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Equilibrium sampling approach to the interpretation of electron density maps


Vitalis, Andreas; Caflisch, Amedeo (2014). Equilibrium sampling approach to the interpretation of electron density maps. Structure, 22(1):156-167.

Abstract

The derivation of molecular models from spatial density data generated by X-ray crystallography or electron microscopy is an active field of research. Here, we introduce and evaluate an approach relying on the equilibrium sampling of energy landscapes describing restraints to experimental input data. Our procedure combines density restraints with replica exchange methodologies in the parameter space of the restraints, and we demonstrate its applicability to both flexible polymers and the assembly of protein complexes from rigid components. For the most difficult system studied, we highlight the importance of advanced data analysis techniques in mining poorly converged data further. Successful and unbiased interpretation of input density maps is a prerequisite for using this approach as an auxiliary restraint term in molecular simulations. Because these simulations will also utilize physical interaction potentials, we hope that they will contribute to deriving families of structural models for input data that are ambiguous per se.

Abstract

The derivation of molecular models from spatial density data generated by X-ray crystallography or electron microscopy is an active field of research. Here, we introduce and evaluate an approach relying on the equilibrium sampling of energy landscapes describing restraints to experimental input data. Our procedure combines density restraints with replica exchange methodologies in the parameter space of the restraints, and we demonstrate its applicability to both flexible polymers and the assembly of protein complexes from rigid components. For the most difficult system studied, we highlight the importance of advanced data analysis techniques in mining poorly converged data further. Successful and unbiased interpretation of input density maps is a prerequisite for using this approach as an auxiliary restraint term in molecular simulations. Because these simulations will also utilize physical interaction potentials, we hope that they will contribute to deriving families of structural models for input data that are ambiguous per se.

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3 citations in Web of Science®
2 citations in Scopus®
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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Department of Biochemistry
07 Faculty of Science > Department of Biochemistry
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:2014
Deposited On:02 Jul 2014 14:07
Last Modified:05 Apr 2016 17:56
Publisher:Cell Press (Elsevier)
ISSN:0969-2126
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1016/j.str.2013.10.014
PubMed ID:24316403

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