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    Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data

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    Author
    Devaurs, Didier; Antunes, Dinler A.; Kavraki, Lydia E.
    Date
    2018
    Abstract
    Both experimental and computational methods are available to gather information about a protein's conformational space and interpret changes in protein structure. However, experimentally observing and computationally modeling large proteins remain critical challenges for structural biology. Our work aims at addressing these challenges by combining computational and experimental techniques relying on each other to overcome their respective limitations. Indeed, despite its advantages, an experimental technique such as hydrogen-exchange monitoring cannot produce structural models because of its low resolution. Additionally, the computational methods that can generate such models suffer from the curse of dimensionality when applied to large proteins. Adopting a common solution to this issue, we have recently proposed a framework in which our computational method for protein conformational sampling is biased by experimental hydrogen-exchange data. In this paper, we present our latest application of this computational framework: generating an atomic-resolution structural model for an unknown protein state. For that, starting from an available protein structure, we explore the conformational space of this protein, using hydrogen-exchange data on this unknown state as a guide. We have successfully used our computational framework to generate models for three proteins of increasing size, the biggest one undergoing large-scale conformational changes.
    Citation
    Devaurs, Didier, Antunes, Dinler A. and Kavraki, Lydia E.. "Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data." International Journal of Molecular Sciences, 19, no. 11 (2018) MDPI: https://doi.org/10.3390/ijms19113406.
    Published Version
    https://doi.org/10.3390/ijms19113406
    Keyword
    hydrogen exchange; mass spectrometry; nuclear magnetic resonance; protein conformational sampling; protein structure
    Type
    Journal article
    Publisher
    MDPI
    Citable link to this page
    https://hdl.handle.net/1911/104979
    Rights
    This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
    Link to License
    https://creativecommons.org/licenses/by/4.0/
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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