Coupled folding and binding with 2D Window-Exchange Umbrella Sampling.

ABSTRACT: Intrinsically disordered regions of proteins can gain structure by binding to a partner. This process, of coupled folding and binding (CFaB), is a fundamental part of many important biological processes. Structure-based models have proven themselves capable of revealing fundamental aspects of how CFaB occurs, however, typical methods to enhance the sampling of these transitions, such as replica exchange, do not adequately sample the transition state region of this extremely rare process. Here, we use a variant of Umbrella Sampling to enforce sampling of the transition states of CFaB of HdeA monomers at neutral pH, an extremely rare process that occurs over timescales ranging from seconds to hours. Using high resolution sampling in the transition state region, we cluster states along the pr

SUBMITTER: Dickson A 

PROVIDER: S-EPMC4744578 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature