Sampling protein-lipid interactions with swarms of trajectories and a transition matrix analysis

Lipid-protein interactions are critical for integral membrane protein function, where lipids can play the role of both solvent and ligand. Because resolving the lipids that solvate a membrane protein is experimentally challenging, simulations have come to play a prominent role in linking lipid solvation and membrane protein function. However, converging the lipid distribution around a membrane protein can require surprisingly long simulations, especially in cholesterol-rich mixtures where lipid diffusion and exchange at the surface of the protein can be quite slow.