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dc.contributor.authorDevaurs, Didier
Antunes, Dinler A.
Papanastasiou, Malvina
Moll, Mark
Ricklin, Daniel
Lambris, John D.
Kavraki, Lydia E.
dc.date.accessioned 2017-05-05T19:00:53Z
dc.date.available 2017-05-05T19:00:53Z
dc.date.issued 2017
dc.identifier.citation Devaurs, Didier, Antunes, Dinler A., Papanastasiou, Malvina, et al.. "Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data." Frontiers in Molecular Biosciences, 4, (2017) Frontiers Media S.A.: https://doi.org/10.3389/fmolb.2017.00013.
dc.identifier.urihttps://hdl.handle.net/1911/94188
dc.description.abstract Monitoring hydrogen/deuterium exchange (HDX) undergone by a protein in solution produces experimental data that translates into valuable information about the protein's structure. Data produced by HDX experiments is often interpreted using a crystal structure of the protein, when available. However, it has been shown that the correspondence between experimental HDX data and crystal structures is often not satisfactory. This creates difficulties when trying to perform a structural analysis of the HDX data. In this paper, we evaluate several strategies to obtain a conformation providing a good fit to the experimental HDX data, which is a premise of an accurate structural analysis. We show that performing molecular dynamics simulations can be inadequate to obtain such conformations, and we propose a novel methodology involving a coarse-grained conformational sampling approach instead. By extensively exploring the intrinsic flexibility of a protein with this approach, we produce a conformational ensemble from which we extract aᅠsingleᅠconformation providing a good fit to the experimental HDX data. We successfully demonstrate the applicability of our method to four small and medium-sized proteins.
dc.language.iso eng
dc.publisher Frontiers Media S.A.
dc.rights This is an open-access article distributed under the terms of theᅠCreative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.title Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data
dc.type Journal article
dc.citation.journalTitle Frontiers in Molecular Biosciences
dc.subject.keywordprotein conformational sampling
coarse-grained conformational sampling
molecular dynamics
experimental data fitting
hydrogen/deuterium exchange
mass spectrometry
nuclear magnetic resonance spectroscopy
X-ray crystallography
dc.citation.volumeNumber 4
dc.type.dcmi Text
dc.identifier.doihttps://doi.org/10.3389/fmolb.2017.00013
dc.identifier.pmcid PMC5344923
dc.identifier.pmid 28344973
dc.type.publication publisher version
dc.citation.articleNumber 13


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