The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models.

ABSTRACT: Coarse-grained elastic network models have been successful in determining functionally relevant collective motions. The level of coarse-graining, however, has usually focused on the level of one point per residue. In this work, we compare the applicability of elastic network models over a broader range of representational scales. We apply normal mode analysis for multiple scales on a high-resolution protein data set using various cutoff radii to define the residues considered to be interacting, or the extent of cooperativity of their motions. These scales include the residue-, atomic-, proton-, and explicit solvent-levels. Interestingly, atomic, proton, and explicit solvent level calculations all provide similar results at the same cutoff value, with the computed mean-square fluctuations s

SUBMITTER: Sen TZ 

PROVIDER: S-EPMC1948848 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature