Molecular dynamics and experimental study of structural behavior of alcohol dehydrogenase enzyme on graphitic sorbent surfaces: orientational features of titratable amino acid residues

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.