FIGURE 7.

This figure shows the difference in the PMF for indole using charge set 2 and charge set 1. Because these are PMFs, this difference is only relative. The absolute free energy difference at any one position, as one would get from a free energy perturbation calculation, is unknown. As expected, increasing the partial charges on the indole atoms destabilizes indole in the low dielectric bilayer core relative to water; however, increasing the partial charges also strongly stabilizes indole high in the interfacial region near the choline groups. It does not appear possible to rationalize this strong interfacial stabilization relative to water by modeling the bilayer as a continuum medium with a spatially dependent dielectric constant unless specific indole-lipid interactions or interactions with the lipid dipolar potential are included.