Change search
ReferencesLink to record
Permanent link

Direct link
MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Univ Massachusetts, Sch Med, Dept Biochem & Mol Pharmacol, RNA Therapeut Inst, 368 Plantat St, Worcester, MA 01605 USA..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
2016 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 44, no 1, 95-105 p.Article in journal (Refereed) PublishedText
Abstract [en]

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.

Place, publisher, year, edition, pages
2016. Vol. 44, no 1, 95-105 p.
National Category
Biochemistry and Molecular Biology
URN: urn:nbn:se:uu:diva-282497DOI: 10.1093/nar/gkv1457ISI: 000371264000016PubMedID: 26673695OAI: diva2:917078
NIH (National Institute of Health), R01 GM106105eSSENCE - An eScience Collaboration
Available from: 2016-04-05 Created: 2016-04-05 Last updated: 2016-04-05Bibliographically approved

Open Access in DiVA

fulltext(5634 kB)92 downloads
File information
File name FULLTEXT01.pdfFile size 5634 kBChecksum SHA-512
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Flores, Samuel Coulbourn
By organisation
Department of Cell and Molecular Biology
In the same journal
Nucleic Acids Research
Biochemistry and Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 92 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 239 hits
ReferencesLink to record
Permanent link

Direct link