School of Chemistry , University of Southampton, Highfield , Southampton , SO17 1BJ United Kingdom.
J Chem Theory Comput. 2019 Apr 9;15(4):2608-2619. doi: 10.1021/acs.jctc.8b01059. Epub 2019 Mar 21.
The outer membrane of Gram-negative bacteria has a highly complex asymmetrical architecture, containing a mixture of phospholipids in the inner leaflet and almost exclusively lipopolysaccharide (LPS) molecules in the outer leaflet. In E. coli, the outer membrane contains a wide range of proteins with a β barrel architecture, that vary in size from the smallest having eight strands to larger barrels composed of 22 strands. Here we report coarse-grained molecular dynamics simulations of six proteins from the E. coli outer membrane OmpA, OmpX, BtuB, FhuA, OmpF, and EstA in a range of membrane environments, which are representative of the in vivo conditions for different strains of E. coli. We show that each protein has a unique pattern of interaction with the surrounding membrane, which is influenced by the composition of the protein, the level of LPS in the outer leaflet, and the differing mobilities of the lipids in the two leaflets of the membrane. Overall we present analyses from over 200 μs of simulation for each protein.
革兰氏阴性细菌的外膜具有高度复杂的不对称结构，包含内层小叶中的磷脂混合物和外层小叶中几乎仅有的脂多糖 (LPS) 分子。在大肠杆菌中，外膜包含多种具有 β 桶结构的蛋白质，其大小从最小的含有 8 个链到较大的由 22 个链组成的桶不等。在这里，我们报告了大肠杆菌外膜 OmpA、OmpX、BtuB、FhuA、OmpF 和 EstA 六种蛋白质在一系列膜环境中的粗粒度分子动力学模拟，这些环境代表了不同大肠杆菌菌株的体内条件。我们表明，每种蛋白质与周围膜的相互作用都具有独特的模式，这受到蛋白质组成、外层 LPS 水平以及膜双层中脂质流动性的不同的影响。总体而言，我们针对每种蛋白质进行了超过 200 μs 的模拟分析。
