Dissecting protein architecture with communication blocks and communicating segment pairs.

ABSTRACT:

Background

Proteins adapt to environmental conditions by changing their shape and motions. Characterising protein conformational dynamics is increasingly recognised as necessary to understand how proteins function. Given a conformational ensemble, computational tools are needed to extract in a systematic way pertinent and comprehensive biological information.

Results

Here, we present a method, Communication Mapping (COMMA), to decipher the dynamical architecture of a protein. The method first extracts residue-based dynamic properties from all-atom molecular dynamics simulations. Then, it integrates them in a graph theoretic framework, where it identifies groups of residues or protein regions that mediate short- and long-range communication. COMMA introduces original concepts

SUBMITTER: Karami Y 

PROVIDER: S-EPMC4959365 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature