Figure 7.

The ArgS orientation required for permeation is shown on the left, at the region z ∼ 4 nm. The carboxylate group of ArgS is interacting with a series of arginine ladder residues. The guanidinium group of the arginine is interacting with D307 and S302 of loop L7 in the protein. ArgS is shown in space-filling format for ease of visualization. Water molecules and the membrane have been omitted for clarity. On the right is a plot showing the orientation of ArgS through OccD1. The green lines indicate a region of specificity, requiring the substrate to be in a conformation such that the guanidinium side chain is pointing toward the periplasmic region, y < 0. The brown lines indicate the periplasmic and extracellular ends of the protein at ∼2.1 nm and ∼7.8 nm, respectively. To see this figure in color, go online.