The interaction of arylazido ubiquinone derivative with mitochondrial ubiquinol-cytochrome c reductase

The bifunctional cytochrome c reductase/processing peptidase complex from plant mitochondria

Cytochrome c reductase from potato has been extensively studied with respect to its catalytic activities, its subunit composition, and the biogenesis of individual subunits. Molecular characterization of all 10 subunits revealed that the high-molecular-weight subunits exhibit striking homologies with the components of the general mitochondrial processing peptidase (MPP) from fungi and mammals. Some of the other subunits show differences in the structure of their targeting signals or in their molecular composition when compared to their counterparts from heterotrophic organisms. The proteolytic activity of MPP was found in the cytochrome c reductase complexes from potato, spinach, and wheat, suggesting that the integration of the protease into this respiratory complex is a general feature of higher plants.

Mitochondrial ubiquinol-cytochrome c reductase complex: crystallization and protein: ubiquinone interaction

The ubiquinol-cytochrome c reductase complex was crystallized in a thin plate form, which diffracts X-rays to 7 A resolution in the presence of mother liquor. This crystalline complex contains ten protein subunits and 140 nmol phospholipid per milligram protein. Over 90% of the phospholipid and ubiquinone in the reductase can be removed by repeated ammonium sulfate precipitation in the presence of 0.5% sodium cholate. The delipidated complex has no enzymatic activity and shows significant changes in the circular dichroism spectrum in the near UV region and in the EPR characteristics of both cytochromes b. Enzyme activity and spectral characteristics can be restored by replenishing the phospholipid and ubiquinone. The structural requirements of ubiquinone for electron transport were studied by measuring the ability of a variety of synthetic ubiquinone derivatives to restore the enzymatic activity and native spectroscopic signatures to the delipidated complex. Q-binding proteins and binding domains were identified using photoaffinity labeled Q-derivatives and HPLC separation of photolabeled peptides. Interaction between ubiquinol-cytochrome c reductase and succinate-Q reductase was established by differential scanning calorimetry and saturation transfer EPR using spin-labeled ubiquinol-cytochrome c reductase. Involvement of iron-sulfur protein in proton translocation by ubiquinol-cytochrome c reductase was investigated by hematorporphyrin-promoted photoinactivation of the complex. The cDNAs encoding the Rieske iron-sulfur protein and a small molecular mass Q-binding protein (QPc-9.5 kDa) were isolated and their nucleotide sequences determined. These will be useful in future structural and mechanistic studies of ubiquinol-cytochrome c reductase via in vitro reconstitution between an over-expressed, mutated subunit and a specific subunit-depleted reductase.

Effect of papain digestion on polypeptide subunits and electron-transfer pathways in mitochondrial b-c1 complex

Papain digestion of subunits of mitochondrial b-c1 complex (ubiquinol-cytochrome-c reductase) isolated from bovine heart and its impact on redox and proton-motive activity of the whole complex were investigated. A 5-min incubation of the oxidized enzyme with papain resulted in digestion of core protein II and the 14-kDa subunit, and limited digestion of the iron-sulfur protein. This was accompanied by a small inhibition of the rate of electron flow and a marked inhibition of proton translocation with decrease of the H+/e- ratio for proton pumping. When papain treatment was performed on the b-c1 complex pre-reduced with ascorbate, partial proteolysis of the iron-sulfur protein and the 14-kDa subunit was greatly accelerated and the electron transfer activity was more markedly inhibited. In all the conditions tested, digestion of the Rieske iron-sulfur protein paralleled the inhibition of reductase activity. Under ascorbate-reduced conditions, papain digestion of the complex gave rise to an alteration of the EPR line shape of the iron-sulfur cluster, namely a broadening and shift of the gx negative peak and destabilization of the protein-bound antimycin-sensitive semiquinone. The latter paralleled the decrease in electron transfer activity and inhibition of antimycin-sensitive cytochrome-b reduction. The results obtained indicate the following. 1. Core protein II and the 14-kDa protein may contribute to the proton-conducting pathway(s) from the matrix aqueous phase to the primary protolytic redox center (protein-bound semiquinone/quinone couple). 2. The iron-sulfur protein contributes, together with other protein(s) (the 14-kDa subunit), to the stabilization of the protein-bound antimycin-sensitive semiquinone species in a protein pocket in the complex. 3. Reduction of the high-potential redox centers induces a change in the quaternary structure of the complex which results in an enhanced surface exposure of segments of the 14-kDa protein and the iron-sulfur protein.

