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    CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations

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    Wu_2014.pdf (709.5Kb)
    Issue Date
    2014-10-15
    Author
    Wu, Emilia L.
    Cheng, Xi
    Jo, Sunhwan
    Rui, Huan
    Song, Kevin C.
    Dávila- Contreras, Eder M.
    Qi, Yifei
    Lee, Jumin
    Monje-Galvan, Viviana
    Venable, Richard M.
    Klauda, Jeffery B.
    Im, Wonpil
    Publisher
    Wiley
    Type
    Article
    Article Version
    Scholarly/refereed, author accepted manuscript
    Metadata
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    Abstract
    CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulation through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builderthat allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types such as phosphoinositides, cardiolipin, sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: cardiolipin lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments.
    Description
    This is the peer reviewed version of the following article: Wu, E. L., Cheng, X., Jo, S., Rui, H., Song, K. C., Dávila-Contreras, E. M., … Im, W. (2014). CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations. Journal of Computational Chemistry, 35(27), 1997–2004. http://doi.org/10.1002/jcc.23702, which has been published in final form at http://doi.org/10.1002/jcc.23702. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
    URI
    http://hdl.handle.net/1808/24265
    DOI
    https://doi.org/10.1002/jcc.23702
    Collections
    • Molecular Biosciences Scholarly Works [581]
    Citation
    Wu, E. L., Cheng, X., Jo, S., Rui, H., Song, K. C., Dávila-Contreras, E. M., … Im, W. (2014). CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations. Journal of Computational Chemistry, 35(27), 1997–2004. http://doi.org/10.1002/jcc.23702

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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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