Relation of the respiratory chain-linked reduced nicotinamide--adenine dinucleotide dehydrogenase to energy-coupling site 1

Using Hyperfine Electron Paramagnetic Resonance Spectroscopy to Define the Proton-Coupled Electron Transfer Reaction at Fe-S Cluster N2 in Respiratory Complex I

Energy-transducing respiratory complex I (NADH:ubiquinone oxidoreductase) is one of the largest and most complicated enzymes in mammalian cells. Here, we used hyperfine electron paramagnetic resonance (EPR) spectroscopic methods, combined with site-directed mutagenesis, to determine the mechanism of a single proton-coupled electron transfer reaction at one of eight iron-sulfur clusters in complex I, [4Fe-4S] cluster N2. N2 is the terminal cluster of the enzyme's intramolecular electron-transfer chain and the electron donor to ubiquinone. Because of its position and pH-dependent reduction potential, N2 has long been considered a candidate for the elusive "energy-coupling" site in complex I at which energy generated by the redox reaction is used to initiate proton translocation. Here, we used hyperfine sublevel correlation (HYSCORE) spectroscopy, including relaxation-filtered hyperfine and single-matched resonance transfer (SMART) HYSCORE, to detect two weakly coupled exchangeable protons near N2. We assign the larger coupling with A(¹H) = [-3.0, -3.0, 8.7] MHz to the exchangeable proton of a conserved histidine and conclude that the histidine is hydrogen-bonded to N2, tuning its reduction potential. The histidine protonation state responds to the cluster oxidation state, but the two are not coupled sufficiently strongly to catalyze a stoichiometric and efficient energy transduction reaction. We thus exclude cluster N2, despite its proton-coupled electron transfer chemistry, as the energy-coupling site in complex I. Our work demonstrates the capability of pulse EPR methods for providing detailed information on the properties of individual protons in even the most challenging of energy-converting enzymes.

The unique chemistry and biology of the piericidins

The piericidin family of microbial metabolites features a 4-pyridinol core linked with a methylated polyketide side chain. Piericidins are exclusively produced by actinomycetes, especially members of the genus Streptomyces. The close structural similarity with coenzyme Q renders the piericidins important NADH-ubiquinone oxidoreductase (complex I) inhibitors in the mitochondrial electron transport chain. Because of the significant activities of the piericidins, which include insecticidal, antimicrobial and antitumor effects, total syntheses of the piericidins were developed using various synthetic strategies. The biosynthetic origin of this class has also been the subject of investigation. This review covers the isolation and structure determination of the natural piericidins, their chemical modification, the total syntheses of natural and unnatural analogs, their biosynthesis, and reported biological activities together with structure-activity relationships. Given the fundamental biology of this class of metabolites, the piericidin family will likely continue to attract attention as biological probes of important biosynthetic processes.

