Fig. 6

Fig. 6

a Mean pore radius profiles and standard deviations averaged across three independent 30 ns equilibrium simulations for GlyR–Apo (left), GlyR–Gly/PTX (middle), and GlyR–Gly (right) along the central pore axis. The final 20 ns of each 30 ns simulation trajectory was used to evaluate these profiles. The one-standard-deviation range between calculations (n = 3, independent repeats of 30 ns simulations) are shown as a gray band and the thick line is the mean between the triplicate 30 ns simulations. Major constriction sites are indicated and the dotted line denotes the radius of hydrated chloride ion. The black traces are the pore radius profile calculated from the cryo-EM structures. b Corresponding mean water free energy profiles and standard deviations. Peaks in free energy profiles are highlighted. c Trajectories along the pore (z)-axis of water molecules and chloride ion coordinates within 5 Å of the channel axis inside the pore, in the presence of a +500 mV transmembrane potential difference (i.e., with the cytoplasmic side having a positive potential). One of five independent 200 ns replicates is shown for each structure. During these and the preceding simulations, positional restraints were placed on the protein backbone, in order to preserve the experimental conformational state while permitting rotameric flexibility in amino acid side chains. The energetic barriers due to the ring of Leu9′ and Pro-2′ are at z ~0 and −20 Å, respectively.