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Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta

2009; Elsevier BV; Volume: 392; Issue: 1 Linguagem: Inglês

10.1016/j.jmb.2009.07.008

1089-8638

Frank DiMaio, Michael D. Tyka, Matthew L. Baker, Wah Chiu, David Baker,

Electron and X-Ray Spectroscopy Techniques

We describe a method based on Rosetta structure refinement for generating high-resolution, all-atom protein models from electron cryomicroscopy density maps. A local measure of the fit of a model to the density is used to directly guide structure refinement and to identify regions incompatible with the density that are then targeted for extensive rebuilding. Over a range of test cases using both simulated and experimentally generated data, the method consistently increases the accuracy of starting models generated either by comparative modeling or by hand-tracing the density. The method can achieve near-atomic resolution starting from density maps at 4–6 Å resolution.