FIGURE 6:

(A–D) Data for four of the AAMD simulation runs with respect to z-distance of each residue on the protein away from the membrane phosphate plane. The simulations were run for 500 ns each. The four systems are (A) WT, (B) I533A, (C) F579A, and (D) K583A. The gray curve on each figure indicates the initial configuration, and the blue curve is the final configuration averaged over the last 100 ns. Similar plots for K339A and Y600L mutant systems are shown in Supplemental Figure S7. (E) PMF profiles of the five systems obtained through umbrella sampling simulations. Right-most end of the graph denoted PHD in solution. The zero of the free energy difference plot is set at the phosphate plane of the membrane.