Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures

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dc.citation.articleNumber243141en_US
dc.citation.issueNumber24en_US
dc.citation.journalTitleThe Journal of Chemical Physicsen_US
dc.citation.volumeNumber143en_US
dc.contributor.authorLammert, Heikoen_US
dc.contributor.authorNoel, Jeffrey K.en_US
dc.contributor.authorHaglund, Ellinoren_US
dc.contributor.authorSchug, Alexanderen_US
dc.contributor.authorOnuchic, José N.en_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2017-06-05T19:27:05Zen_US
dc.date.available2017-06-05T19:27:05Zen_US
dc.date.issued2015en_US
dc.description.abstractThe diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an essential part of a protein’s functional native state. The dynamics in the native state are controlled by the same funneled energy landscape that guides the entire folding process. SBMs apply the principle of minimal frustration, drawn from energy landscape theory, to construct a funneled folding landscape for a given protein using only information from the native structure. On an energy landscape smoothed by evolution towards minimal frustration, geometrical constraints, imposed by the native structure, control the folding mechanism and shape the native dynamics revealed by the model. Native-state fluctuations can alternatively be estimated directly from the diversity in the set of NMRstructures for a protein. Based on this information, we identify a highly flexible loop in the ribosomal protein S6 and modify the contact map in a SBM to accommodate the inferred dynamics. By taking into account the probable native state dynamics, the experimental transition state is recovered in the model, and the correct order of folding events is restored. Our study highlights how the shared energy landscape connects folding and function by showing that a better description of the native basin improves the prediction of the folding mechanism.en_US
dc.identifier.citationLammert, Heiko, Noel, Jeffrey K., Haglund, Ellinor, et al.. "Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures." <i>The Journal of Chemical Physics,</i> 143, no. 24 (2015) AIP Publishing LLC.: http://dx.doi.org/10.1063/1.4936881.en_US
dc.identifier.doihttp://dx.doi.org/10.1063/1.4936881en_US
dc.identifier.urihttps://hdl.handle.net/1911/94778en_US
dc.language.isoengen_US
dc.publisherAIP Publishing LLC.en_US
dc.rightsArticle is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.en_US
dc.titleConstructing a folding model for protein S6 guided by native fluctuations deduced from NMR structuresen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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