Figure 5
Isoflurane binding is more stable in the closed channel.
Probabilities of finding an isoflurane molecule (center of mass) in molecular dynamics (MD) simulations at position z along the pore axis, P(z) and at the distance r from the pore axis, P(r), were calculated for (a,c) the closed channel and (b,d) a desensitized channel. A probability is defined as the ratio of the number of snapshots where isoflurane was found at the position z or at the distance r to the total snapshots chosen from the simulation. The bin widths of 1 Å and 0.5 Å were used for position z and distance r, respectively. Isoflurane motion in each pore conformation was evaluated every 0.1 ns from 100 ns simulations. Color indicates starting positions of isoflurane, 6′ (red) or 13′ (blue), in the MD simulations.
