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    Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly

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    Park_2014.pdf (1.104Mb)
    Issue Date
    2013
    Author
    Park, Soohyung
    Im, Wonpil
    Publisher
    American Chemical Society
    Type
    Article
    Article Version
    Scholarly/refereed, author accepted manuscript
    Rights
    This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1021/ct3008556.
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    Abstract
    The method of window exchange umbrella sampling molecular dynamics (WEUSMD) with a pre-optimized parameter set was recently used to obtain the most probable conformations and the energetics of transmembrane (TM) helix assembly of a generic TM sequence. When applied to glycophorin A TM domain (GpA-TM) using the restraint potentials along the helix-helix distance, however, tight interfacial packing of GpA-TM resulted in insufficient conformational sampling at short helix-helix separation. This sampling issue is addressed by extending the WEUSMD into two dimensions with the restraint potentials along the helix-helix distance and crossing angle. The two-dimensional WEUSMD results demonstrate that the incomplete sampling in the one-dimensional WEUSMD arises from high barriers along the crossing angle between the GpA-TM helices. Together with the faster convergence in both the assembled conformations and the potential of mean force, the 2D-WEUSMD can be a general and efficient approach in computational studies of TM helix assembly.
    URI
    http://hdl.handle.net/1808/24233
    DOI
    https://doi.org/10.1021/ct3008556
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    • Molecular Biosciences Scholarly Works [581]
    Citation
    Park, S., & Im, W. (2013). Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly. Journal of Chemical Theory and Computation, 9(1), 13–17. http://doi.org/10.1021/ct3008556

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    Contact KU ScholarWorks
    785-864-8983
    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    785-864-8983

    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    Image Credits
     

     

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