Work

Unusual Arrangement of Catalytic Loops of the Alcohol Dehydrogenase Enzyme During the Adsorption Process on a Graphitic Carbon Surface

Year: 2025

Type: article

Abstract: Molecular dynamics simulations (MDs) were conducted to investigate the alcohol dehydrogenase (ADH) enzyme and its cofactor, nicotinamide adenine dinucleotide (NAD), solvated in an aqueous system on a graphite-carbon surface. The study focuses on key structural aspects of ADH, particularly its conformational changes, including the rotation of the catalytic domain, the coenzyme binding domain, and the rearrangement of the active center required for catalytic activation. MDs were performed for 100 ns to track the conformational and rotational changes of the ADH+NAD complex in an aqueous environment. The diffusion process of ADH+NAD was observed for approximately 50–60 ns, after which the complex made contact with the graphite surface, leading to final relaxation. Upon adsorption of ADH onto the carbon surface, NAD exhibited fluctuations between 55 and 60 ns, coinciding with the opening of two catalytic loops associated with the NAD-binding region. Experimental and kinetic studies suggest that these structural changes may significantly impact the enzymatic activity of ADH in the presence of a carbon surface.

Source: Molecular Modeling Connect

DOI: 10.69709/molmodc.2025.101003

Authors: Kholmirzo T. Kholmurodov, Ivan A. Baigunov, Pavel P. Gladyshev, Mirzoaziz A. Husenzoda, Hanan G. Elhaes, Medhat A. Ibrahim