Delineating Protein-Protein Curvilinear Dissociation Pathways and Energetics with Naïve Multiple-Walker Umbrella Sampling Simulations.

Abstract

The protein-protein interaction energetics can be obtained by calculating the potential of mean force (PMF) from umbrella sampling (US) simulations, in which samplings are often enhanced along a predefined vector as the reaction coordinate. However, any slight change in the vector may significantly vary the calculated PMF, and therefore the energetics using a random choice of vector may mislead. A non-predefined curve path-based sampling enhancement approach is a natural alternative, but was relatively less explored for protein-protein systems. In this work, dissociation of the barnase-barstar complex is simulated by implementing non-predefined curvilinear pathways in US simulations. A simple variational principle is applied to determine the lower bound PMF, which could be used to derive the standard free energy of binding. Two major dissociation pathways, which include interactions with the RNA-binding loop and the Val 36 to Gly 40 loop, are observed. Further, the proposed approach was used to discriminate the decoys from protein-protein docking studies. © 2019 Wiley Periodicals, Inc.