Electron transfer in complex I from Escherichia coli was investigated by an ultrafast freeze-quench approach. The reaction of complex I with NADH was stopped in the time domain from 90 s to 8 ms and analyzed by electron paramagnetic resonance (EPR) spectroscopy at low temperatures. The data show that after binding of the first molecule of NADH, two electrons move via the FMN cofactor to the iron-sulfur (Fe/S) centers N1a and N2 with an apparent time constant of Ϸ90 s, implying that these two centers should have the highest redox potential in the enzyme. The rate of reduction of center N2 (the last center in the electron transfer sequence) is close to that predicted by electron transfer theory, which argues for the absence of coupled proton transfer or conformational changes during electron transfer from FMN to N2. After fast reduction of N1a and N2, we observe a slow, Ϸ1-ms component of reduction of other Fe/S clusters. Because all elementary electron transfer rates between clusters are several orders of magnitude higher than this observed rate, we conclude that the millisecond component is limited by a single process corresponding to dissociation of the oxidized NAD ؉ molecule from its binding site, where it prevents entry of the next NADH molecule. Despite the presence of approximately one ubiquinone per enzyme molecule, no transient semiquinone formation was observed, which has mechanistic implications, suggesting a high thermodynamic barrier for ubiquinone reduction to the semiquinone radical. Possible consequences of these findings for the proton translocation mechanism are discussed.EPR spectroscopy ͉ Escherichia coli ͉ freeze-quench ͉ iron-sulfur clusters ͉ reactive oxygen species C omplex I is one of the three key enzymes of the mitochondrial respiratory chain. The simpler prokaryotic version contains the same cofactors and performs the same major function as its eukaryotic counterpart (1). Complex I couples electron transfer from NADH to ubiquinone to translocation of 2 H ϩ /e Ϫ across the membrane (2). It is a true redox-linked proton pump, as is complex IV (3), but is distinct from complex III, which generates the electrochemical proton gradient across the membrane by a redox loop mechanism (4). Complex I consists of membrane and extramembrane domains (1). A recent structure of the latter (5) established the relative positions of the NADH-oxidizing cofactor FMN and several iron-sulfur (Fe/S) clusters that provide an electron transfer pathway to the electron acceptor, ubiquinone, in the membrane domain (Fig. 1). There is no high-resolution structure of the membrane domain, which must contain the machinery of proton translocation. Electron paramagnetic resonance (EPR) spectroscopy of complex I reveals individual signals of two binuclear and several tetranuclear Fe/S clusters (6). Equilibrium redox titrations have shown that the tetranuclear cluster N2, the last in the chain (Fig. 1), has the highest midpoint redox potential (E m ), approximately Ϫ150 mV vs. NHE. One of the binuclear clusters, N1a, has b...