Fig. 3.

Ion/water permeation properties as a function of the z axis. (A) Average channel radii during the sampling MD of the nonprotonated and protonated Asp32, Val43Met, and Val43Leu. (B) Number of H bonds (or Na⁺−O interactions) between MotA/B and H₃O⁺, Na⁺, and H₂O during permeation. (C) Water distribution in the channel during H₃O⁺ permeation at Z = 0, ±5, and ±10. (D) Side-chain χ₁ angle of Leu46 (MotB) during H₃O⁺ permeation. (E) Angles between the membrane normal and the dipole moment of H₃O⁺ and H₂O. The values in B–E are averaged over 10 SMD2 trajectories. (F) Free energy profiles for H₃O⁺, Na⁺, and H₂O permeation. (G) Free energy barrier heights ΔG and rate constants for water/ion permeation, k and k′. Here $k^{\text{'}}$ was deduced from experimental values with ω = 300 s⁻¹, n = 1,240 (*), and N = 10 for Streptococcus (40), n/2N = 50 for E. coli (41) (†), and n/2N = 65 for E. coli (42) (‡).