Алкогольдегидрогеназа: молекулярно-динамическое изучение конформационного и ориентационного поведения фермента в комплексе с НАД при сорбции на поверхности электродных материалов на примере графита
https://doi.org/10.17586/2220-8054-2025-16-2-192-198
Аннотация
В данной работе проведены исследования методом компьютерной молекулярной динамики (МД) ориентации и структурных конформаций фермента алкогольдегидрогеназы (далее АДГ) в комплексе с никотинамидиндинуклеотидом (далее НАД) при сорбции на поверхности электродных материалов на примере графита.
Об авторах
И. А. Байгунов
Dubna State University, Department of Chemistry, New Technologies and Materials
Россия
Россия
Иван Андреевич Байгунов
Х. Т. Холмуродов
Dubna State University, Department of Chemistry, New Technologies and Materials; Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research; Lomonosov Moscow State University, Department of Fundamental Nuclear Interactions; S. U. Umarov Physical-Technical Institute (PhTI)
Россия
Россия
Холмирзо Тагойкулович Холмуродов
П. П. Гладышев
Dubna State University, Department of Chemistry, New Technologies and Materials
Россия
Россия
Гладышев Павел Павлович
Список литературы
1. Wagenknecht P.S., Penney J.M., Hembre R.T. Transition-metal-catalyzed regeneration of nicotinamide coenzymes with hydrogen. Organometallics, 2003, 22 (6), P. 1180–1182.
2. Nakamura K., Yamanaka R. Light mediated cofactor recycling system in biocatalytic asymmetric reduction of ketone. Chemical Communications, 2002, 16, P. 1782–1783.
3. Bilan D.S., Belousov V.V. Genetically encoded probes for NAD+/NADH monitoring. Free Radical Biology and Medicine, 2016, 100, P. 32–42.
4. Presecki A.V., Vasi ˇ c-Ra ´ cki D. Modelling of the alcohol dehydrogenase production in baker’s yeast. ˇ Process biochemistry, 2005, 40 (8), P. 2781– 2791.
5. Tusek A., ˇ Sali ˇ c A., Kurtanjek ´ Z., Zeli ˇ c B. Modeling and kinetic parameter estimation of alcohol dehydrogenase-catalyzed hexanol oxidation in a ´ microreactor. Engineering in Life Sciences, 2012, 12 (1), P. 49–56.
6. Orlich B., Berger H., Lade M., Schomacker R. Stability and activity of alcohol dehydrogenases in W/O-microemulsions: Enantioselective reduction ¨ including cofactor regeneration. Biotechnology and Bioengineering, 2000, 70 (6), P. 638–646.
7. Hohn S., Zheng K., Romeis S., Brehl M., Peukert W., de Ligny D., Boccaccini A.R. Effects of medium pH and preconditioning treatment on ¨ protein adsorption on 45S5 bioactive glass surfaces. Advanced Materials Interfaces, 2020, 7 (15), 2000420.
8. Benavidez T.E., Torrente D., Marucho M., Garcia C.D. Adsorption and catalytic activity of glucose oxidase accumulated on OTCE upon the application of external potential. J. of colloid and interface science, 2014, 435, P. 164–170.
9. Wang F., Zhang Y.Q. Bioconjugation of silk fibroin nanoparticles with enzyme and peptide and their characterization. Advances in protein chemistry and structural biology, 2015, 98, P. 263–291.
10. Welborn V.V. Structural dynamics and computational design of synthetic enzymes. Chem. Catalysis, 2022, 2 (1), P. 19–28.
11. Norde W., Lyklema J. Why proteins prefer interfaces. J. of Biomaterials Science, Polymer Edition, 1991, 2 (3), P. 183–202.
12. Andrade J.D. (Ed.). Surface and interfacial aspects of biomedical polymers, 1985, Plenum Press, New York, 1985, 1, P. 249–292.
13. Gladyshev P.P., Shapovalov Yu.A., Kvasova V.P. Reconstructed oxidoreductase systems, Science, Alma-ata, KazSSR, 1987, 187 p.
14. Gladyshev P.P., Goriaev M.I., Shpil’berg I.G., Iu A.S. Sorption immobilization of NAD-dependent enzyme systems. I. Influence of electrostatic interactions on the orientation of alcohol dehydrogenase on the sorbent surface. Molekuliarnaia Biologiia, 1982, 16 (5), P. 938–942. (in Russian).
15. Gladyshev P.P., Goriaev M.I., Shpil’berg I.G. Sorption immobilization of NAD-dependent enzyme systems. II. Influence of hydrophobic interactions on the orientation of alcohol dehydrogenase on the sorbent surface. Molekuliarnaia Biologiia, 1982, 16 (5), P. 943–947. (in Russian).
16. Foresman J., Frish E. Exploring chemistry, Gaussian Inc., Pittsburg, USA, 1996, 21, P. 93–123
17. Leach A.R. Molecular modelling: principles and applications. Pearson education, Harlow, 2001, 727 p.
18. Case D.A., Cheatham III T.E., Darden T., Gohlke H., Luo R., Merz Jr. K.M., Woods R.J. The Amber biomolecular simulation programs. J. of Computational Chemistry, 2005, 26 (16), P. 1668–1688.
19. Case D.A., Aktulga H.M., Belfon K., Cerutti D.S., Cisneros G.A., Cruzeiro V.W.D., Merz Jr. K.M. AmberTools. J. of Chemical Information and Modeling, 2023, 63 (20), P. 6183–6191.
20. Lee T.S., Cerutti D.S., Mermelstein D., Lin C., LeGrand S., Giese T.J., York D.M. GPU-accelerated molecular dynamics and free energy methods in Amber18: performance enhancements and new features. J. of Chemical Information and Modeling, 2018, 58 (10), P. 2043–2050.
21. Cruzeiro V.W.D., Amaral M.S., Roitberg A.E. Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation. The J. of Chemical Physics, 2018, 149 (7).
22. Kholmurodov K.T. Models in bioscience and materials research: Molecular dynamics and related techniques, Nova Science Publishers Ltd., New York, 2013, 208 p.
23. Kholmurodov K.T. Computational materials and biological sciences, Nova Science Publishers Ltd., New York, 2015, 188 p.
Рецензия
Для цитирования:
Байгунов И.А., Холмуродов Х.Т., Гладышев П.П. Алкогольдегидрогеназа: молекулярно-динамическое изучение конформационного и ориентационного поведения фермента в комплексе с НАД при сорбции на поверхности электродных материалов на примере графита. Наносистемы: физика, химия, математика. 2025;16(2):192-198. https://doi.org/10.17586/2220-8054-2025-16-2-192-198
For citation:
Baigunov I.A., Kholmurodov Kh.T., Gladyshev P.P. Alcohol dehydrogenase: molecular dynamics study of conformational and orientational behaviour of the enzyme in complex with nad during sorption on the surface of electrode materials using graphite as an example. Nanosystems: Physics, Chemistry, Mathematics. 2025;16(2):192-198. https://doi.org/10.17586/2220-8054-2025-16-2-192-198
Просмотров:
18
Послать статью по эл. почте 