FIG 7.

MD simulation-predicted binding of the inhibitors PAβN and NMP, with the substrate minocycline shown as a reference. The positions of ligands initially predicted by docking (Autodock Vina) are shown as thin gray sticks, and those in the final phase of MD simulation are shown as thick blue sticks. AcrB residues within 3.5 Å of the ligand are shown in stick models (red, green, or yellow, if they belong to the distal pocket, proximal pocket, or G-loop, respectively). For NMP, two somewhat different equilibrium positions were obtained, and only one is shown here. (Modified from reference 93.)