Computing the relative stabilities and the per-residue components in protein conformational changes.

ABSTRACT: Protein molecules often undergo conformational changes. In order to gain insights into the forces that drive such changes, it would be useful to have a method that computes the per-residue contributions to the conversion free energy. Here, we describe the "confine-convert-release" (CCR) method, which is applicable to large conformational changes. We show that CCR correctly predicts the stable states of several "chameleon" sequences that have previously been challenging for molecular simulations. CCR can often discriminate better from worse predictions of native protein models in critical assessment of protein structure prediction (CASP). We show how the total conversion free energies can be parsed into per-residue free-energy components. Such parsing gives insights into which amino acids a

SUBMITTER: Roy A 

PROVIDER: S-EPMC3905753 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature