Campus Units

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

Document Type

Article

Publication Version

Accepted Manuscript

Publication Date

6-2009

Journal or Book Title

Proteins: Structure, Function, and Bioinformatics

Volume

75

Issue

4

First Page

837

Last Page

845

DOI

10.1002/prot.22292

Abstract

The collective dynamics of the nascent polypeptide exit tunnel are investigated with the computationally efficient elastic network model using normal mode analysis. The calculated normal modes are considered individually and in linear combinations with different coefficients mimicking the phase angles between modes, in order to follow the mechanistic motions of tunnel wall residues. The low frequency fluctuations indicate three distinct regions along the tunnel - the entrance, the neck and the exit – each having distinctly different domain motions. Generally the lining of the entrance region moves in the exit direction, with the exit region having significantly larger motions, but in a perpendicular direction, whereas the confined neck region generally has rotational motions. Especially the universally conserved extensions of ribosomal proteins L4 and L22 located at the narrowest and mechanistically strategic region of tunnel undergo generally anti- or non-correlated motions, which may have an important role in nascent polypeptide gating mechanism. These motions appear to be sufficiently robust so as to be unaffected by the presence of a peptide chain in the tunnel.

Comments

This is the peer reviewed version of the following article: Kurkcuoglu, Ozge, Zeynep Kurkcuoglu, Pemra Doruker, and Robert L. Jernigan. "Collective dynamics of the ribosomal tunnel revealed by elastic network modeling." Proteins: Structure, Function, and Bioinformatics 75, no. 4 (2009): 837-845., which has been published in final form at doi: 10.1002/prot.22292. 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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