Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach.

ABSTRACT: In this article, a second-order mean-field-based approach is introduced for characterizing the complete set of residue-residue couplings consistent with a given protein structure. This information is subsequently used to classify protein hybrids with respect to their potential to be functional based on the presenceabsence and severity of clashing residue-residue interactions. First, atomistic representations of both the native and denatured states are used to calculate rotamer-backbone, rotamer-intrinsic, and rotamer-rotamer conformational energies. Next, this complete conformational energy table is coupled with a second-order mean-field description to elucidate the probabilities of all possible rotamer-rotamer combinations in a minimum Helmholtz free-energy ensemble. Computational results

SUBMITTER: Moore GL 

PROVIDER: S-EPMC154303 | biostudies-literature | 2003 Apr

REPOSITORIES: biostudies-literature