Probing the flexibility of large conformational changes in protein structures through local perturbations.

ABSTRACT: Protein conformational changes and dynamic behavior are fundamental for such processes as catalysis, regulation, and substrate recognition. Although protein dynamics have been successfully explored in computer simulation, there is an intermediate-scale of motions that has proven difficult to simulate - the motion of individual segments or domains that move independently of the body the protein. Here, we introduce a molecular-dynamics perturbation method, the Rotamerically Induced Perturbation (RIP), which can generate large, coherent motions of structural elements in picoseconds by applying large torsional perturbations to individual sidechains. Despite the large-scale motions, secondary structure elements remain intact without the need for applying backbone positional restraints. Owing to

SUBMITTER: Ho BK 

PROVIDER: S-EPMC2660149 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature