Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II.

ABSTRACT: Structure-based elastic network models (ENMs) have been remarkably successful in describing conformational transitions in a variety of biological systems. Low-frequency normal modes are usually calculated from the ENM that characterizes elastic interactions between residues in contact in a given protein structure with a uniform force constant. To explore the dynamical effects of nonuniform elastic interactions, we calculate the robustness and coupling of the low-frequency modes in the presence of nonuniform variations in the ENM force constant. The variations in the elastic interactions, approximated here by Gaussian noise, approximately account for perturbation effects of heterogeneous residue-residue interactions or evolutionary sequence changes within a protein family. First-order pertu

SUBMITTER: Zheng W 

PROVIDER: S-EPMC2717279 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature