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
https://doi.org/10.17586/2220-8054-2025-16-2-192-198
Abstract
In this work, computer molecular dynamics (MD) studies of the orientation and structural conformations of the alcohol dehydrogenase enzyme (hereinafter ADH) in complex with nicotine adenine dinucleotide (hereinafter NAD) during sorption on the surface of electrode materials using graphite as an example were carried out.
About the Authors
I. A. BaigunovRussian Federation
Ivan A. Baigunov
Universitetskaya, 19, Dubna, Moscow Region, 141980
Kh. T. Kholmurodov
Russian Federation
Kholmirzo T. Kholmurodov
Universitetskaya, 19, Dubna, Moscow Region, 141980
Joliot-Curie, 6, Dubna, Moscow Region, 141980
Leninskiye Gory, GSP-1, Moscow, 119991
Aini ave., 299/1, Dushanbe, 734063
P. P. Gladyshev
Russian Federation
Pavel P. Gladyshev
Universitetskaya, 19, Dubna, Moscow Region, 141980
References
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.
Review
For citations:
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