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Structure. 2011 Sep 7;19(9):1211-8. doi: 10.1016/j.str.2011.07.017.

Symmetry-restrained flexible fitting for symmetric EM maps.

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1
Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Abstract

Many large biological macromolecules have inherent structural symmetry, being composed of a few distinct subunits, repeated in a symmetric array. These complexes are often not amenable to traditional high-resolution structural determination methods, but can be imaged in functionally relevant states using cryo-electron microscopy (cryo-EM). A number of methods for fitting atomic-scale structures into cryo-EM maps have been developed, including the molecular dynamics flexible fitting (MDFF) method. However, quality and resolution of the cryo-EM map are the major determinants of a method's success. In order to incorporate knowledge of structural symmetry into the fitting procedure, we developed the symmetry-restrained MDFF method. The new method adds to the cryo-EM map-derived potential further restraints on the allowed conformations of a complex during fitting, thereby improving the quality of the resultant structure. The benefit of using symmetry-based restraints during fitting, particularly for medium to low-resolution data, is demonstrated for three different systems.

PMID:
21893283
PMCID:
PMC3412758
DOI:
10.1016/j.str.2011.07.017
[Indexed for MEDLINE]
Free PMC Article
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