Figure 2
From: Uptake dynamics in the Lactose permease (LacY) membrane protein transporter
Simulated structural rearrangements in the sugar-bound state. The crystal structure (transparent) and last frame from the simulation (solid) show the helical simulated shifts of (A) helices 2 and 11 and (B) helices 5 and 8. The TDG molecule and Phe 27 are shown in their crystallographic positions. (C) The Cα-Cα distances in helix pair 2 (Gly 46) – 11 (Gly 370) and helix pair 5 (Gly 159) – 8 (Gly 262) for the sugar-bound simulation, the repeat simulation, and the apo state simulation. (D) One-hundred pore radii extracted from the final 100 ns of the sugar-bound simulation (gray). The pore radii from the occluded (PDB ID: 4OAA) and periplasmic open (PDB ID: 5GXB) crystal structures are shown in black and red, respectively. Dashed lines correspond to the TDG position in the crystal structure (black) and the average simulated centers-of-mass of residues Glu 269 (red) and Phe 27 (blue).
