Department of Chemistry, Jilin University, Changchun, Jilin, China.
School of Physics, Georgia Institute of Technology, Atlanta, GA, USA.
Methods Mol Biol. 2021;2302:237-251. doi: 10.1007/978-1-0716-1394-8_13.
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.
在过去的 20 年中，膜蛋白的分子动力学模拟取得了巨大的发展。运行这些模拟首先需要将蛋白质的三维结构嵌入到具有合适组成的脂质双层中，该脂质双层类似于其天然环境。这一步远非微不足道，特别是对于建模脂质的不均匀混合物。CHARMM-GUI 是一个用于模拟系统准备的网络服务器，它极大地简化了这一步骤，允许构建复杂的不均匀和/或不对称的膜。在这里，我们展示如何使用 CHARMM-GUI 构建外膜蛋白 BamA 的膜。
