FIGURE 3.

Geometrical parameters of the barrel and the degree of pore hydration in the course of a 15-ns MD simulation. (A) Effective radii of the periplasmic and cytoplasmic rims, outer chamber and of the constriction over the stages of simulation with the restricted backbone (rsbb), first unrestrained simulation (sim1), symmetry-driven annealing (symm1), the second unrestrained simulation (sim2), and the second symmetric annealing (symm2) (estimated every 50 ps). (B) Distances from the pore axis to the closest and the most distant α-carbons of equivalent residues in the heptamer that illustrate the ellipticity of the outer chamber (A98 and A102) and constriction (L105 and L109), estimated every 10 ps. (C) Conformational exchange in the pore illustrated by the radial motion of subunits. Positions of the α-carbons of A102 residues in individual subunits (numbered 1–7) were tracked every 10 ps. Residues closest to the pore axis at a given moment are marked by a magenta dot, whereas those most deviating from the axis are designated by a blue dot. Plots for the residues A98, L105, and L109 (not presented) illustrated the ellipticity of the barrel in the same way as this one for A102. (D) Z-coordinates of water molecules illustrating the degree of hydration of the pore constriction and vestibules scored every 1 ps.