Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of, Bioinformatics and Computational Biology, Baker Center for Bioinformatics and Biological Statistics
Journal or Book Title
Journal of Chemical Theory and Computation
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 highresolution 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 showing only a slightly higher correlation (0.61) with the experimental temperature factors from crystallography than the results of the residue-level coarse-graining. The qualitative behavior of each level of coarse graining is similar at different cutoff values. The correlations between these fluctuations and the number of internal contacts improve with increased cutoff values. Our results demonstrate that atomic level elastic network models provide an improved representation for the collective motions of proteins compared to the coarse-grained models.
American Chemical Society
Sen, Taner Z.; Feng, Yaping; Garcia, John V.; Kloczkowski, Andrzej; and Jernigan, Robert L., "The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models" (2006). Biochemistry, Biophysics and Molecular Biology Publications. 302.