 2016. V. 116. P. 7854. https://doi.org/10.1021/acs.chemrev.6b00174
- Almendros M., Berenguer J., Sinisterra J.V. // Appl. Environmental Microbiology. 2012. V. 78. P. 3128. https://doi.org/10.1128/AEM.07605-11
- Fateev I.V., Kharitonova M.I., Antonov K.V. et al. // Chemistry. 2015. V. 21. P. 13401. https://doi.org/10.1002/chem.201501334
Supplementary files
