Diversity of function-related conformational changes in proteins: coordinate uncertainty, fragment rigidity, and stability.

ABSTRACT: It was found that the variety of function-related conformational changes ("movements") in proteins is beyond the earlier simple classifications. Here we offer biochemists a more comprehensive, transparent, and easy-to-use approach allowing a detailed and accurate interpretation of such conformational changes. It makes possible a more multifaceted characterization of protein flexibility via identification of rigidly and nonrigidly repositioned fragments, stable and nonstable fragments, and domain and nondomain repositioning. "Coordinate uncertainty thresholds" derived from computed differences between independently determined coordinates of the same molecules are used as the criteria for conformational identity. "Identical" rigid substructures are localized in the distance difference matric

SUBMITTER: Rashin AA 

PROVIDER: S-EPMC2978001 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature