Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
Fig 4
Binding preference of charged and/or aromatic ligands to the solvent-exposed surface of EmrE.
(A) 3D densities of the central atom near the solvent-exposed surface of EmrE, looking from the “open” (top) and “closed” (bottom) side. Aromatic side chains exposed at the surface are shown in yellow, charged in orange. In each set of simulation, 10 ligands were initially placed in the water phase and allowed to interact with the protein. (B) Ligand density as in (A), but projected on the z-axis. Note that entered into spaces between the protein and the lipid bilayer, occasionally achieving z<0.5 nm but outside of the main ligand-binding channel. (C) A sample structure of ligand-bound EmrE in which the ligand spontaneously passed from bulk solvent to z = 0.8 nm (see extended simulations in S7 Fig).