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

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    Author
    Rohrdanz, Mary A.; Zheng, Wenwei; Lambeth, Bradley; Vreede, Jocelyne; Clementi, Cecilia
    Date
    2014
    Abstract
    The 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.
    Citation
    Rohrdanz, Mary A., Zheng, Wenwei, Lambeth, Bradley, et al.. "Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble." PLoS Computational Biology, 10, no. 10 (2014) Public Library of Science: e1003797. http://dx.doi.org/10.1371/journal.pcbi.1003797.
    Published Version
    http://dx.doi.org/10.1371/journal.pcbi.1003797
    Type
    Journal article
    Publisher
    Public Library of Science
    Citable link to this page
    https://hdl.handle.net/1911/78899
    Rights
    This 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.
    Link to License
    https://creativecommons.org/licenses/by/4.0/
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    • Chemistry Publications [694]
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    Home | FAQ | Contact Us | Privacy Notice | Accessibility Statement
    Managed by the Digital Scholarship Services at Fondren Library, Rice University
    Physical Address: 6100 Main Street, Houston, Texas 77005
    Mailing Address: MS-44, P.O.BOX 1892, Houston, Texas 77251-1892
    Site Map