Three Molecules of Ubiquinone Bind Specifically to Mitochondrial Cytochrome bc1 Complex (original) (raw)
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Journal of Biological Chemistry
NADH-quinone oxidoreductase (complex I) couples electron transfer from NADH to quinone with proton translocation across the membrane. Quinone reduction is a key step for energy transmission from the site of quinone reduction to the remotely located proton-pumping machinery of the enzyme. Although structural biology studies have proposed the existence of a long and narrow quinone-access channel, the physiological relevance of this channel remains debatable. We investigated here whether complex I in bovine heart submitochondrial particles (SMPs) can catalytically reduce a series of oversized ubiquinones (OS-UQs), which are highly unlikely to transit the narrow channel because their side chain includes a bulky “block” that is ~13 Å across. We found that some OS-UQs function as efficient electron acceptors from complex I, accepting electrons with an efficiency comparable to ubiquinone-2. The catalytic reduction and proton translocation coupled with this reduction were completely inhibit...
Bioscience, biotechnology, and biochemistry, 2016
We previously produced the unique ubiquinone QT ("decoupling" quinone), the catalytic reduction of which in NADH-quinone oxidoreduction with bovine heart mitochondrial NADH-ubiquinone oxidoreductase (complex I) is completely decoupled from proton translocation across the membrane domain. This feature is markedly distinct from those of typical short-chain quinones such as ubiquinone-1. To further characterize the features of the QT reaction with complex I, we herein synthesized three QT analogs, QT2-QT4, and characterized their electron transfer reactions. We found that all aspects of electron transfer (e.g. electron-accepting activity and membrane potential formation) vary significantly among these analogs. The features of QT2 as decoupling quinone were slightly superior to those of original QT. Based on these results, we conclude that the bound positions of QTs within the quinone binding cavity susceptibly change depending on their side-chain structures, and the positions...
A New Ubiquinone Metabolite and Its Activity at the Mitochondrial bc 1 Complex
Chemical Research in Toxicology, 2007
Ubichromanol, a reductive cyclization product of ubiquinone, acts as radical scavenging antioxidant and is similarly effective as R-tocopherol. However, nothing is known so far on the two-electron oxidation product of this antioxidant and its bioactivity. This study demonstrates that ubichromanol yields a ubiquinone-like compound with a hydroxyl-substituted side chain (UQOH) on oxidation. HPLC/MS and HPLC/ECD measurements revealed its natural presence in bovine liver mitochondria. The bioactivity of this formerly unknown compound as substrate for mitochondrial complex III was tested by measurements of the quinol:cytochrome c oxidoreductase activity in bovine submitochondrial particles and isolated mitochondrial bc 1 complex. Consistently in both model systems, reduced UQOH exhibited substrate efficiencies below that of native ubiquinone but a significantly higher efficiency than R-tocopheryl quinone. Model calculations revealed that on binding of reduced UQOH to the bc 1 complex the polar hydroxyl group was located close to hydrophobic amino acid residues. This fact could in part explain the lower efficiency of reduced UQOH in comparison to ubiquinone as a substrate for the mitochondrial bc 1 complex. Therefore, the hydroxylation of the aliphatic or isoprenoid side chains of bioquinones, which is typical for quinoid oxidation products of chromanols, such as R-tocopherol and ubichromanol, disturbs substrate binding at the mitochondrial electron-transfer complexes, which usually interact with ubiquinone.
Archives of Biochemistry and Biophysics, 2000
Determination of the number of ubiquinone-and inhibitor-binding sites in the mitochondrial complex I (NADH:ubiquinone oxidoreductase) is a controversial question with a direct implication for elaborating a suitable model to explain the bioenergetic mechanism of this complicated enzyme. We have used combinations of both selective inhibitors and common ubiquinone-like substrates to demonstrate the multiplicity of the reaction centers in the complex I in contrast with competition studies that have suggested the existence of a unique binding site for ubiquinone. Our results provide new evidence for the existence of at least two freely exchangeable ubiquinone-binding sites with different specificity for substrates, as well as for a different kinetic interaction of inhibitors with the enzyme.
Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2000
NADH-ubiquinone oxidoreductase (called complex I for mitochondrial enzyme and NDH-1 for bacterial counterparts) is an energy transducer, which utilizes the redox energy derived from the oxidation of NADH with ubiquinone to generate an electrochemical proton gradient vW H across the membrane. The complex I/NDH-1 contain one non-covalently bound flavin mononucleotide and as many as eight iron-sulfur clusters as electron transfer components in common. In addition, electron paramagnetic resonance (EPR) spectroscopic studies have revealed that three ubisemiquinone (SQ) species with distinct spectroscopic and thermodynamic properties are detectable in complex I and function as electron/proton translocators. Thus, the understanding of molecular properties of the individual quinone species is prerequisite to elucidate the energy-coupling mechanism of complex I. We have investigated these SQ species using EPR spectroscopy and found that the three SQ species have strikingly different properties. We will report characteristics of these SQ species and discuss possible functional roles of individual quinone species in the electron/proton transfer reaction of complex I/NDH-1.
