Title
MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory
UMMS Affiliation
RNA Therapeutics Institute; Department of Biochemistry and Molecular Pharmacology
Publication Date
2016-01-08
Document Type
Article
Disciplines
Bioinformatics | Computational Biology | Molecular Biology | Structural Biology
Abstract
Easy-to-use macromolecular viewers, such as UCSF Chimera, are a standard tool in structural biology. They allow rendering and performing geometric operations on large complexes, such as viruses and ribosomes. Dynamical simulation codes enable modeling of conformational changes, but may require considerable time and many CPUs. There is an unmet demand from structural and molecular biologists for software in the middle ground, which would allow visualization combined with quick and interactive modeling of conformational changes, even of large complexes. This motivates MMB-GUI. MMB uses an internal-coordinate, multiscale approach, yielding as much as a 2000-fold speedup over conventional simulation methods. We use Chimera as an interactive graphical interface to control MMB. We show how this can be used for morphing of macromolecules that can be heterogeneous in biopolymer type, sequence, and chain count, accurately recapitulating structural intermediates. We use MMB-GUI to create a possible trajectory of EF-G mediated gate-passing translocation in the ribosome, with all-atom structures. This shows that the GUI makes modeling of large macromolecules accessible to a wide audience. The morph highlights similarities in tRNA conformational changes as tRNA translocates from A to P and from P to E sites and suggests that tRNA flexibility is critical for translocation completion.
Rights and Permissions
Copyright © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
DOI of Published Version
10.1093/nar/gkv1457
Source
Nucleic Acids Res. 2016 Jan 8;44(1):95-105. doi: 10.1093/nar/gkv1457. Epub 2015 Dec 15. Link to article on publisher's site
Journal/Book/Conference Title
Nucleic acids research
Related Resources
PubMed ID
26673695
Repository Citation
Tek A, Korostelev AA, Flores SC. (2016). MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory. Open Access Publications by UMass Chan Authors. https://doi.org/10.1093/nar/gkv1457. Retrieved from https://escholarship.umassmed.edu/oapubs/2643
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Bioinformatics Commons, Computational Biology Commons, Molecular Biology Commons, Structural Biology Commons