Figure 7: Comparison of ion-binding site accessibility and coordination in the substrate-free Ce (a) and substrate-bound CeS (b) states of BetP-G153D observed using molecular dynamics simulations.
The green surface indicates the density of water molecules occupying the extracellular pathway (defined as waters within 16 Å of D153) during three 200 ns trajectories. Protein snapshots were taken at 81 and 83 ns of the trajectories of the Ce and CeS states, respectively. BetP protein is shown as a cut-away surface. Sodium ions are shown as violet spheres. Oxygen atoms of water and protein that form the Na2- and Na1′-binding site in the closed CcS state are shown as red spheres. Oxygen atoms in addition to those from the closed-state structure coordinating the ion during molecular simulations of the corresponding state are shown as yellow spheres. Selected helices are shown as cartoons: TMH1′ and its symmetry equivalent TMH6′ (red), and TMH3′ and its symmetry equivalent TMH8′ (blue), with substrate choline shown as sticks.
