Replica exchange simulations of transient encounter complexes in protein-protein association.

ABSTRACT: Recent paramagnetic relaxation enhancement (PRE) studies on several weakly interacting protein complexes have unequivocally demonstrated the existence of transient encounter complexes. Here, we present a computational method to study protein-protein binding by creating equilibrium ensembles that include both specific and nonspecific protein complexes. In a joint analysis of simulation and experiment we explore the physical nature and underlying physicochemical characteristics of encounter complexes involving three protein-protein interactions of the bacterial phosphotransferase system. Replica exchange Monte Carlo simulations using a coarse-grained energy function recover the structures of the specific complexes and produce binding affinities in good agreement with experiment. Together wit

SUBMITTER: Kim YC 

PROVIDER: S-EPMC2529066 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature