Figure 8. Membrane deformation induced by the Na⁺-dicarboxylate symporter VcINDY, based on coarse-grained MD simulations in POPC at 298 K.

(A) Structure of the VcINDY dimer in the outward-facing state, viewed along the membrane perpendicular from the extracellular space. The protein is represented as Glt_Ph in Figure 1. (B) Deflection of the membrane mid-plane induced by VcINDY in the outward- and inward-facing states (left and right, respectively) based on three independent simulations for either state. The view is from the extracellular space. From left to right, the standard error of the data (N = 3) across each map is, on average, 1.0 Å and 0.8 Å. (C) Structures of outward- and inward-facing VcINDY (represented as in panel A), alongside calculated density maps for lipid alkyl chains within 10 Å from the protein surface (yellow), based on all the simulation data obtained for either state. Note the outward-facing state is a model, constructed on the basis of the experimental inward-facing structure through repeat-swapping (Mulligan et al., 2016).