Identification of ubiquinol binding motifs at the Qo-site of the cytochrome bc1 complex
The journal of physical chemistry. B, 2015
Enzymes of the bc1 complex family power the biosphere through their central role in respiration and photosynthesis. These enzymes couple the oxidation of quinol molecules by cytochrome c to the transfer of protons across the membrane, to generate a proton-motive force that drives ATP synthesis. Key for the function of the bc1 complex is the initial redox process that involves a bifurcated electron transfer in which the two electrons from a quinol substrate are passed to different electron acceptors in the bc1 complex. The electron transfer is coupled to proton transfer. The overall mechanism of quinol oxidation by the bc1 complex is well enough characterized to allow exploration at the atomistic level, but details are still highly controversial. The controversy stems from the uncertain binding motifs of quinol at the so-called Qo active site of the bc1 complex. Here we employ a combination of classical all atom molecular dynamics and quantum chemical calculations to reveal the bindi...
Concerted Two-Electron Reduction of Ubiquinone in Respiratory Complex I
Journal of Physical Chemistry B, 2019
Respiratory complex I catalyzes two-electron/two-proton reduction of a ubiquinone (Q) substrate bound at its Q-binding pocket; upon reduction, ubiquinole carries electrons further down the electron transport chain. The mechanism of this twoelectron transfer reaction is poorly-understood. Here we consider a hypothetical scheme in which two electrons transfer together with two protons in a concerted fashion. On one side a coupled electron/proton transfer occurs from the reduced N2 FeS cluster and protonated His 38 residue respectively, while on the other side a hydrogen atom transfer occurs from the neutral Tyr 87 residue, generating a tyrosyl radical. A method to evaluate the coupling matrix element that corresponds to a concerted tunneling of two electrons was developed. Overall, our calculations indicate that the concerted reaction is feasible, in which case a transient tyrosyl radical is formed during the catalytic cycle of the enzyme.
The specificity of mitochondrial complex I for ubiquinones
Biochemical Journal, 1996
We report the first detailed study on the ubiquinone (coenzyme Q; abbreviated to Q) analogue specificity of mitochondrial complex I, NADH: Q reductase, in intact submitochondrial particles. The enzymic function of complex I has been investigated using a series of analogues of Q as electron acceptor substrates for both electron transport activity and the associated generation of membrane potential.
Journal of bioenergetics and biomembranes, 2001
Studies of the structure-activity relationships of ubiquinones and specific inhibitors are helpful to probe the structural and functional features of the ubiquinone reduction site of bovine heart mitochondrial complex I. Bulky exogenous short-chain ubiquinones serve as sufficient electron acceptors from the physiological ubiquinone reduction site of bovine complex I. This feature is in marked contrast to other respiratory enzymes such as mitochondrial complexes II and III. For various complex I inhibitors, including the most potent inhibitors, acetogenins, the essential structural factors that markedly affect the inhibitory potency are not necessarily obvious. Thus, the loose recognition by the enzyme of substrate and inhibitor structures may reflect the large cavity like structure of the ubiquinone (or inhibitor) binding domain in the enzyme. On the other hand, several phenomena are difficult to explain by a simple one-catalytic site model for ubiquinone.
Biochemistry, 1999
Native structures of ubihydroquinone:cytochrome c oxidoreductase (bc 1 complex) from different sources, and structures with inhibitors in place, show a 16-22 Å displacement of the [2Fe-2S] cluster and the position of the C-terminal extrinsic domain of the iron sulfur protein. None of the structures shows a static configuration that would allow catalysis of all partial reactions of quinol oxidation. We have suggested that the different conformations reflect a movement of the subunit necessary for catalysis. The displacement from an interface with cytochrome c 1 in native crystals to an interface with cytochrome b is induced by stigmatellin or 5-n-undecyl-6-hydroxy-4,7-dioxobenzothiazole (UHDBT) and involves ligand formation between His-161 of the [2Fe-2S] binding cluster and the inhibitor. The movement is a rotational displacement, so that the same conserved docking surface on the iron sulfur protein interacts with cytochrome c 1 and with cytochrome b. The mobile extrinsic domain retains essentially the same tertiary structure, and the anchoring N-terminal tail remains in the same position. The movement occurs through an extension of a helical segment in the short linking span. We report details of the protein structure for the two main configurations in the chicken heart mitochondrial complex and discuss insights into mechanism provided by the structures and by mutant strains in which the docking at the cytochrome b interface is impaired. The movement of the iron sulfur protein represents a novel mechanism of electron transfer, in which a tethered mobile head allows electron transfer through a distance without the entropic loss from free diffusion. † We acknowledge with gratitude the support for this research provided by NIH Grants GM 35438 (to A.R.C.) and DK 44842 (to E.paramagnetic resonance; [2Fe-2S], iron sulfur cluster of the Rieske-type iron sulfur protein; ISP, Rieske-type iron sulfur protein; ISP ox and ISP red , oxidized and reduced states of the iron sulfur protein; ISPB or ISPC, iron sulfur protein with the mobile extrinsic domain docked at cytochrome b or cytochrome c1 interface, respectively; LH1, light-harvesting complex 1 of bacterial photosynthesis; MOA-, -methoxyacrylate, or similar group, acting as the pharmacophore of a class of inhibitors acting at the Qo site; QH2, ubihydroquinone or quinol; Q, ubiquinone or quinone; Qi site, quinone reducing site; Qo site, quinol oxidizing site; Qos and Qow, postulated strongly and weakly binding quinone molecules bound to the quinol oxidizing site; -PEWY-, highly conserved span with this sequence in single-letter amino acid code; UHDBT, 5-n-undecyl-6-hydroxy-4,7dioxobenzothiazole.