Atomistic simulations of cholesterol in asymmetric lipid bilayers with varying degrees of lipid chain unsaturation

Asymmetric membranes consisting of DOPC, cholesterol, and a lipid with a varying level of unsaturation were simulated at 310 K. The DOPC leaflet consisted of 130 molecules, whereas the other leaflet consisted of either 125 DLiPC with 2 double bonds in both chains, 120 DAPC with 4 double bonds in both chains, or 115 DDPC with 6 double bonds in both chains. These numbers were adjusted to prevent membrane bending. All systems contained 28 molecules (10 mol%) of cholesterol. The CHARMM36 force field [1] was used and the membranes were generated using CHARMM-GUI [2].

The simulations were run for 1 microsecond using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file.

The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:

• Topology files (top) and molecular definitions (itp)
• Index files (ndx)
• A common run parameter file (mdp)
• A run input file (tpr)
• Trajectory file (xtc) written every 100 ps
• Energy file (edr)
• Log file (log)
• Final structure file (gro)
• Continue point file (cpt)

The files are named DOPC_LLLL_AA_CHOLXX_TTT.FFF, where

• LLLL is the type of phospholipid paired with DOPC
• AA stands for all atom (Coarse-grained data in a separate upload)
• CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)
• TTT is the temperature
• FFF is the tile type (see above)

[1] DOI: 10.1021/jp101759q

[2] DOI: 10.1021/acs.jctc.5b00935

[3] DOI: 10.1016/j.softx.2015.06.001