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Finding rigid bodies in protein structures: application to flexible fitting into cryoEM maps

Pandurangan, Arun and Topf, Maya (2012) Finding rigid bodies in protein structures: application to flexible fitting into cryoEM maps. Journal of Structural Biology 177 (2), pp. 520-531. ISSN 1047-8477.

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Official URL: http://dx.doi.org/10.1016/j.jsb.2011.10.011

Abstract

We present RIBFIND, a method for detecting flexibility in protein structures via the clustering of secondary structural elements (SSEs) into rigid bodies. To test the usefulness of the method in refining atomic structures within cryoEM density we incorporated it into our flexible fitting protocol (Flex-EM). Our benchmark includes 13 pairs of protein structures in two conformations each, one of which is represented by a corresponding cryoEM map. Refining the structures in simulated and experimental maps at the 5-15 Å resolution range using rigid bodies identified by RIBFIND shows a significant improvement over using individual SSEs as rigid bodies. For the 15 Å resolution simulated maps, using RIBFIND-based rigid bodies improves the initial fits by 40.64% on average, as compared to 26.52% when using individual SSEs. Furthermore, for some test cases we show that at the sub-nanometer resolution range the fits can be further improved by applying a two-stage refinement protocol (using RIBFIND-based refinement followed by an SSE-based refinement). The method is stand-alone and could serve as a general interactive tool for guiding flexible fitting into EM maps.

Item Type: Article
Keyword(s) / Subject(s): Flexible fitting, rigid bodies, clustering, optimisation, low-resolution maps, cryo electron microscopy density fitting
School or Research Centre: Birkbeck Schools and Research Centres > School of Science > Biological Sciences
Depositing User: Administrator
Date Deposited: 09 Nov 2011 09:25
Last Modified: 17 Apr 2013 12:21
URI: http://eprints.bbk.ac.uk/id/eprint/4270

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