Anharmonic normal mode analysis of elastic network model improves the modeling of atomic fluctuations in protein crystal structures.

ABSTRACT: Protein conformational dynamics, despite its significant anharmonicity, has been widely explored by normal mode analysis (NMA) based on atomic or coarse-grained potential functions. To account for the anharmonic aspects of protein dynamics, this study proposes, and has performed, an anharmonic NMA (ANMA) based on the C(alpha)-only elastic network models, which assume elastic interactions between pairs of residues whose C(alpha) atoms or heavy atoms are within a cutoff distance. The key step of ANMA is to sample an anharmonic potential function along the directions of eigenvectors of the lowest normal modes to determine the mean-squared fluctuations along these directions. ANMA was evaluated based on the modeling of anisotropic displacement parameters (ADPs) from a list of 83 high-resolutio

SUBMITTER: Zheng W 

PROVIDER: S-EPMC2884254 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature