Coarse-grained simulations of protein-protein association: an energy landscape perspective.

ABSTRACT: Understanding protein-protein association is crucial in revealing the molecular basis of many biological processes. Here, we describe a theoretical simulation pipeline to study protein-protein association from an energy landscape perspective. First, a coarse-grained model is implemented and its applications are demonstrated via molecular dynamics simulations for several protein complexes. Second, an enhanced search method is used to efficiently sample a broad range of protein conformations. Third, multiple conformations are identified and clustered from simulation data and further projected on a three-dimensional globe specifying protein orientations and interacting energies. Results from several complexes indicate that the crystal-like conformation is favorable on the energy landscape eve

SUBMITTER: Ravikumar KM 

PROVIDER: S-EPMC3443792 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature