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Preparing Membrane Proteins for Simulation Using CHARMM-GUI

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Structure and Function of Membrane Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2302))

Abstract

Molecular dynamics simulations of membrane proteins have grown dramatically in the last 20 years. Running these simulations first requires embedding the protein’s three-dimensional structure in a lipid bilayer of a suitable composition, one that resembles its native environment. This step is far from trivial, especially for modeling heterogeneous mixtures of lipids. CHARMM-GUI, a webserver for simulation system preparation greatly simplifies this step, allowing for the construction of complex heterogeneous and/or asymmetric membranes. Here, we demonstrate how to use CHARMM-GUI to build the membrane for the outer-membrane protein BamA.

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Acknowledgments

This work was supported by the National Institutes of Health (R01-GM123169). Computational resources were provided through the Extreme Science and Engineering Discovery Environment (XSEDE; TG-MCB130173), which is supported by NSF Grant ACI-1548562.

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Authors and Affiliations

  1. Department of Chemistry, Jilin University, Changchun, Jilin, China

    Yupeng Li & Jinchan Liu

  2. School of Physics, Georgia Institute of Technology, Atlanta, GA, USA

    Yupeng Li, Jinchan Liu & James C. Gumbart

  3. School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA

    Yupeng Li, Jinchan Liu & James C. Gumbart

Authors
  1. Yupeng Li
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  2. Jinchan Liu
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  3. James C. Gumbart
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Corresponding author

Correspondence to James C. Gumbart .

Editor information

Editors and Affiliations

  1. School of Biological Sciences and School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA

    Ingeborg Schmidt-Krey

  2. School of Physics, Georgia Institute of Technology, Atlanta, GA, USA

    James C. Gumbart

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Li, Y., Liu, J., Gumbart, J.C. (2021). Preparing Membrane Proteins for Simulation Using CHARMM-GUI. In: Schmidt-Krey, I., Gumbart, J.C. (eds) Structure and Function of Membrane Proteins. Methods in Molecular Biology, vol 2302. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1394-8_13

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  • DOI: https://doi.org/10.1007/978-1-0716-1394-8_13

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1393-1

  • Online ISBN: 978-1-0716-1394-8

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