All-atom cytoPlus model of mammalian cell plasma membranes

All-atom trajectory of a data-driven model of mammalian plasma membranes. The phospholipid compositions of the two leaflets were modeled after data from lipidomics analysis of the individual leaflets of red blood cell membranes. The overall cholesterol concentration was also taken from lipidomics analysis, but its interleaflet distribution was determined from a long atomistic simulation of the bilayer on Anton (15 us) followed by a shorter simulation in NAMD (2 us, uploaded here). The converged membrane model has fewer phospholipids and more cholesterol in the exoplasmic (sphingomyelin-rich) leaflet, and more phospholipids and less cholesterol in the cytoplasmic (PUFA-rich) leaflet. Detailed information about the lipid and cholesterol compositions of the two leaflets, together with experimental validation of the model and direct illustrations of its biophysical and physiological effects can be found in https://doi.org/10.1101/2023.07.30.551157. Uploaded files include: a structure file for the system (.psf), an all-atom trajectory centered on the average z position of the terminal methyl carbons of all lipids (.dcd), the parameter files and a sample NAMD input file used for the simulation. The uploaded trajectory is the last 1.2 us from the NAMD run with frames output every 120 ps.哺乳动物质膜数据驱动模型的全原子轨迹。两个脂单层（leaflet）的磷脂组成参考红细胞膜各脂单层的脂质组学分析数据构建。整体胆固醇浓度同样取自脂质组学分析结果，但其脂单层间的分布则通过两步模拟确定：首先在Anton超级计算机上对脂双层开展长达15微秒的全原子模拟，随后在NAMD中完成2微秒的短时间模拟（本次上传的即后者的模拟结果）。该收敛后的膜模型中，外质面（富含鞘磷脂）脂单层的磷脂占比更低、胆固醇占比更高；而胞质面（富含多不饱和脂肪酸（PUFA））脂单层则磷脂占比更高、胆固醇占比更低。关于两个脂单层的脂质与胆固醇组成、该模型的实验验证结果，以及其生物物理与生理效应的详细信息与直观阐释，均可查阅 https://doi.org/10.1101/2023.07.30.551157。 本次上传的文件包括：体系结构文件（.psf）、以所有脂质末端甲基碳的平均z坐标为中心的全原子轨迹文件（.dcd）、模拟所用的参数文件，以及一份NAMD模拟输入示例文件。本次上传的轨迹为NAMD模拟运行的最后1.2微秒片段，轨迹帧的输出间隔为120皮秒。