Quantum dynamics of proton transfer processes in enzymatic reactions. Simulations of phospholipase A2

Abstract

AbstractFor the past few years we have been developing a theoretical model capable of describing quantum dynamical processes which occur in molecular systems and in enzymatic active sites. This, in particular, includes proton transfer processes.Our most advanced studies have been performed for phospholipase A2, an enzyme which hydrolyzes phospholipids. The potential energy function for the active site is computed using an Approximate Valence Bond (AVB) method. The dynamics of the key proton in the enzyme's active site is described either by the classical molecular dynamics (MD/AVB model) or by the time‐dependent Schroedinger equation. The dynamics of the remaining atoms of the enzyme are described using classical MD. The coupling between the quantum proton and the classical atoms is accomplished via Hellmann‐Feynman forces, as well as the time‐dependence of the potential energy function in the Schroedinger equation (QCMD/AVB model).The quantum proton transfer from the water molecule to histidine is followed by a nucleophilic attack of the created OH− group. The processes are simulated using the parallelized QCMD code.