Locating the Route of Entry and Binding Sites of Benzocaine and Phenytoin in a Bacterial Voltage Gated Sodium Channel
Figure 6
Lipid and water in the fenestrations as a function of drug position.
(A) A representative snapshot showing lipid occupying the lateral fenestrations while benzocaine sits at its minimum energy position in the activation gate. The position of F203 (orange) and T138 (yellow surface) are also shown. (B) The extent to which lipid penetrates into the fenestration is plotted as a function of the position of each drug. Low values indicate extension further into the fenestration. (C) A snapshot showing an extreme example of a water chain extending from the channel lumen to phenytoin on the exterior surface of the protein. In most cases the water chain does not extend this far. (D) The probability that a continuous water chain extends from each drug back to the channel lumen as a function of drug position (solid lines). Also shown is the probability that a water chain extends from the drug directly to bulk water (dashed lines). In B and D the data for individual windows are shown in points and a moving average of 5 data points is indicated by the line.