Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins.

ABSTRACT: Proteins have often evolved sequences so as to acquire the ability for regulation via allosteric conformational change. Here we investigate how allosteric dynamics is designed through sequences with nonlinear interaction features. First, for 71 allosteric proteins of which two, open and closed, structures are available, a statistical survey of interactions using an all-atom model with effective solvation shows that those residue contact interactions specific to one of the two states are significantly weaker than are the contact interactions shared by the two states. This interaction feature indicates there is underlying sequence design to facilitate conformational change. Second, based on the energy landscape theory, we implement these interaction features into a new atomic-interaction-bas

SUBMITTER: Li W 

PROVIDER: S-EPMC3048140 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature