Campus Units

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

Document Type

Article

Publication Version

Accepted Manuscript

Publication Date

8-2017

Journal or Book Title

Proteins: Structure, Function, and Bioinformatics

Volume

85

Issue

8

First Page

1422

Last Page

1434

DOI

10.1002/prot.25302

Abstract

It is known that over half of the proteins encoded by most organisms function as oligomeric complexes. Oligomerization confers structural stability and dynamics changes in proteins. We investigate the effects of oligomerization on protein dynamics and its functional significance for a set of 145 multimeric proteins. Using coarse-grained elastic network models, we inspect the changes in residue fluctuations upon oligomerization and then compare with residue conservation scores to identify the functional significance of these changes. Our study reveals conservation of about ½ of the fluctuations, with ¼ of the residues increasing in their mobilities and ¼ having reduced fluctuations. The residues with dampened fluctuations are evolutionarily more conserved and can serve as orthosteric binding sites, indicating their importance. We also use triosephosphate isomerase as a test case to understand why certain enzymes function only in their oligomeric forms despite the monomer including all required catalytic residues. To this end, we compare the residue communities (groups of residues which are highly correlated in their fluctuations) in the monomeric and dimeric forms of the enzyme. We observe significant changes to the dynamical community architecture of the catalytic core of this enzyme. This relates to its functional mechanism and is seen only in the oligomeric form of the protein, answering why proteins are oligomeric structures.

Comments

This is the peer reviewed version of the following article: Mishra, Sambit Kumar, Kannan Sankar, and Robert L. Jernigan. "Altered dynamics upon oligomerization corresponds to key functional sites." Proteins: Structure, Function, and Bioinformatics 85, no. 8 (2017): 1422-1434, which has been published in final form at doi:10.1002/prot.25302. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.

Copyright Owner

Wiley Periodicals, Inc.

Language

en

File Format

application/pdf

Published Version

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