Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method

A global potential energy surface has been constructed through interpolation of our recently developed reaction path potential for chemical reactions in enzymes which is derived from combined ab initio quantum mechanical and molecular mechanical calculations. It has been implemented for the activated molecular dynamics simulations of the initial proton transfer reaction catalyzed by triosephosphate isomerase. To examine the dynamical effects on the rate constants of the enzymatic reaction, the classical transmission coefficient $\mathrm{\kappa (t)}$ is evaluated to be 0.47 with the reactive flux approach, demonstrating considerable deviations from transition state theory. In addition, the fluctuations of protein environments have small effects on the barrier recrossing, and the transmission coefficient $\mathrm{\kappa (t)}$ strongly depends on the fluctuations of atoms near the active site of the enzyme.