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    Exploring the free energy landscape of nucleosome assembly

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    Author
    Zhang, B.; Zheng, W.; Papoian, G.A.; Wolynes, P.G.
    Date
    2016
    Abstract
    The nucleosome is the fundamental unit for packaging the genome. A detailed molecular picture for its conformational dynamics is crucial for understanding transcription and gene regulation. We investigate the disassembly of single nucleosomes using a predictive coarse-grained protein DNA model with transferable force fields. This model quantitatively describes the thermodynamic stability of both the histone core complex and the nucleosome and predicts rates of transient nucleosome opening that match experimental measurements. Quantitative characterization of the free-energy landscapes reveals the mechanism of nucleosome unfolding in which DNA unwinding and histone protein disassembly are coupled. The interfaces between H2A-H2B dimers and the (H3-H4)2 tetramer are first lost when the nucleosome opens releasing a large fraction but not all of its bound DNA. For the short strands studied in single molecule experiments, the DNA unwinds asymmetrically from the histone proteins, with only one of its two ends preferentially exposed. The detailed molecular mechanism revealed in this work provides a structural basis for interpreting experimental studies of nucleosome unfolding.
    Citation
    Zhang, B., Zheng, W., Papoian, G.A., et al.. "Exploring the free energy landscape of nucleosome assembly." Journal of the American Chemical Society, 138, no. 26 (2016) American Chemical Society: 8126-8133. http://dx.doi.org/10.1021/jacs.6b02893.
    Published Version
    http://dx.doi.org/10.1021/jacs.6b02893
    Type
    Journal article
    Publisher
    American Chemical Society
    Citable link to this page
    https://hdl.handle.net/1911/93967
    Rights
    Article 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.
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    • Chemistry Publications [636]
    • Faculty Publications [4988]
    • Physics and Astronomy Publications [1771]

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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