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Originally published as Biophys J. BioFAST on August 4, 2006.
doi:10.1529/biophysj.106.085894
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Biophysical Journal 91:2760-2767 (2006)
© 2006 The Biophysical Society

Optimization and Evaluation of a Coarse-Grained Model of Protein Motion Using X-Ray Crystal Data

Dmitry A. Kondrashov *, Qiang Cui {dagger} and George N. Phillips, Jr. {dagger} {ddagger}

* Department of Biochemistry, {dagger} Department of Chemistry and Theoretical Chemistry Institute, and {ddagger} Departments of Biochemistry and Computer Science, University of Wisconsin-Madison, Madison, Wisconsin

Correspondence: Address reprint requests to George N. Phillips, Tel.: 608-263-6142; E-mail: phillips{at}biochem.wisc.edu.

Simple coarse-grained models, such as the Gaussian network model, have been shown to capture some of the features of equilibrium protein dynamics. We extend this model by using atomic contacts to define residue interactions and introducing more than one interaction parameter between residues. We use B-factors from 98 ultra-high resolution (≤1.0 Å) x-ray crystal structures to optimize the interaction parameters. The average correlation between Gaussian network-model fluctuation predictions and the B-factors is 0.64 for the data set, consistent with a previous large-scale study. By separating residue interactions into covalent and noncovalent, we achieve an average correlation of 0.74, and addition of ligands and cofactors further improves the correlation to 0.75. However, further separating the noncovalent interactions into nonpolar, polar, and mixed yields no significant improvement. The addition of simple chemical information results in better prediction quality without increasing the size of the coarse-grained model.




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