Complex I (NADH-ubiquinone oxidoreductase) in the respiratory chain of mitochondria and several bacteria functions as a redoxdriven proton pump that contributes to the generation of the protonmotive force across the inner mitochondrial or bacterial membrane and thus to the aerobic synthesis of ATP. The stoichiometry of proton translocation is thought to be 4 H þ per NADH oxidized (2 e − ). Here we show that a H þ ∕2 e − ratio of 3 appears more likely on the basis of the recently determined H þ ∕ATP ratio of the mitochondrial F 1 F o -ATP synthase of animal mitochondria and of a set of carefully determined ATP∕2 e − ratios for different segments of the mitochondrial respiratory chain. This lower H þ ∕2 e − ratio of 3 is independently supported by thermodynamic analyses of experiments with both mitochondria and submitochondrial particles. A reduced H þ ∕2 e − stoichiometry of 3 has important mechanistic implications for this proton pump. In a rough mechanistic model, we suggest a concerted proton translocation mechanism in the three homologous and tightly packed antiporterlike subunits L, M, and N of the proton-translocating membrane domain of complex I.cell respiration | proton pumping | conformational changes | phosphorylation potential C omplex I is the entry point of the respiratory chain in mitochondria and many bacteria and structurally by far the most complicated of the three respiratory chain complexes with protonmotive activity, viz. I, III, and IV. Complex I is an L-shaped integral membrane protein. Its hydrophilic arm, which protrudes out of the membrane on the negatively charged N side, contains the NADH-oxidizing FMN site, a set of iron sulfur centers, and a binding site for ubiquinone (1-3). The membrane domain includes seven subunits that in mitochondria are all encoded by mtDNA and that are present also in bacteria (see Fig. 1). Three of these subunits*, L, M, and N, are homologous to one another as well as to certain bacterial proton/cation antiporters (2, 3, 6). They share structural features, such as two disrupted transmembrane α-helices (4) and conserved lysines within the membrane domain, which appear to be important in the proton-pumping mechanism (7-9).When considering possible mechanisms of redox-linked proton translocation by complex I, some kind of conformational coupling has appeared obvious due to the long distance between the redoxactive cofactors in the hydrophilic domain and the likely protontranslocating subunits in the membrane domain. The crystal structures (4, 10) revealed a most uncommon long amphipathic α-helix that is part of the distal subunit L. It passes along almost the entire N surface of the membrane domain and is followed by a transmembrane helix on the proximal side of subunit N, thus "wrapping up" the three antiporter-like subunits. This helix has been suggested to communicate redox-dependent conformational changes in the hydrophilic domain to the membrane subunits (4, 10).Here we first reexamine the stoichiometry of redox-coupled proton translocation in complex I and...