Cytochrome b is necessary for the assembly of subunit VII in the cytochrome b-c1 complex of yeast mitochondria

The synthesis and assembly of subunit VII, the Q-binding protein of the cytochrome b-c1 complex, into the inner mitochondrial membrane has been compared in wild-type yeast cells and in a mutant cell line lacking cytochrome b. Both immunoblotting and immunoprecipitation analysis with specific antiserum against subunit VII indicated that this subunit is not detectable in the mutant as compared to the wild-type mitochondria. However, labeling in vivo of the cytochrome b deficient yeast cells in the presence of the uncoupler carbonyl cyanide m-chlorophenylhydrazone clearly demonstrated that subunit VII was synthesized in the mutant cells to the same extent as in the wild-type cells. Incubation of subunit VII, synthesized in vitro in a reticulocyte lysate programmed with yeast RNA, with mitochondria isolated from both wild-type and cytochrome b deficient yeast cells revealed that the subunit VII was transported into the wild-type mitochondria into a compartment where it was resistant to digestion by exogenous proteinase K. By contrast, subunit VII was bound in lowered amounts to the cytochrome b deficient mitochondria where it remained sensitive to digestion by exogenous proteinase K, suggesting that the import of subunit VII may be impaired due to the lack of cytochrome b. Furthermore, subunit VII was synthesized both in vivo and in vitro with the same molecular mass as the mature form of this protein.

Purification of highly active cytochrome bc1 complexes from phylogenetically diverse species by a single chromatographic procedure

A method has been developed for purification of highly active ubiquinol-cytochrome c oxidoreductase (cytochrome bc1) complexes from wild-type Rhodobacter sphaeroides, Rhodobacter capsulatus MT1131, bovine heart and yeast mitochondria. This is the first report of the isolation of cytochrome bc1 complex from a wild-type strain of Rb. sphaeroides and from any strain of Rb. capsulatus. The purification involves extraction of membranes with dodecyl maltoside and two successive DEAE column chromatography steps. All of the resulting bc1 complexes are free of succinate dehydrogenase and cytochrome c oxidase activities. The purified bc1 complexes from both photosynthetic bacteria contain four polypeptide subunits, although the molecular weights of some of their subunits differ. They are also free of reaction center and light-harvesting pigments and polypeptides. The turnover number of the Rb. sphaeroides complex is 128 s-1, and that of the Rb. capsulatus complex is 64 s-1. The bc1 complex from bovine heart contains eight polypeptides and has a turnover number of 1152 s-1, while the yeast complex contains nine polypeptides and has a turnover number of 219 s-1. The activities of these complexes are equal to or better than those commonly obtained by previously reported methods. This method of purification is relatively simple, reproducible, and yields cytochrome bc1 complexes which largely retain the turnover number of the starting material and are pure on the basis of optical spectra, enzymatic activities and polypeptide composition. The purification of cytochrome bc1 complexes from energy-transducing membranes which differ markedly in their lipid and protein composition makes it likely that with minor modifications this method could be applied to species other than those described here.

Phospholipid-dependent interaction between dibromothymoquinone and iron-sulfur protein in mitochondrial ubiquinol-cytochrome c reductase

Dibromothymoquinone (DBMIB) inhibits antimycin A-sensitive ubiquinol-cytochrome c reductase activity; the maximal inhibition is 90%. DBMIB alters the EPR spectra of reduced iron-sulfur protein in intact ubiquinol-cytochrome c reductase. The maximal spectral change occurs with 60 mol inhibitor per mol cytochrome c1 in the reductase. DBMIB causes little alteration in the EPR characteristics of iron-sulfur protein when ubiquinol-cytochrome c reductase is delipidated. When delipidated ubiquinol-cytochrome c reductase is replenished with phospholipid, the effect of DBMIB reappears. However, when DBMIB is added to delipidated protein prior to replenishment with phospholipid, very little spectral alteration is observed. DBMIB does not alter the EPR spectra of purified iron-sulfur protein, with or without phospholipid in the preparation. Reduced DBMIB does not alter the EPR characteristics of iron-sulfur protein in intact or delipidated ubiquinol-cytochrome c reductase. Cysteine and other thiol compounds can reverse the spectral alternation caused by DBMIB. This reversal probably results from the reduction of DBMIB.

