Computational study of the dimethylphosphate hydrolysis as thereference system for the understanding of the restrictionendonucleases mechanism

Understanding enzymatic mechanisms is essential knowledge for further medicine and biotechnology development. Our long-standing effort is aimed at the explanation of the reaction mechanism of endonucleases (enzymes cleaving DNA chain(s)) using computational approaches. According to the published experimental and theoretical results, the suggested mechanism is SN2 hydrolysis of the phosphate backbone. [1] Presented work is focused on the study of simplified model of the enzymatic reaction. This model consists of dimethylphosphate and the nucleophile (water, hydroxyl ion) attacking the phosphodiester bond. The hydrolysis was simulated using Car Parrinello Molecular Dynamics (CPMD) [2] in vacuum and in water. The reaction free energy profiles were evaluated using metadynamics [3] and obtained results were compared to the experimental data [4]. The model serves as a reference system for the upcoming simulation of the enzymatic reactions.