A reductant-induced oxidation mechanism for complex I

A model for energy conversion in Complex I is proposed that is a conservative expansion of Mitchell's Q-cycle using a simple mechanistic variation of that already established experimentally for Complex III. The model accommodates the following proposals. (1) The large number of flavin and iron-sulfur redox cofactors integral to Complex I form a simple but long electron transfer chain guiding submillisecond electron transfer from substrate NADH in the matrix to the [4Fe-4S] cluster N2 close to the matrix-membrane interface. (2) The reduced N2 cluster injects a single electron into a ubiquinone (Q) drawn from the membrane pool into a nearby Qnz site, generating an unstable transition state semiquinone (SQ). The generation of a SQ species is the primary step in the energy conversion process in Complex I, as in Complex III. In Complex III, the SQ at the Qo site near the cytosolic side acts as a strong reductant to drive electronic charge across the membrane profile via two hemes B to a Qi site near the matrix side. We propose that in Complex I, the SQ at the Qnz site near the matrix side acts as a strong oxidant to pull electronic charge across the membrane profile via a quinone (Qny site) from a Qnx site near the cytosolic side. The opposing locations of matrix side Qnz and cytosolic side Qo, together with the opposite action of Qnz as an oxidant rather than a reductant, renders the Complex I and III processes vectorially and energetically complementary. The redox properties of the Qnz and Qo site occupants can be identical. (3) The intervening Qny site of Complex I acts as a proton pumping element (akin to the proton pump of Complex IV), rather than the simple electron guiding hemes B of Complex III. Thus the transmembrane action of Complex I doubles to four (or more) the number of protons and charges translocated per NADH oxidized and Q reduced. The Qny site does not exchange with the pool and may even be covalently bound. (4) The Qnx site on the cytosol side of Complex I is complementary to the Qi site on the matrix side of Complex III and can have the same redox properties. The Qnx site draws QH2 from the membrane pool to be oxidized in two single electron steps. Besides explaining earlier observations and making testable predictions, this Complex I model re-establishes a uniformity in the mechanisms of respiratory energy conversion by using engineering principles common to Complexes III and IV: (1) all the primary energy coupling reactions in the different complexes use oxygen chemistry in the guise of dioxygen or ubiquinone, (2) these reactions are highly localized structurally, utilizing closely placed catalytic redox cofactors, (3) these reactions are also highly localized energetically, since virtually all the free energy defined by substrates is conserved in the form of transition state that initiates the transmembrane action and (4) all complexes possess apparently supernumerary oxidation-reduction cofactors which form classical electron transfer chains that operate with high directional specificity to guide electron at near zero free energies to and from the sites of localized coupling.

Identification of the TYKY homologous subunit of complex I from Neurospora crassa

A polypeptide subunit of complex I from Neurospora crassa, homologous to bovine TYKY, was expressed in Escherichia coli, purified and used for the production of rabbit antiserum. The mature mitochondrial protein displays a molecular mass of 21280 Da and results from cleavage of a presequence consisting of the first 34 N-terminal amino acids of the precursor. This protein was found closely associated with the peripheral arm of complex I.

Proton-translocation by membrane-bound NADH:ubiquinone-oxidoreductase (complex I) through redox-gated ligand conduction

For the catalytic mechanism of proton-translocating NADH-dehydrogenase (complex I, EC 1.6.99.3) a number of hypothetical models have been proposed over the last three decades. These models are discussed in the light of recent substantial progress on the structure and function of this very complicated multiprotein complex. Only the high-potential iron-sulfur center N-2 and ubiquinone seem to contribute to the proton-translocating machinery of complex I: Based on the pH dependent midpoint potential of iron-sulfur cluster N-2 and the physical properties of ubiquinone intermediates a novel mechanism is proposed. The model builds on a series of defined chemical reactions taking place at three different ubiquinone-binding sites. Therefore, some aspects of this redox-gated ligand conduction mechanism are reminiscent to the proton-motive Q-cycle. However, its central feature is the abstraction of a proton from ubihydroquinone by a redox-Bohr group associated with iron-sulfur cluster N-2. Thus, in the proposed mechanism proton translocation is driven by a direct linkage between redox dependent protonation of iron-sulfur cluster N-2 and the redox chemistry of ubiquinone.

Bacterial NADH-quinone oxidoreductases: iron-sulfur clusters and related problems

Many bacteria contain proton-translocating membrane-bound NADH-quinone oxidoreductases (NDH-1), which demonstrate significant genetic, spectral, and kinetic similarity with their mitochondrial counterparts. This review is devoted to the comparative aspects of the iron-sulfur cluster composition of NDH-1 from the most well-studied bacterial systems to date.: Paracoccus denitrificans, Rhodobacter sphaeroides, Escherichia coli, and Thermus thermophilus. These bacterial systems provide useful models for the study of coupling Site I and contain all the essential parts of the electron-transfer and proton-translocating machinery of their eukaryotic counterparts.

