Active site dynamics in protein molecules: A stochastic boundary molecular‐dynamics approach

Abstract The stochastic boundary molecular‐dynamics approach for studying chemical events in liquids is extended to proteins. A method for simulating the localized dynamics of a portion of a protein is developed and illustrated by an application to the bovine pancreatic trypsin inhibitor (BPTI). The dynamics of the aromatic ring atoms of Tyr 21 of BPTI are targeted as the “active site,” and the results from several different localized models are compared with those from a simulation of the entire molecule. The most consistent results are obtained with a model that consists of a buffer region composed of harmonically constrained Langevin atoms surrounding the active site region whose atoms are treated by molecular dynamics. Possible applications of the model are discussed.