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. 2020 Jun 8;119(1):190–205. doi: 10.1016/j.bpj.2020.05.030

Figure 6.

Figure 6

Hydration of VSDs. (a) Free energy profiles estimated from probabilities of water distribution along the VSD principal axis (z) of NavMs, NavPaS, wild-type HCN1, and mutant HCN1, averaged over 200 ns. Note that the free energy barriers are cut at 6 kcal/mol. (b) Correlation between the height of the free energy barrier and the time of the first ion passage (either Na+ or Cl−) through a VSD. Ion passage times are taken from all simulations reported in Table S2. Gray dots represent VSDs that were not porated in any of the simulations. The outlier at (600 ns, 2.3 kcal/mol) corresponds to VSD2 of HCN1 mutant; note that we performed only two simulations for this channel. (c) Positions of water molecules in each VSD of NavPaS projected along the VSD radius (r) and the VSD principal axis (z). The VSDs’ center of mass is located at (0,0). Blue circles show all positions extracted from 200 frames of the last 200 ns of the equilibration trajectory. To see this figure in color, go online.