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. 2016 Mar 29;110(6):1334–1345. doi: 10.1016/j.bpj.2016.02.014

Figure 3.

Figure 3

The 2D PMFs of WT, with Cl–cen present, calculated with MS-RMD. For (A), CV1 (the horizontal axis) is defined as the distance between E148 and E203, and CV2 (the vertical axis) is the difference in the two distances from the excess proton CEC to either E148 or E203. For (B), CV1 is the distance of the CEC along the proton pathway sampled by the MetaD, and CV2 is the water density in the central region. The red line on each 2D PMF represents the minimum free energy path for the transition from E203(H) to E148(H). The plot below each 2D PMF is the PMF calculated along that minimum free energy path. The boxes R, T, and P in (A) represent the positions of the reactant, transition state, and product state, respectively. The inset in (B) highlights the free energy in the reactant minimum more clearly with a finer color scale of purple through red corresponding to the PMF range of 7.5–10.5 kcal/mol. To see this figure in color, go online.