Water dynamics and side chain conformational changes at the gate. (a) Equilibrium snapshots depicting the pattern of pore hydration in WT closed (PDB ID: 7QKO), mutated channels (βL9′S, α₂L9′S, βδεL9′S), and WT open (PDB ID: 7QL6). A clear gap in the water distribution is apparent in the constricted hydrophobic gating region of the closed channel. Note the progressive increase in water density in the mutant channels and the open conformations. The channel subunit in the front has been removed for clarity. The time-averaged water density values for WT closed and open channel in Fig. 6 d agree with the snapshots of pore hydration. (b) Fluctuation of water density with time (x-axis) in the middle of the pore for the WT closed, open, and mutant channels. Note the increase in water fluctuations (pore wetting–dewetting events) with an increasing number of mutations at L9′. Also, note that in the open pore (7QL6), water density is not continuous but interrupted by complete aperiodic wetting transitions (several nanoseconds long). (c) Averaged superimposed structures of C and O conformations of AChRs (synaptic view [i–iii], and membrane view [iv]) obtained from the equilibrated part of the all-atom simulations. Blue, C (7QKO) and silver, O (7QL6). Dotted lines represent asymmetric pentagons (1 each for the C versus O states) which roughly mark the position of the side chains at 9′ (i), 13′ (ii), and 16′ (iii) positions. Note the increase in pore diameter due to side chain rotations, orthogonal translation (iv), and straightening of the M2 helices in the O structure.