Coarse-grained free energy functions for studying protein conformational changes: a double-well network model.

ABSTRACT: In this work, a double-well network model (DWNM) is presented for generating a coarse-grained free energy function that can be used to study the transition between reference conformational states of a protein molecule. Compared to earlier work that uses a single, multidimensional double-well potential to connect two conformational states, the DWNM uses a set of interconnected double-well potentials for this purpose. The DWNM free energy function has multiple intermediate states and saddle points, and is hence a "rough" free energy landscape. In this implementation of the DWNM, the free energy function is reduced to an elastic-network model representation near the two reference states. The effects of free energy function roughness on the reaction pathways of protein conformational change is

SUBMITTER: Chu JW 

PROVIDER: S-EPMC2084241 | biostudies-literature | 2007 Dec

REPOSITORIES: biostudies-literature