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Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution.


ABSTRACT: Structural studies of large proteins and protein assemblies are a difficult and pressing challenge in molecular biology. Experiments often yield only low-resolution or sparse data that are not sufficient to fully determine atomistic structures. We have developed a general geometry-based algorithm that efficiently samples conformational space under constraints imposed by low-resolution density maps obtained from electron microscopy or X-ray crystallography experiments. A deformable elastic network (DEN) is used to restrain the sampling to prior knowledge of an approximate structure. The DEN restraints dramatically reduce over-fitting, especially at low resolution. Cross-validation is used to optimally weight the structural information and experimental data. Our algorithm is robust even for noise-added density maps and has a large radius of convergence for our test case. The DEN restraints can also be used to enhance reciprocal space simulated annealing refinement.

SUBMITTER: Schroder GF 

PROVIDER: S-EPMC2213367 | biostudies-literature | 2007 Dec

REPOSITORIES: biostudies-literature

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Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolution.

Schröder Gunnar F GF   Brunger Axel T AT   Levitt Michael M  

Structure (London, England : 1993) 20071201 12


Structural studies of large proteins and protein assemblies are a difficult and pressing challenge in molecular biology. Experiments often yield only low-resolution or sparse data that are not sufficient to fully determine atomistic structures. We have developed a general geometry-based algorithm that efficiently samples conformational space under constraints imposed by low-resolution density maps obtained from electron microscopy or X-ray crystallography experiments. A deformable elastic networ  ...[more]

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