Campus Units

Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of, Computer Science, Bioinformatics and Computational Biology

Document Type

Article

Publication Version

Accepted Manuscript

Publication Date

7-2009

Journal or Book Title

Proteins: Structure, Function, and Bioinformatics

Volume

76

Issue

1

First Page

164

Last Page

175

DOI

10.1002/prot.22328

Abstract

Because of its appealing simplicity, the anisotropic network model (ANM) has been widely accepted and applied to study many molecular motion problems: such as ribosome motions, the molecular mechanisms of GroEL-GroES function, allosteric changes in hemoglobin, motor-protein motions, and conformational changes in general. However, the validity of the ANM has not been closely examined. In this work, we use ANM to predict the anisotropic temperature factors of proteins obtained from X-ray and NMR data. The rich, directional anisotropic temperature factor data available for hundreds of proteins in the Protein Data Bank (PDB) are used as validation data to closely test the ANM model. The significance of this work is that it presents a timely, important evaluation of the model, shows the extent of its accuracy in reproducing experimental anisotropic temperature factors, and suggests ways to improve the model. An improved model will help us better understand the internal dynamics of proteins, which in turn can greatly expand the usefulness of the models, which has already been demonstrated in many applications.

Comments

This is the peer reviewed version of the following article: Yang, Lei, Guang Song, and Robert L. Jernigan. "Comparisons of experimental and computed protein anisotropic temperature factors." Proteins: Structure, Function, and Bioinformatics 76, no. 1 (2009): 164-175, which has been published in final form at doi: 10.1002/prot.22328. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.

Copyright Owner

Wiley-Liss, Inc.

Language

en

File Format

application/pdf

Published Version

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