Computer Simulations of Lipid Translocation and Desorption in Model Membranes

Lipid membranes are crucial structures in cells, composed of a bilayer of lipids, membrane associated proteins, and many other molecules. There is increasing evidence that membranes and lipids have important bioactive roles in many cellular processes. The thin, soft, dynamic, and chemically complex structure of lipid bilayers makes their characterization difficult. Atomistic molecular dynamics computer simulations have provided valuable insight into the structure and dynamics of model membrane systems. I used MD simulations to study free energies of lipids in various model membranes. The method of umbrella sampling was used to calculate the free energy for moving a single lipid from water to the center of a lipid bilayer. From these calculations, we have determined the free energy barrier for lipid flip-flop, and the free energy for lipid desorption. Phospholipids with relatively large and zwitterionic head groups were shown to translocate in a pore-mediated mechanism, whereas ceramide, cholesterol, and diacylglycerol with small polar head groups crossed in a solubility-diffusion mechanism. The presence of cholesterol in membranes increased the free energy barrier for DPPC flip-flop, cholesterol flip-flop, and pore formation. For different membranes, we calculate the free energy difference of a lipid monomer in the bilayer compared to bulk water, which is the excess chemical potential for the lipid monomer in that environment. We found that cholesterol prefers more ordered and rigid lipid bilayers, while DPPC had a lower excess chemical potential in a pure DPPC bilayer compared to a DPPC bilayer with 40 mol% cholesterol. Neither ceramide nor diacylglycerol had a strong preference for a model lipid raft bilayer, compared to a POPC bilayer, while cholesterol did have a large preference for the raft bilayer. This work expands our understanding of lipid membranes

Molecular View of Cholesterol Flip-Flop and Chemical Potential in Different Membrane Environments

The relative stability of cholesterol in cellular membranes and the thermodynamics of fluctuations from equilibrium have important consequences for sterol trafficking and lateral domain formation. We used molecular dynamics computer simulations to investigate the partitioning of cholesterol in a systematic set of lipid bilayers. In addition to atomistic simulations, we undertook a large set of coarse grained simulations, which allowed longer time and length scales to be sampled. Our results agree with recent experiments that the rate of cholesterol flip-flop can be fast on physiological time scales, while extending our understanding of this process to a range of lipids. We predicted that the rate of flip-flop is strongly dependent on the composition of the bilayer. In polyunsaturated bilayers, cholesterol undergoes flip-flop on a submicrosecond time scale, while flip-flop occurs in the second range in saturated bilayers with high cholesterol content. We also calculated the free energy of cholesterol desorption, which can be equated to the excess chemical potential of cholesterol in the bilayer compared to water. The free energy of cholesterol desorption from a DPPC bilayer is 80 kJ/mol, compared to 67 kJ/mol for a DAPC bilayer. In general, cholesterol prefers more ordered and rigid bilayers and has the lowest affinity for bilayers with two polyunsaturated chains. Overall, the simulations provide a detailed molecular level thermodynamic description of cholesterol interactions with lipid bilayers, of fundamental importance to eukaryotic life.