Method for Identifying Common Features in Reactive Trajectories of a Transition Path Sampling Ensemble.

Abstract

Simulation methods like transition path sampling (TPS) generate an abundance of information buried in the collection of reactive trajectories that they generate. However, only limited use has been made of this information, mainly for the identification of the reaction coordinate. The standard TPS tools have been designed for monitoring the progress of the system from reactants to products. However, the reaction coordinate does not contain all the information regarding the mechanism. In our earlier work, we have used TPS on enzymatic systems and have identified important motions in the reactant well that prepares the system for the reaction. Since these events take place in the reactant well, they are beyond the reach of standard TPS postprocessing methods. We present a simple scheme for identifying the common trends in enzymatic trajectories. This scheme was designed for a specific class of enzymatic reactions: it can be used for identifying motions that guide the system to reaction-ready conformations. We have applied it to two enzymatic systems that we have studied in the past, formate dehydrogenase and purine nucleoside phosphorylase, and we were able to identify interactions, far from the transition state, that are important for preparing the system for the reaction but that had been overlooked in earlier work.