Supplementary information: The free-energy barriers against expansion of the metastable fusion stalk and its implication for the protein fusion machinery
نویسندگان
چکیده
System setup. All vesicles were obtained by spontaneous aggregation of randomly placed lipids. This method is described in detail elsewhere [1]. An additional long equilibration run of 20 μs was performed for the mixed lipid systems (two artificial pores were present) [2]. In all cases, equilibrium of the vesicle was defined by the flux convergence of the lipid components. The pure POPC vesicle/dimples consisted of 2217 lipids. The mixed POPC:POPE system, 1330 POPC and 887 POPE (40%) lipids. The mixed POPC:cholesterol system, 1980 POPC and 834 cholesterol (30%) molecules. The box dimensions in our (umbrella) simulations were 21× 22× 20 nm. About 50000 solvent beads were present. All vesicles were equilibrated with 2 artificial pores of 1.6 nm radius. Equilibrium is defined by the absence of net flux/flip-flops for each individual component, which can take upto 20 μs in the mixed vesicles [2].
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