Fig. 9: The coupling mechanism of complex I.

The two main states of the complex are shown in green (major-like MJ states, represented by CXI_INT, CXI_NADH, and CXI_MJ structures) and blue (minor-like MN states, represented by CXI_DQ and CXI_MN structures). It is expected that in the membrane such two states would largely correspond to the proton channels opened either to the cytosol (MJ) or to the periplasm (MN). In state 1 the enzyme is waiting for quinone to bind. The complex is reduced so that key Nqo4 β1–β2 loop with H38 is flipped into the Q cavity (black arc). In state 2, upon quinone binding, this loop retracts, allowing quinone to reach the deep end of the cavity. The cavity “tightens” around the headgroup (blue arrows), the enzyme converts into the MN state and conformational changes propagate into the E-channel (red arrows). In state 3, two electrons from NADH arrive to quinone via cluster N2, the quinone is protonated to quinol and the double negative charge resides on proton-donating residues H38₄ and Y87₄ (depicted as red Q headgroup for simplicity). Electrostatic interactions with charged residues in the E-channel initiate further changes propagating (either conformationally or electrostatically) into antiporter-like subunits (red arrows), resulting in the ejection of protons into the periplasm. In state 4, the enzyme is quickly re-reduced and H38₄ flips out (black arc). Facilitated by this and the expansion of the cavity (blue arrows), quinol is ejected into the lipid bilayer and the enzyme reverts to a MJ-like state. The cycle resumes at state 1, with further details outlined in the text.