Respiratory complex I (NADH:ubiquinone oxidoreductase) is a key enzyme in metabolism and is the least understood protein in the mitochondrial electron transfer chain (ETC). It couples the energy released from NADH oxidation and ubiquinone (Q) reduction to the translocation of four protons across the inner mitochondrial membrane, contributing to the proton motive force (PMF) used to synthesise ATP. Although structural knowledge of complex I is now extensive, the mechanism by which it couples the redox energy for proton translocation remains unclear.

First, the rate-limiting step of catalysis in complex I was investigated from the point of view of the proton. Using the proteoliposomes system, the pH and solvent isotope dependence of kinetic parameters of purified bovine and Yarrowia lipolytica complex I mutants were measured under a range of conditions. I find complex I robustly displays a solvent kinetic isotope effect (KIE), signifying that the rate-limiting step involves a proton transfer. This isotopic sensitive step is dependent on Q-chain length, Q binding-site mutations, and Qconcentration, but not dependent on Δp, suggesting that this step is Q-reduction. Proton inventory experiments suggest that a single proton is transferred in the rate-limiting step, and that complex I is rate-limited by a combination of a proton transfer step and an isotopically insensitive step, which was assigned as the product release of ubiquinol.

Next, the role of conserved charged residues in the central axis were investigated using the Paracoccus denitrificans model system. Mutants of residues involved in the energy propagation pathway and subunit hydration channel gating were evaluated using solvent isotope effect and proton pumping experiments. These mutations all exhibited a greater isotope dependence than WT, showing that proton pumping steps have become robustly rate-limiting. Then, experimental results were evaluated against computational and mechanistic proposals, to identify the role of these residues.

Finally, the role of a putative re-protonation channel in NUCM was investigated using the Yarrowia lipolytica model system. Point mutations, made up of conserved buried charged residues connecting the Q-binding site to the matrix were generated. Characterisation of mutants revealed that residues with strong ionic interactions (arginine and glutamate) did not express complex I, and that mutation effects were inconsistent with the abrogation of a protonation channel. I conclude that these residues likely play no role in re-protonation, but instead may be important for structural stabilisation.