Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES.

ABSTRACT: Large macromolecular assemblies are often important for biological processes in cells. Allosteric communications between different parts of these molecular machines play critical roles in cellular signaling. Although studies of the topology and fluctuation dynamics of coarse-grained residue networks can yield important insights, they do not provide characterization of the time-dependent dynamic behavior of these macromolecular assemblies. Here we develop a novel approach called Perturbation-based Markovian Transmission (PMT) model to study globally the dynamic responses of the macromolecular assemblies. By monitoring simultaneous responses of all residues (>8,000) across many (>6) decades of time spanning from the initial perturbation until reaching equilibrium using a Krylov subspace proj

SUBMITTER: Lu HM 

PROVIDER: S-EPMC2741606 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature