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g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation

Authors

  • Maarten G. Wolf,

    Corresponding author
    1. Computational Biomolecular Chemistry Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen D-37077, Germany
    • Computational Biomolecular Chemistry Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen D-37077, Germany
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  • Martin Hoefling,

    1. Department for Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Göttingen D-37077, Germany
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  • Camilo Aponte-Santamaría,

    1. Department for Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Göttingen D-37077, Germany
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  • Helmut Grubmüller,

    1. Department for Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Göttingen D-37077, Germany
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  • Gerrit Groenhof

    1. Computational Biomolecular Chemistry Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen D-37077, Germany
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Errata

This article is corrected by:

  1. Errata: Corrigendum: g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation Volume 37, Issue 21, 2038, Article first published online: 28 June 2016

Abstract

To efficiently insert a protein into an equilibrated and fully hydrated membrane with minimal membrane perturbation we present a computational tool, called g_membed, which is part of the Gromacs suite of programs. The input consists of an equilibrated membrane system, either flat or curved, and a protein structure in the right position and orientation with respect to the lipid bilayer. g_membed first decreases the width of the protein in the xy-plane and removes all molecules (generally lipids and waters) that overlap with the narrowed protein. Then the protein is grown back to its full size in a short molecular dynamics simulation (typically 1000 steps), thereby pushing the lipids away to optimally accommodate the protein in the membrane. After embedding the protein in the membrane, both the lipid properties and the hydration layer are still close to equilibrium. Thus, only a short equilibration run (less then 1 ns in the cases tested) is required to re-equilibrate the membrane. Its simplicity makes g_membed very practical for use in scripting and high-throughput molecular dynamics simulations. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

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