Organization and function of cytochrome b and ubiquinone in the cristae membrane of beef heart mitochondria

The arrangement and function of the redox centers of the mammalian bc1 complex is described on the basis of structural data derived from amino acid sequence studies and secondary structure predictions and on the basis of functional studies (i.e., EPR data, inhibitor studies, and kinetic experiments). Two ubiquinone reaction centers do exist--a QH2 oxidation center situated at the outer, cytosolic surface of the cristae membrane (Q0 center), and a Q reduction center (Qi center) situated more to the inner surface of the cristae membrane. The Q0 center is formed by the b-566 domain of cytochrome b, the FeS protein, and maybe an additional small subunit, whereas the Qi center is formed by the b-562 domain of cytochrome b and presumably the 13.4 kDa protein ("QP-C"). The "Q binding proteins" are proposed to be protein subunits of the Q reaction centers of various multiprotein complexes. The path of electron flow branches at the Q0 center, half of the electrons flowing via the high-potential cytochrome chain to oxygen and half of the electrons cycling back into the Q pool via the cytochrome b path connecting the two Q reaction centers. During oxidation of QH2, 2H+ are released to the cytosolic space and during reduction of Q, 2H+ are taken up from the matrix side, resulting in a net transport across the membrane of 2H+ per e- flown from QH2 to cytochrome c, the H+ being transported across the membrane as H (H+ + e-) by the mobile carrier Q. The authors correct their earlier view of cytochrome b functioning as a H+ pump, proposing that the redox-linked pK changes of the acidic groups of cytochrome b are involved in the protonation/deprotonation processes taking place during the reduction and oxidation of Q. The reviewers stress that cytochrome b is in equilibrium with the Q pool via the Qi center, but not via the Q0 center. Their view of the mechanisms taking place at the reductase is a Q cycle linked to a Q-pool where cytochrome b is acting as an electron pump.

Experimental observations on the structure and function of mitochondrial complex III that are unresolved by the protonmotive ubiquinone-cycle hypothesis

The current model of the protonmotive ubiquinone cycle as applied to mitochondrial ubiquinol-cytochrome c reductase complex (Complex III) is able to explain a number of previously puzzling observations concerning electron-transfer and proton translocating functions of the complex. However, a number of pertinent experimental observations concerning the structure and function of this complex cannot as yet be incorporated into the present version of the ubiquinone cycle. The yet unresolved problems of electron transfer uncovered by these observations include some kinetic and thermodynamic problems, uncertainties in the binding site(s) and mode of binding of ubiquinol and inhibitors, the observed multiple spectroscopic, electrochemical, and kinetic forms of cytochromes b, iron-sulfur protein, and cytochrome c1, the multiple and overlapping effects of inhibitors, and the functional role of conformational changes in the complex. It is concluded that although the Q cycle is a valuable base for the design of future experiments, its mechanism must be reconciled with the above uncertainties as well as with the accumulated evidence that Complex III can exist in two or more interchangeable forms, exhibiting different properties with respect to electron-transfer pathways, inhibitor binding, and spectral and electrochemical properties of the electron-carrier subunits.

Isolation and amino acid sequence of the 9.5 kDa protein of beef heart ubiquinol:cytochrome c reductase

The 9.5 kDa protein of beef heart ubiquinol:cytochrome c reductase was isolated by a series of chromatographic steps involving dissociation of the complex by urea and guanidine. A clear distinction between the 9.5 kDa protein and the 9.2 kDa protein described earlier [(1982) J. Biochem. 91, 2077-2085] by SDS-PAGE was only achieved when the electrophoresis was performed according to Schägger et al. [(1985) FEBS Lett. 190, 89-94; (1986) Methods Enzymol. 126, 22] because in this gel system the apparent molecular mass of the 9.5 kDa protein is shifted to 11 kDa. The amino acid sequence was determined by solid-phase Edman degradation of the whole protein up to amino acid residue 80 and of the proteolytic cleavage fragments. The protein consists of 81 amino acid residues; its Mr was calculated to be 9507. Structure predictions have been made from average and sided hydropathy profiles. The 9.5 kDa protein is either bound to the core proteins within a 9.5 kDa-core protein subcomplex or else it aggregates easily with the core proteins during the isolation procedure.

