Molecular Dynamics and Experimental Study of the Structural Behavior of Alcoholdehydrogenase Enzyme on a Graphitic Sorbent Surface: Features of the Orientation of Titrable Amino Acid Residues

Abstract

Identifying characteristic structural conformations of enzymes and proteins, especially key titratable amino acids, could become a mandatory stage of further research in performing natural and computational experiments by varying the pH values, charges, and concentrations of water–salt environments. The authors of this work perform 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. Images are obtained of the adsorption of ADH + NAD on the surface of a graphitic carbon surface during long-term 100 ns dynamic conformational and rotational changes. MD analysis allows the orientation of ADH + NAD enzyme adsorption to be mapped, thereby providing detailed observations of changes in the conformation of proteins in the region of titratable amino acid residues of ADH. An extension of MD modeling is used to consider the mechanism of conformational changes in the ADH + NAD + water/graphitic carbon surface system, along with the orientation adsorption of the protein system and the key titratable amino acids. Finally, data from MD modeling are compared to experimental observations.