Campus Units

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

Document Type

Article

Publication Version

Accepted Manuscript

Publication Date

2-27-2016

Journal or Book Title

Journal of Molecular Biology

Volume

428

Issue

5, Part A

First Page

802

Last Page

810

DOI

10.1016/j.jmb.2015.12.003

Abstract

The essential aspects of the ribosome’s mechanism can be extracted from coarse-grained simulations, including the ratchet motion, the movement together of critical bases at the decoding center, as well as movements of the peptide tunnel lining that assist in the expulsion of the synthesized peptide. Because of its large size, coarse-graining helps to simplify and to aid in the understanding of its mechanism. Results presented here utilize coarse-grained elastic network modeling to extract the dynamics, and both RNAs and proteins are coarse-grained. We review our previous results, showing the well-known ratchet motions and the motions in the peptide tunnel and in the mRNA tunnel. The motions of the lining of the peptide tunnel appear to assist in the expulsion of the growing peptide chain, and clamps at the ends of the mRNA tunnel with three proteins, ensure that the mRNA is held tightly during decoding and essential for the helicase activity at the entrance. The entry clamp may also assist in base recognition to ensure proper selection of the incoming tRNA. The overall precision with which the ribosome operates as a machine is remarkable.

Comments

This is a manuscript of an article published as Zimmermann, Michael T., Kejue Jia, and Robert L. Jernigan. "Ribosome mechanics informs about mechanism." Journal of molecular biology 428, no. 5 (2016): 802-810. doi:10.1016/j.jmb.2015.12.003. Posted with permission.

Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

Copyright Owner

Elsevier Ltd.

Language

en

File Format

application/pdf

Published Version

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