Fig. 5: Molecular dynamics simulations to investigate the pore hydration profile. | Nature Communications

Fig. 5: Molecular dynamics simulations to investigate the pore hydration profile.

From: Cryo-EM structures of prokaryotic ligand-gated ion channel GLIC provide insights into gating in a lipid environment

Fig. 5

a, b The mean pore radius of GLICpH7.5 (purple) and GLICpH4.0-O (deep pink) along with the corresponding standard deviation in gray (simulation average and standard deviation from one out of three independent equilibrium simulation runs of 200 ns with a sampling interval of 0.1 ns). Black dashed lines represent the diameter of one water molecule. c, d Free-energy profiles of a water molecule along the central axis are shown for the corresponding structures with standard deviation in gray. e, f Time series of the water molecules (blue) and Na+ ions (salmon) are plotted for a simulation time of 200 ns for each corresponding structure. The location of I9´ is pointed out by an arrow. White stretches reflect regions lacking water.

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