Fig. 6: Propagation of conformational changes from the Q-site towards E-channel.

a, b Overlay of CXI_INT (grey) with CXI_DQ structure (coloured subunits, Nqo8 in orange, Nqo10 in light green, Nqo11 in light blue and Nqo14 in yellow). The structures were aligned by the MDs. The distances between the key residues from the E-channel and the central hydrophilic axis, involved in proton translocation, change due to both global and local shifts and rotations of the side chains. A grey mesh indicates Q cavity. Key charged residues from the E-channel and hydrophobic residues undergoing large conformational changes are indicated. Y59₁₀ sits on a π-bulge in the key TM3 of Nqo10. a Side view and b top view from the cytoplasm. The conformational change extends from the Nqo8 loop (red) towards Nqo11, coupled with major shifts in the hydrophobic protein environment. c Analysis of modelled water molecules distribution. In the crystal structure CXI_DQ, rotation of the Nqo10 TM3 helix and the associated Y59₁₀ leads to subsequent rotation of E32₁₁, which allows for inclusion of a single water molecule between E32₁₁ and E67₁₁. The key water in CXI_DQ system is shown as transparent van der Waals spheres. All other modelled waters are shown as sticks with oxygen coloured according to the structure and hydrogen grey.