Extended Data Fig. 5: Prestin’s cross-sectional area changes upon transition from Down to Up states.

a, Upon the transition from Down to Up state and the movement of the anion-binding site, the most obvious changes are seen in the peripheral helices TM5b, TM6-TM7, and TM8. b, MD simulation of prestin in Up state is compared with the Inhibited II state (Cl⁻ and Salicylate) equilibrated in POPC lipid bilayers. The cross-sectional area of outer and inner monolayers with mapped leaflet coordinate in the Z direction (across the membrane thickness) using all-atom molecular dynamics simulations (1µs). Δz shows movement of the phosphate group of the lipids in the Z (thickness) direction. The comparison was made between Up (Cl⁻) and Inhibited II (SO₄²⁻) states. The largest difference was observed at the location of the TM6 helix. c, Cross-sectional area calculations of the transmembrane domain of SLC26A9(12) along the hydrophobic thickness using CHARMM-membrane builder. Cross-sectional area change of SLC26A9 from Inward-facing to Intermediate states (6RTC and 6RTF) per monomer¹⁹. Note that prior to area calculation, the spatial arrangements of all the structures with respect to the hydrocarbon core of the lipid bilayer were first adjusted using the PPM server(30). The structures were aligned based on residues 460 to 505 (TM13-TM14). d, Comparison of the change in the micelle morphology between two salicylate-inhibited structures Inhibited I (Cl⁻) and Inhibited II (SO₄²⁻ + Salicylate) states. The overlay of the two states shows drastic changes in the micelle thickness especially around TM6 region in addition to the overall changes in the micelle in-lane direction, both indicative of major structural rearrangements between the two states. ChimeraX was used for illustration.