RNA Therapeutics Institute; Department of Biochemistry and Molecular Pharmacology
Bioinformatics | Computational Biology | Molecular Biology | Structural Biology
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.
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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
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
Nucleic acids research
Tek, Alex; Korostelev, Andrei A.; and Flores, Samuel Coulbourn, "MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory" (2016). Open Access Articles. 2643.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.