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.