Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity.

ABSTRACT: Given the three-dimensional structure of a protein, its thermodynamic properties are calculated using a recently introduced distance constraint model (DCM) within a mean-field treatment. The DCM is constructed from a free energy decomposition that partitions microscopic interactions into a variety of constraint types, i.e., covalent bonds, salt-bridges, hydrogen-bonds, and torsional-forces, each associated with an enthalpy and entropy contribution. A Gibbs ensemble of accessible microstates is defined by a set of topologically distinct mechanical frameworks generated by perturbing away from the native constraint topology. The total enthalpy of a given framework is calculated as a linear sum of enthalpy components over all constraints present. Total entropy is generally a nonadditive proper

SUBMITTER: Jacobs DJ 

PROVIDER: S-EPMC1305163 | biostudies-literature | 2005 Feb

REPOSITORIES: biostudies-literature