Molecular dynamics and experimental study of structural behavior of alcohol dehydrogenase enzyme on graphitic sorbent surfaces: orientational features of titratable amino acid residues
- Authors: Baigunov I.A.1, Gladyshev P.P.1, Kholmurodov K.T.1,2,3, Elhaes H.4, Ibrahim M.5
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Affiliations:
- Dubna State University
- Joint Institute for Nuclear Research
- Lomonosov Moscow State University S. U. Umarov Physical-Technical Institute (PhTI)
- Ain Shams University
- National Research Centre
- Issue: Vol 99, No 3 (2025)
- Pages: 484–498
- Section: БИОФИЗИЧЕСКАЯ ХИМИЯ И ФИЗИКО-ХИМИЧЕСКАЯ БИОЛОГИЯ
- Submitted: 03.06.2025
- Published: 29.05.2025
- URL: https://rjonco.com/0044-4537/article/view/682039
- DOI: https://doi.org/10.31857/S0044453725030147
- EDN: https://elibrary.ru/FNWAJO
- ID: 682039
Cite item
Abstract
The identification of the characteristic structural conformations of enzymes and proteins, especially key titratable amino acids, may become a necessary stage of further research in the implementation of natural and computational experiments, which are carried out by varying the pH values, charges and concentrations of the water-salt environment. In this work, computer molecular dynamics (MD) and experimental studies of the enzyme alcohol dehydrogenase and its cofactor (ADH+NAD) solvated with water on a graphite carbon surface are carried out. The snapshots of the adsorption process of ADH+NAD on the surface of a graphitic carbon surface during long-term 100 nanosecond dynamical conformational and rotational changes are obtained. The MD-analysis provides mapping of the ADH+NAD enzyme orientation adsorption, thereby allowing for the detailed observation of changes in protein conformation in the region of titratable amino acid residues of ADH. Next, based on an extension of the MD-model implementation, the mechanism of conformational changes in the entire system (ADH+NAD + water / graphitic carbon surface), as well as the orientation adsorption of the entire protein system along with key titratable amino acids are considered and the MD simulation data are compared with the experimental observations.
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About the authors
I. A. Baigunov
Dubna State University
Email: kholmirzo@gmail.com
Department of Chemistry, New Technologies and Materials
Russian Federation, Dubna, Moscow Region, 141980P. P. Gladyshev
Dubna State University
Email: kholmirzo@gmail.com
Department of Chemistry, New Technologies and Materials
Russian Federation, Dubna, Moscow Region, 141980Kh. T. Kholmurodov
Dubna State University; Joint Institute for Nuclear Research; Lomonosov Moscow State UniversityS. U. Umarov Physical-Technical Institute (PhTI)
Author for correspondence.
Email: kholmirzo@gmail.com
Department of Chemistry, New Technologies and Materials, Frank Laboratory of Neutron Physics, Faculty of Physics, Department of Fundamental Nuclear Interactions
Russian Federation, Dubna, Moscow Region, 141980; Dubna, Moscow Region, 141980; Moscow, 119991; Dushanbe, 734063, Republic of TajikistanH. Elhaes
Ain Shams University
Email: kholmirzo@gmail.com
Physics Department, Faculty of Women for Arts, Science and Education
Egypt, Cairo, 11757M. Ibrahim
National Research Centre
Email: kholmirzo@gmail.com
Molecular Spectroscopy and Modeling Unit, Spectroscopy Department
Egypt, Dokki, Giza, 12622References
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