Campus Units

Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of, Computer Science, Statistics, Bioinformatics and Computational Biology, Baker Center for Bioinformatics and Biological Statistics

Document Type

Article

Publication Version

Accepted Manuscript

Publication Date

2-12-2008

Journal or Book Title

Structure

Volume

16

Issue

2

First Page

321

Last Page

330

DOI

10.1016/j.str.2007.12.011

Abstract

The large number of available HIV-1 protease structures provides a remarkable sampling of conformations of the different conformational states, which can be viewed as direct structural information about its dynamics. After structure matching, we apply principal component analysis (PCA) to obtain the important apparent motions, including bound and unbound structures. There are significant similarities between the first few key motions and the first few low-frequency normal modes calculated from a static representative structure with an elastic network model (ENM), strongly suggesting that the variations among the observed structures and the corresponding conformational changes are facilitated by the low-frequency, global motions intrinsic to the structure. Similarities are also found when the approach is applied to an NMR ensemble, as well as to molecular dynamics (MD) trajectories. Thus, a sufficiently large number of experimental structures can directly provide important information about protein dynamics, but ENM can also provide similar sampling of conformations.

Comments

This is a manuscript of an article published as Yang, Lei, Guang Song, Alicia Carriquiry, and Robert L. Jernigan. "Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes." Structure 16, no. 2 (2008): 321-330. doi: 10.1016/j.str.2007.12.011. Posted with permission.

Copyright Owner

Elsevier Ltd.

Language

en

File Format

application/pdf

Published Version

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