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Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
2014 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 42, no 2, e9- p.Article in journal (Refereed) Published
Abstract [en]

Determining the conformational rearrangements of large macromolecules is challenging experimentally and computationally. Case in point is the ribosome; it has been observed by high-resolution crystallography in several states, but many others are known only from low-resolution methods including cryoelectron microscopy. Combining these data into dynamical trajectories that may aid understanding of its largest-scale conformational changes has so far remained out of reach of computational methods. Most existing methods either model all atoms explicitly, resulting in often prohibitive cost, or use approximations that lose interesting structural and dynamical detail. In this work, I introduce Internal Coordinate Flexible Fitting, which uses full atomic forces and flexibility in limited regions of a model, capturing extensive conformational rearrangements at low cost. I use it to turn multiple low-resolution density maps, crystallographic structures and biochemical information into unified all-atoms trajectories of ribosomal translocation. Internal Coordinate Flexible Fitting is three orders of magnitude faster than the most comparable existing method.

Place, publisher, year, edition, pages
2014. Vol. 42, no 2, e9- p.
National Category
Natural Sciences
URN: urn:nbn:se:uu:diva-221062DOI: 10.1093/nar/gkt906ISI: 000331138100002OAI: oai:DiVA.org:uu-221062DiVA: diva2:708161
Available from: 2014-03-26 Created: 2014-03-25 Last updated: 2014-03-26Bibliographically approved

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Flores, Samuel Coulbourn
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