QM/MM study of the enzymatic catalysis

Abstract

Enzyme catalysis generally includes multiple physical and chemical processes, such as the substrate transportion and binding to the active site, the chemical reaction in the protein confined environment, and the product release, where any chemical or nonchemical step is probably to dominate the activity of enzyme. In order to understand the enzymatic efficiency, the classical molecular dynamics (MM MD) and combined quantum and classical molecular dynamics (QM/MM MD) simulations, in combination with the umbrella sampling, have been used to explore mechanisms for the enzymatic catalysis and the substrate transportion in several biological systems, including the detoxification of the G-type nerve agent sarin by phosphotriesterase (PTE), the hydrolysis of uridine by the pyrimidine-specific nucleoside hydrolase Yeik (CU-NH), and the transportation of naphthalimide-polyamine compounds into the drug sites by the bovine serum albumin (BSA). Extensive QM/MM MD and MM MD simulations show that the wild-type PTE enzyme is capable of hydrolyzing sarin but with a low catalytic efficiency. Dissociation of the degraded product from the binuclear zinc center is predicted to be the rate-determining step with the free-energy barrier of 21.0 kcal/mol, and the multiple chemical steps are involved in the dissociation process. The P-F cleavage of the substrate sarin follows a two-step mechanism, in which the nucleophilic attack of the bridging hydroxide leads to the P-Oµ formation with the free-energy barrier of 9.8 kcal/mol, and the subsequent P-F cleavage and the proton transfer from the µ-OH to the residue Asp301 yields the degraded product with the free-energy span of 12.3 kcal/mol. The relatively strong hydrogen-bond interactions between the substrate uridine and key residues in the active site of CU-NH play an important role in the substrate specificity. The enzymatic N -glycosidic bond cleavage of uridine by CU-NH is the rate-limiting step with the free energy barrier of about 20 kcal/mol, and the substrate protonation less influences the activity of CU-NH, completely different from other nucleoside hydrolases. The combined random acceleration molecular dynamics and MD simulations (RAMD MD) have been used to explore possible transportation channels and the most favorable pathways for the delivery of the naphthalimide-polyamine complex to two drug sites of BSA, as well as their thermodynamic and dynamic properties. MM MD and RAMD MD simulations show that the selective specificity of these two drug sites strongly depends on the electron-withdrawing and electron-donating substituents of the substrate, which can be used for the design of new naphthalimide drugs. Such site-selectivity-dependence design strategy may open up an avenue in drug discovery. With the fast development of low-scaling QM methodologies and the application of artificial intelligence neural network approaches to theoretical and computational chemistry, it can be expected to reduce the computational costs of QM treatment and improve the efficiency of QM/MM, which makes the direct QM/MM study of larger and more complex systems become possible. In addition, the improvement and development of coarse-grained models can surmount the spatial and temporal limitation of multiscale calculations and simulations. Accordingly, global simulations of extremely large and complicated biosystems can be realized in the future, which may provide a theoretical basis for further expanding the application of enzyme engineering.