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

2006

Journal or Book Title

Biochemistry

Volume

45

Issue

4

First Page

1173

Last Page

1182

DOI

10.1021/bi0518085

Abstract

The internal dynamics of triosephosphate isomerase have been investigated with elastic networks, with and without a substrate bound. The slowest modes of motion involve large domain motions but also a loop motion that conforms to the changes observed between the crystal structures 8TIM and 1TPH. Our computations confirm that the different motions of this loop are important in several of the computed slowest modes. We have shown that elastic network computations on this protein system can combine atoms for the functional parts of the structure with coarse-grained (cg) representations of the remainder of the structure in several different ways. Similar loop motions are seen with elastic network models for atomistic and mixed cg models. The loop motions are reproduced with an overlap of 0.75–0.79 by combining the four slowest modes of motion for the free and complex forms of the enzyme.

Comments

This is a manuscript of an article published as Kurkcuoglu, Ozge, Robert L. Jernigan, and Pemra Doruker. "Loop motions of triosephosphate isomerase observed with elastic networks." Biochemistry 45, no. 4 (2006): 1173-1182. doi:10.1021/bi0518085. Posted with permission.

Copyright Owner

American Chemical Society

Language

en

File Format

application/pdf

Published Version

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