Figure 5
Hydration of AP in the Loose protomer of AcrB and AcrD. (a) Comparison of RDF profiles of water oxygen atoms around AP (all atoms) in the Loose protomer of AcrB (red solid line) and AcrD (brown dash-dotted line) extracted from the equilibrium MD trajectories. (b) Comparison of SDF of waters within the AP of Loose protomer. The SDF was calculated over the configurations forming the most populated cluster of AcrB (left) and AcrD (right). The isosurfaces are shown at density isovalue of 6, meaning that the represented surfaces correspond to 6 times higher average number density of solvent molecules than bulk (see Subsection Hydration in Methods). The AP and DP are marked in green and red while the G-loop in yellow cartoon representations. The hydrophobic/aromatic residues of the pocket are shown as cyan sticks in the respective structures.