Evidence for two independent pathways of electron transfer in mitochondrial NADH:Q oxidoreductase. II. Kinetics of reoxidation of the reduced enzyme

The pre-steady-state kinetics of reoxidation of NADH:Q oxidoreductase present in submitochondrial particles has been studied by the freeze-quench method. It was found that at pH 8 only 50% of the Fe-S clusters 2 and 4 and 75% of the clusters 3 were rapidly reoxidised after transient and complete reduction by a pulse of NADH in the presence of excess NADPH. Thus, NADPH keeps 50% of the clusters 2 and 4 and 25% of the clusters 3 permanently reduced at this pH. Since NADH oxidation is nearly optimal at this pH, whereas NADPH oxidation is virtually absent, it was concluded that these permanently reduced clusters were not involved in the NADH oxidation activity. Incomplete reoxidation of the clusters 2, 3 and 4 after a pulse of NADH was also found in the absence of NADPH, both at pH 6.5 and at pH 8. A pulse of NADPH given at pH 6.5, where NADPH oxidation by oxygen is nearly optimal, caused a slow reduction of 50% of clusters 2 and 4 and 30% of the clusters 3, which persisted for a period of at least 15 s. It was concluded that these clusters were not involved in the oxidation of NADPH by oxygen, as catalysed by the particles. As a working hypothesis a dimeric model for NAD(P)H:Q oxidoreductase is proposed, consisting of two different protomers. One of the protomers, containing FMN and the Fe-S clusters 1-4 in stoichiometric amounts, only reacts with NADH, and its oxidation by ubiquinone is rapid at pH but slow at pH 6.5. The other protomer, containing FMN and the clusters 2, 3 and 4, reacts with both NADH and NADPH and has a pH optimum at 6-6.5 for the reaction with ubiquinone.

Studies of the ferricyanide reductase activities of the mitochondrial reduced nicotinamide adenine dinucleotide-ubiquinone reductase (complex I) utilizing arylazido-beta-alanyl NAD+ and arylazido-beta-alanyl NADP+

The NADH and NADPH ferricyanide reductase activities present in mitochondrial NADH-CoQ reductase preparations have been studied utilizing two photoaffinity pyridine nucleotide analogues: arylazido-beta-alanyl NAD+ (A3'-O-[3-[N-(4-azido-2-nitrophenyl)amino]propionyl]NAD+) and arylazido-beta-alanyl NADP+ (N3'-O-[3-[N-(4-azido-3-nitrophenyl)amino]propionyl]NADP+). For the NADH-K3Fe(CN)6 reductase activity, arylazido-beta-alanyl NAD+ was found to be, in the dark, a competitive inhibitor with respect to both NADH and K3Fe(CN)6 with Ki,app values of 9.7 and 15.5 microM, respectively. In comparison the NADP+ analogue exhibited weak noncompetitive inhibitor activity for this reaction against both substrates. Upon photoirradiation arylazido-beta-alanyl NAD+ inhibited NADH-K3Fe(CN)6 reductase up to 70% in the presence of a 25-fold molar excess of analogue over the enzyme concentration. This photodependent inhibition could be prevented by the presence, during irradiation, of the natural substrate NADH. In contrast complex kinetic results were obtained with studies of the effects of the pyridine nucleotide analogues of NADPH-K3Fe(CN)6 reductase activity in the dark. Photoirradiation of either analogue in the presence of the enzyme complex resulted in an activation of NADPH-dependent activity. The possibility that the NADPH-K3Fe(CN)6 reductase activity of complex I represents a summation of the combined ferricyanide reductase activity of the NADPH-NAD+ transhydrogenase and NADH oxidoreductase is suggested.

An analysis of some thermodynamic properties of iron-sulphur centres in site I of mitochondria

1. The midpoint potentials of the various iron-sulphur centres in Site I were determined at different pH values by the technique of redox potentiometry. An interesting feature is the pH-dependence of Centre N-2, the highest potential component of the NADH dehydrogenase segment of the respiratory chain. 2. The apparent midpoint potentials of Centre N-2 (NADH dehydrogenase) and S-1 (succinate dehydrogenase) and their pH-dependence was also determined by using the succinate/fumarate couple. Again Centre N-2 is pH-dependent in midpoint potential, and Centre S-1 is not. The results obtained by titrating with the succinate/fumarate couple are in quantitative agreement with those obtained for these centres by redox potentiometry. 3. Oxidation-reduction titrations of iron-sulphur centres with the couple NADH/NAD+ and an analogue APADH/APAD+ in the presence of rotenone gave results substantially different from those obtained by redox potentiometry; these differences may be due to the mechanism of action of NADH dehydrogenase and its specific interaction with NADH. 5. The addition of ATP to an NAD+/NADH-poised system induces an uncoupler-sensitive oxidation of Centre N-4.

