Fig. 1. Prestin simulation systems.
a MARTINI-based CG model of prestin from the side and extracellular views. In the side view, the two protomers are outlined in green and magenta, respectively, and the approximate position of the membrane is marked with yellow lines. In the extracellular view, the core and gate domains are colored in orange and blue, respectively. b Simulation system to probe lipid-protein interactions, including four prestin dimers, separated by 200 Å, and embedded in a square membrane patch of side length 400 Å. The composition of the membrane is shown in the legend, with lipid types represented with different colors. c Simulation system to study protein-protein cross-talks. Each system includes two prestin dimers at a 200-Å separation, embedded in a 400 × 200 Å2 bilayer, and with different relative orientations d. In each system, the two dimers are rotated around the membrane normal (z axis) in 45° increments. Given the two-fold symmetry of the protein, combinations of four different orientations per protein dimer (0°, 45°, 90°, and 135°, labeled as 1–4) cover all relative orientations of the two proteins at 45° intervals. Identical orientations are numbered the same, e.g., 45° and 225° are both labeled 2.