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Abstract <p>In this work, computer molecular dynamics and experimental studies of the enzyme alcohol dehydrogenase (ADH) and its cofactor nicotinamide adenine dinucleotide (NAD) solvated with water on a graphite carbon surface were carried out. Computational molecular dynamics (MD) simulations of the (ADH + NAD + water) system were performed to track the adsorption process on the surface of graphitic carbon during long-term 100 ns dynamic conformational and rotational changes. MD analysis provides mapping of the adsorption orientation of the ADH+NAD enzyme, which allows detailed observation of changes in protein conformation in the region of titratable amino acid residues of ADH. Identification of the characteristic conformation of key titratable amino acids may become a necessary stage in further <sup>1</sup>research and implementation of a numerical experiment, which will be carried out by varying the pH and charge values. MD simulation data are compared with experimental observations, which indicate the atomic-molecular mechanism of the influence of solution pH on the conformation and orientation of protein adsorption.</p>

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Arrangement of Catalytic Loops Correlated with Conenzyme Vibrations for Alcoholdehydrogenase Enzyme in Adsorption on a Carbon Surface

  • 期刊论文

  • 发表日期：

    2025年10月1日

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  • Kholmirzo T. Kholmurodov,
  • I. A. Baigunov,
  • P. P. Gladyshev,
  • Mirzo aziz Husenzoda,
  • Hanan Elhaes,
  • Medhat Ibrahim

摘要

Abstract

In this work, computer molecular dynamics and experimental studies of the enzyme alcohol dehydrogenase (ADH) and its cofactor nicotinamide adenine dinucleotide (NAD) solvated with water on a graphite carbon surface were carried out. Computational molecular dynamics (MD) simulations of the (ADH + NAD + water) system were performed to track the adsorption process on the surface of graphitic carbon during long-term 100 ns dynamic conformational and rotational changes. MD analysis provides mapping of the adsorption orientation of the ADH+NAD enzyme, which allows detailed observation of changes in protein conformation in the region of titratable amino acid residues of ADH. Identification of the characteristic conformation of key titratable amino acids may become a necessary stage in further 1research and implementation of a numerical experiment, which will be carried out by varying the pH and charge values. MD simulation data are compared with experimental observations, which indicate the atomic-molecular mechanism of the influence of solution pH on the conformation and orientation of protein adsorption.