Campus Units

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

Document Type

Article

Publication Version

Submitted Manuscript

Publication Date

1-27-2018

Journal or Book Title

The Journal of Physical Chemistry B

Volume

122

Issue

21

First Page

5409

Last Page

5417

DOI

10.1021/acs.jpcb.7b11668

Abstract

Predicting protein motions is important for bridging the gap between protein structure and function. With growing numbers of structures of the same, or closely related proteins becoming available, it is now possible to understand more about the intrinsic dynamics of a protein with principal component analysis (PCA) of the motions apparent within ensembles of experimental structures. In this paper, we compare the motions extracted from experimental ensembles of 50 different proteins with the modes of motion predicted by several types of coarse-grained elastic network models (ENMs) which additionally take into account more details of either the protein geometry or the amino acid specificity. We further compare the structural variations in the experimental ensembles with the motions sampled in molecular dynamics (MD) simulations for a smaller subset of 17 proteins with available trajectories. We find that the correlations between the motions extracted from MD trajectories and experimental structure ensembles are slightly different than for the ENMs, possibly reflecting potential sampling biases. We find that there are small gains in the predictive power of the ENMs in reproducing motions present in either experimental or MD ensembles by accounting for the protein geometry rather than the amino acid specificity of the interactions.

Comments

This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in The Journal of Physical Chemistry B, copyright © American Chemical Society after peer review. To access the final edited and published work see doi: 10.1021/acs.jpcb.7b11668.

Copyright Owner

American Chemical Society

Language

en

File Format

application/pdf

Published Version

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