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Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):237-42. doi: 10.1073/pnas.1302823110. Epub 2013 Dec 20.

Protein structural ensembles are revealed by redefining X-ray electron density noise.

Author information

1
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.

Abstract

To increase the power of X-ray crystallography to determine not only the structures but also the motions of biomolecules, we developed methods to address two classic crystallographic problems: putting electron density maps on the absolute scale of e(-)/Å(3) and calculating the noise at every point in the map. We find that noise varies with position and is often six to eight times lower than thresholds currently used in model building. Analyzing the rescaled electron density maps from 485 representative proteins revealed unmodeled conformations above the estimated noise for 45% of side chains and a previously hidden, low-occupancy inhibitor of HIV capsid protein. Comparing the electron density maps in the free and nucleotide-bound structures of three human protein kinases suggested that substrate binding perturbs distinct intrinsic allosteric networks that link the active site to surfaces that recognize regulatory proteins. These results illustrate general approaches to identify and analyze alternative conformations, low-occupancy small molecules, solvent distributions, communication pathways, and protein motions.

KEYWORDS:

Ringer; electron number density; molecular motions; protein dynamics; refinement against perturbed input data

PMID:
24363322
PMCID:
PMC3890839
DOI:
10.1073/pnas.1302823110
[Indexed for MEDLINE]
Free PMC Article
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