Coenzyme Q analogues reconstitute electron transport and proton ejection but not the antimycin-induced "red shift" in mitochondria from coenzyme Q deficient mutants of the yeast Saccharomyces cerevisiae

Mitochondria isolated from coenzyme Q deficient yeast cells had no detectable NADH:cytochrome c reductase or succinate:cytochrome c reductase activity but contained normal amounts of cytochromes b and c1 by spectral analysis. Addition of the exogenous coenzyme Q derivatives including Q2, Q6, and the decyl analogue (DB) restored the rate of antimycin- and myxothiazole-sensitive cytochrome c reductase with both substrates to that observed with reduced DBH2. Similarly, addition of these coenzyme Q analogues increased 2-3-fold the rate of cytochrome c reduction in mitochondria from wild-type cells, suggesting that the pool of coenzyme Q in the membrane is limiting for electron transport in the respiratory chain. Preincubation of mitochondria from the Q-deficient yeast cells with DBH2 at 25 degrees C restored electrogenic proton ejection, resulting in a H+/2e- ratio of 3.35 as compared to a ratio of 3.22 observed in mitochondria from the wild-type cell. Addition of succinate and either coenzyme Q6 or DB to mitochondria from the Q-deficient yeast cells resulted in the initial reduction of cytochrome b followed by a slow reduction of cytochrome c1 with a reoxidation of cytochrome b. The subsequent addition of antimycin resulted in the oxidant-induced extrareduction of cytochrome b and concomitant oxidation of cytochrome c1 without the "red" shift observed in the wild-type mitochondria. Similarly, addition of antimycin to dithionite-reduced mitochondria from the mutant cells did not result in a red shift in the absorption maximum of cytochrome b as was observed in the wild-type mitochondria in the presence or absence of exogenous coenzyme Q analogues.(ABSTRACT TRUNCATED AT 250 WORDS)

Identification of ubiquinone-binding proteins in yeast mitochondrial ubiquinol-cytochrome c reductase using an azido-ubiquinone derivative

An azido-ubiquinone derivative, 3-azido-2-methyl-5-methoxy-6-(3,7-dimethyloctyl)-1,4-benzoquinone, was used to study the ubiquinone-protein interaction and to identify the ubiquinone-binding proteins in yeast mitochondrial ubiquinone-cytochrome c reductase. The phospholipids and Q6 in purified reductase were removed by repeated ammonium sulfate precipitation in the presence of 0.5% sodium cholate. The resulting phospholipid- and ubiquinone-depleted reductase shows no enzymatic activity; activity can be completely restored by the addition of phospholipids and Q6 or Q2. The ubiquinone- and phospholipid-replenished ubiquinonol-cytochrome c reductase is also fully active upon reconstituting with bovine succinate-ubiquinone reductase to form succinate-cytochrome c reductase. When an azido-ubiquinone derivative was added to the ubiquinone and phospholipid-depleted reductase in the dark, followed by the addition of phospholipids, partial reconstitutive activity was restored, while full ubiquinol-cytochrome c reductase activity was observed when Q2H2 was used as substrate in the assay mixture. Apparently, the large amount of Q2H2 present in the assay mixture displaces the azido-ubiquinone in the system. Photolysis of the azido-Q-treated reductase with long-wavelength ultraviolet light abolishes about 70% of both the restored reconstitutive activity and Q2H2-cytochrome c reductase activity. The activity loss is directly proportional to the covalent binding of [3H]azido-ubiquinone to the reductase protein. When the photolyzed, [3H]azido-ubiquinone-treated sample was subjected to SDS-polyacrylamide gel electrophoresis followed by analysis of the distribution of radioactivity among the subunits, the cytochrome b protein and a protein with an apparent molecular weight of 14 000 were heavily labeled. The amount of radioactive labeling in both these proteins was affected by the presence of phospholipids.

Syntheses and biological activities of azido ubiquinone derivatives

A general method for the synthesis of azido-ubiquinone derivatives has been developed directly by substituting one hydrogen atom on the benzoquinone ring with an azido group under weakly acidic conditions. The reaction takes several hours and the yield is generally low. The azido-ubiquinone was purified by preparative thin layer chromatography, and identified by NMR, IR and mass spectra. All the synthesized azido-ubiquinone derivatives show partial activity in mediating biological electron transfer in the dark, and show partial or complete inhibition upon photolysis.