Literature DB >> 33877631

Preparing Membrane Proteins for Simulation Using CHARMM-GUI.

Yupeng Li1,2,3, Jinchan Liu1,2,3, James C Gumbart4,5.   

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.

Entities:  

Keywords:  Gram-negative bacteria; Lipid bilayer; Molecular dynamics; Outer-membrane protein

Mesh：

Substances：

Year:  2021        PMID： 33877631      PMCID： PMC8158057          DOI： 10.1007/978-1-0716-1394-8_13

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  42 in total

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Authors:  Vlad Cojocaru; Kia Balali-Mood; Mark S P Sansom; Rebecca C Wade
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8.  Formation and Characterization of Supported Lipid Bilayers Composed of Hydrogenated and Deuterated Escherichia coli Lipids.

Authors:  Tania Kjellerup Lind; Hanna Wacklin; Jürgen Schiller; Martine Moulin; Michael Haertlein; Thomas Günther Pomorski; Marité Cárdenas
Journal:  PLoS One       Date:  2015-12-11       Impact factor: 3.240

9.  Modeling the conformational changes underlying channel opening in CFTR.

Authors:  Kazi S Rahman; Guiying Cui; Stephen C Harvey; Nael A McCarty
Journal:  PLoS One       Date:  2013-09-27       Impact factor: 3.240

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