Fig. 1
From: Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting
Alternating-access transport in PaNhaP. a Inward-open dimer with bound Na+ ions (yellow spheres) embedded in a lipid bilayer. Arrows indicate gradient-driven Na+ import (yellow) coupled to H+ export (green) from the cytosol (bottom) to the exterior (top). b Inward- and outward-open structures of protomers A and B, respectively, with a section through the average water density in the 1-μs free MD simulation of the asymmetric dimer (red: no water; blue: water at bulk density). The green sphere indicates Hδ of the protonated Asp159, and the green arrows its water accessibility. c Motion of six-helix-bundle transporter domains between inward-open (blue) and outward-open states (red), after superposition of the dimerization domains (gray) of the respective average structures. Left: Translation normal to membrane in side view; right: domain rotation (axis indicated by green arrow) seen from above. d Projection of the 1-μs equilibrium MD run of the asymmetric dimer onto the plane of vertical displacement Δzin and rotation angle Δϕin relative to the inward-open structure (blue: inward-open protomer A; red: outward-open protomer B)
