OPRLM: Orientations of proteins in realistic lipid membranes
OPRLM: Orientations of proteins in realistic lipid membranes
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OPRLM：真实脂质膜中蛋白质的方向
DOI：
10.1016/j.bpj.2022.11.1608
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发表时间：
2023
影响因子：
3.4
通讯作者：
Im, Wonpil
中科院分区：
文献类型：
--
作者：
Park, Sang-Jun;Todd, Spencer C.;Pogozheva, Irina D.;Lomize, Andrei L.;Im, Wonpil
基于OPM数据库和广泛使用的GHARMM-GUI工具集，创建了一个新的网络工具和数据库OPRLM（逼真脂膜中的蛋白质取向）。该数据库提供了一套完整的实验三维结构的整体和外周膜蛋白的蛋白质数据库，定位在平面和弯曲的脂质双层使用隐式和显式膜表示。膜系统从单组分人工脂质双分子层到具有复杂脂质组成的多组分双分子层，对应于18种生物膜，脂质类型在两个小叶之间不对称或对称分布：14“平均”真核细胞和细胞器膜（哺乳动物、植物和真菌的质膜，哺乳动物和真菌的内质网和高尔基体膜，哺乳动物的核内体和溶酶体膜，线粒体外膜和内膜，植物液泡膜，植物和蓝藻的类囊体膜），革兰氏阴性细菌（大肠杆菌）的外膜和内膜，革兰氏阳性细菌和古细菌的“平均”细胞膜。所有这些膜系统都可以在CHARMM-GUI Archive （https://www）中公开使用。charmm-gui。org/docs/archive/biomembrane)。该网络工具允许用户的任何专业水平的一个简单的设置蛋白质膜系统的原子分子动力学（MD）模拟在预组装现实的脂质膜形成明确的脂质混合物。OPRLM可在https://oprlm上公开获取。org/。
A new web tool and a database, OPRLM (Orientations of Proteins in Realistic Lipid Membranes), has been created based on the OPM database and the broadly used GHARMM-GUI toolset. The database provides a complete set of experimental 3D structures of integral and peripheral membrane proteins from the Protein Data Bank that are positioned in planar and curved lipid bilayers using implicit and explicit membrane representations. Membrane systems vary from single-component artificial lipid bilayers to multi-component bilayers with complex lipid composition corresponding to 18 biomembranes with either asymmetric or symmetric distribution of lipid types between two leaflets: 14 “average” eukaryotic cellular and organelle membranes (plasma membranes of mammals, plants, and fungi, endoplasmic reticulum and apparatus Golgi membranes of mammals and fungi, mammalian membranes of endosomes and lysosomes, mitochondrial outer and inner membranes, plant vacuole membranes, thylakoid membranes of plants and cyanobacteria), the outer and the inner membranes of Gram-negative bacteria (E. coli), and “average” cell membranes of Gram-positive bacteria and archaebacteria. All these membrane systems are accessible for public use in CHARMM-GUI Archive (https://www. charmm-gui. org/docs/archive/biomembrane). The web tool allows users of any level of expertise an easy setup of protein-membrane systems for atomic molecular dynamics (MD) simulations in pre-assembled realistic lipid membranes formed by mixtures of explicit lipids. OPRLM is publicly available at https://oprlm. org/.