Studies on the mechanism of site I energy conservation

1. Of the several iron-sulfur centers detected in the site I segment of the respiratory chain, centers N-2 and N-1a alone exhibit apparent phosphate-potential dependent half-reduction potentials, indicating their possible involvement in energy conservation. 2. At high phosphate potential, the apparent half-reduction potential of center N-2 shifts positively by 125 +/- 20 mV, while center N-1a shifts negatively by approximately 60 mV. 3. The redox state of individual iron-sulfur centers in various metabolic states was analyzed. Center N-2 is highly reduced (greater than 90%) in "state 4" mitochondria, while center N-1a stays mostly oxidized. 4. In a submitochondrial system, ATP addition induced reduction of center N-2 if the Eh of the suspension was poised from the high potential side of site I using the succinate/fumarate couple. In contrast, center N-2 was oxidized upon energization, if the Eh of the system was poised from the low potential side using the NADH/NAD couple. 5. Based on these redox behaviors of center N-2, a tentative hypothesis of site I energy transduction was proposed.

A protective function of superoxide dismutase during respiratory chain activity

(1) Aerobic incubation of heart muscle submitochondrial particles in phosphate buffer after treatment with NADH causes a progressive and substantial inhibition of the NADH oxidation system. Succinate oxidation remains almost unaffected by NADH treatment. (2) The loss of NADH oxidase activity is due to an inhibition of the respiratory chain-linked NADH dehydrogenase. This inhibition of the enzyme is very similar to that caused by combination of the organic mercurial mersalyl with NADH dehydrogenase. (3) The inhibition of NADH oxidation is largely prevented by compounds that are known to react with superoxide ions (02-.), including superoxide dismutase, cytochrome c, tiron and Mn2+. EDTA also has a protective effect, but a number of other metal chelating agents, and several proteins, including catalase, are without effect. (4) It is concluded that the inhibition of NADH oxidation of NADH oxidation by superoxide ions or by mersalyl is reversible and is therefore not due to the loss of oxidoreduction components from the respiratory chain or to an irreversible change in protein conformation. (6) The function of mitochondrial superxide dismutase is discussed in relation to the key role of NADH dehydrogenase in energy-conserving reactions and the formation of hydrogen peroxide during mitochondrial oxidations.

Proton translocation coupled to quinone reduction by reduced nicotinamide--adenine dinucleotide in rat liver and ox heart mitochondria

Measurements were made of the stoicheiometry of proton-translocation coupled to NAD(P)H oxidation by several quinones (duroquinone, ubiquinone(0), ubiquinone(1), ubiquinone(2)) in mitochondria from rat liver and ox heart. Observed stoicheiometries of protons translocated per mol of NADH oxidized (-->H(+)/2e(-) ratios; Mitchell, 1966) ranged from 0.75 (rat liver mitochondria with ubiquinone(1)) to 1.55 (ox heart mitochondria with ubiquinone(1) or ubiquinone(2)). Only the rotenone-sensitive pathway of NADH oxidation by quinone was able to support proton translocation. Correction of the observed -->H(+)/2e(-) ratios for the loss of reducing equivalents to the rotenone-insensitive pathway increased their value to approx. 2.0. It is concluded that the rotenone-sensitive NADH- ubiquinone reductase activity of the respiratory chain may be organized in the mitochondrial membrane as a proton-translocating oxidoreduction loop. The number of such loops between NADH and ubiquinone is one, and not two, as initially proposed by Mitchell (1966).