X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals

TitleX-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals
Publication TypeJournal Article
Year of Publication2014
AuthorsKuzmanic, A., N.S. Pannu, B. Zagrovic
JournalNature Communications
Volume5
Date PublishedFeb
ISBN Number2041-1723
Accession NumberWOS:000332664900001
Keywordsb-factors, conformational entropy, flexibility, force-fields, high-resolution, molecular-dynamics simulations, motion, particle mesh ewald, protein crystal, villin headpiece
Abstract

Biomolecular X-ray structures typically provide a static, time- and ensemble-averaged view of molecular ensembles in crystals. In the absence of rigid-body motions and lattice defects, B-factors are thought to accurately reflect the structural heterogeneity of such ensembles. In order to study the effects of averaging on B-factors, we employ molecular dynamics simulations to controllably manipulate microscopic heterogeneity of a crystal containing 216 copies of villin headpiece. Using average structure factors derived from simulation, we analyse how well this heterogeneity is captured by high-resolution molecular-replacement-based model refinement. We find that both isotropic and anisotropic refined B-factors often significantly deviate from their actual values known from simulation: even at high 1.0 angstrom resolution and R-free of 5.9%, B-factors of some well-resolved atoms underestimate their actual values even sixfold. Our results suggest that conformational averaging and inadequate treatment of correlated motion considerably influence estimation of microscopic heterogeneity via B-factors, and invite caution in their interpretation.

DOI10.1038/Ncomms4220
Alternate JournalNat Commun

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