Figure 4.

Atomistic simulation of the spinach chloroplast ATP synthase rotor ring. (A) Comparison of the assembled model with 17 lipids inside the c-ring at 250 ns with the experimental Cryo-EM map EMD_4273 (Hahn et al., 2018) contoured at the level of 3σ (black). Excellent correspondence between positions of protein atoms (green) and experimental map is observed. The lipids (magenta) fit very well into the densities in the membrane region. (B) Density distributions of outer (left) and inner (right) POPC phosphate (red) and diacylglycerol (blue) moieties overlaid with three exemplary trajectories of permeating water molecules. Average position of Glu61 centers of mass is shown using the solid line. (C) Contact maps between water molecules and Glu61 side chains. Presence of water molecules whose oxygen atoms are within 4 Å of Glu61 O_ε1 and O_ε2 atoms is indicated using gray (1 molecule) and black (2 molecules).