Fig. 5. Proposed coupling mechanism of complex I.

a) Overview showing key helices and residues. Upon electron transfer from cluster N2, negatively charged quinone initiates a cascade of conformational changes, propagating from the E-channel (Nqo8/10/11) to the antiporters via the central axis (red arrows) of charged and polar residues located around flexible breaks in key TM helices. Cluster N2-driven shifts of Nqo4/6 helices²⁷ (blue arrows) likely assist overall conformational changes. Helix HL and the βH element help coordinate conformational changes by linking discontinuous TM helices between the antiporters. In the antiporters, LysTM7 from the first half-channel is assumed to be protonated (via the link to cytoplasm) in the oxidised state²⁹. Upon reduction of quinone and subsequent conformational change, the first half-channel closes to the cytoplasm, GluTM5 moves out and LysTM7 donates its proton to the connecting Lys/HisTM8 and then onto Lys/GluTM12 from the second half-channel. Lys/GluTM12 ejects its proton into periplasm upon return from reduced to oxidised state. A fourth proton per cycle is translocated in the E-channel in a similar manner. TM helices are numbered and key charged residues (GluTM5, LysTM7, Lys/GluTM12, Lys/HisTM8 from Nqo12-14, 11_Glu67, 11_Glu32, interacting with 10_Tyr59, 8_Glu213 and some residues from the connection to Q cavity) are indicated by red circles for Glu and blue circles for Lys/His. b) Schematic drawing illustrating conformational changes between the two main (low energy) conformations. Analysis of networks of polar residues and modelled waters in the structure suggests that in the oxidised state (as crystallised) periplasmic half-channels are likely to be open. Residues shown as black circles indicate conserved prolines from the break in TM12.