Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble

dc.citation.firstpagee1003797en_US
dc.citation.issueNumber10en_US
dc.citation.journalTitlePLoS Computational Biologyen_US
dc.citation.volumeNumber10en_US
dc.contributor.authorRohrdanz, Mary A.en_US
dc.contributor.authorZheng, Wenweien_US
dc.contributor.authorLambeth, Bradleyen_US
dc.contributor.authorVreede, Jocelyneen_US
dc.contributor.authorClementi, Ceciliaen_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2015-01-06T19:20:34Zen_US
dc.date.available2015-01-06T19:20:34Zen_US
dc.date.issued2014en_US
dc.description.abstractThe nature of the optical cycle of photoactive yellow protein (PYP) makes its elucidation challenging for both experiment and theory. The long transition times render conventional simulation methods ineffective, and yet the short signaling-state lifetime makes experimental data difficult to obtain and interpret. Here, through an innovative combination of computational methods, a prediction and analysis of the biological signaling state of PYP is presented. Coarse-grained modeling and locally scaled diffusion map are first used to obtain a rough bird's-eye view of the free energy landscape of photo-activated PYP. Then all-atom reconstruction, followed by an enhanced sampling scheme; diffusion map-directed-molecular dynamics are used to focus in on the signaling-state region of configuration space and obtain an ensemble of signaling state structures. To the best of our knowledge, this is the first time an all-atom reconstruction from a coarse grained model has been performed in a relatively unexplored region of molecular configuration space. We compare our signaling state prediction with previous computational and more recent experimental results, and the comparison is favorable, which validates the method presented. This approach provides additional insight to understand the PYP photo cycle, and can be applied to other systems for which more direct methods are impractical.en_US
dc.identifier.citationRohrdanz, Mary A., Zheng, Wenwei, Lambeth, Bradley, et al.. "Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble." <i>PLoS Computational Biology,</i> 10, no. 10 (2014) Public Library of Science: e1003797. http://dx.doi.org/10.1371/journal.pcbi.1003797.en_US
dc.identifier.doihttp://dx.doi.org/10.1371/journal.pcbi.1003797en_US
dc.identifier.urihttps://hdl.handle.net/1911/78899en_US
dc.language.isoengen_US
dc.publisherPublic Library of Scienceen_US
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titleMultiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensembleen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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