The NADH-binding subunit of the energy-transducing NADH-ubiquinone oxidoreductase of Paracoccus denitrificans: gene cloning and deduced primary structure

The NADH dehydrogenase complex isolated from Paracoccus denitrificans is composed of approximately 10 unlike polypeptides and contains noncovalently bound FMN, non-heme iron, and acid-labile sulfide [Yagi, T. (1986) Arch. Biochem. Biophys. 250, 302-311]. The NADH-binding subunit (Mr = 50,000) of this enzyme complex was identified by direct photoaffinity labeling with [32P]NADH [Yagi, T., & Dinh, T.M. (1990) Biochemistry 29, 5515-5520]. Primers were synthesized on the basis of the N-terminal amino acid sequence of this polypeptide, and these primers were used to synthesize an oligonucleotide probe by the polymerase chain reaction. This probe was utilized to isolate the gene encoding the NADH-binding subunit from a genomic library of P. denitrificans. The nucleotide sequence of the gene and the deduced amino acid sequence of the entire NADH-binding subunit were determined. The NADH-binding subunit has 431 amino acid residues and a calculated molecular weight of 47,191. The encoded protein contains a putative NAD(H)-binding and an iron-sulfur cluster-binding consensus sequence. The deduced amino acid sequence of the Paracoccus NADH-binding subunit shows remarkable similarity to the alpha subunit of the NAD-linked hydrogenase of Alcaligenes eutrophus H16. When partial DNA sequencing of the regions surrounding the gene encoding the NADH-binding subunit was carried out, sequences homologous to the 24-, 49-, and 75-kDa polypeptides of bovine complex I were detected, suggesting that the structural genes of the Paracoccus NADH dehydrogenase complex constitute a gene cluster.

Studies on the mechanism of oxidative phosphorylation. ADP promotion of GDP phosphorylation

The process of ATP or GTP synthesis by bovine heart submitochondrial particles involves the binding of ADP or GDP to 3 exchangeable sites I, II, and III, and only upon substrate occupation of site III does rapid ATP or GTP synthesis take place. The dissociation constants determined for ADP were KADPI less than or equal to 10(-8) M, KADPII approximately 10(-7) M, and KADPIII (equivalent to apparent KADPm), approximately 3 x 10(-6) M in the low Km mode and KADPIII approximately 150 x 10(-6) M in the high Km mode. For GDP, these constants were KGDPI approximately 10(-6)-10(-5) M, KGDPII approximately 10(-4) M, and KGDPIII approximately 10(-3) M when NADH was the respiratory substrate (Matsuno-Yagi, A., and Hatefi, Y. (1990) J. Biol. Chem. 265, 82-88). Because of its low affinity for the above binding sites, GDP at micromolar concentrations does not lead to GTP synthesis. However, as shown in this paper, micromolar [GDP] undergoes phosphorylation in the presence of micromolar concentrations of ADP. Under these conditions, both ATP and GTP are synthesized. GDP inhibits ATP synthesis with KGDPi congruent to 7 microM, while ADP promotes GTP synthesis in a reaction that requires inorganic phosphate (apparent KPim = 2-3 mM) and is inhibited by uncouplers and inhibitors of the ATP synthase complex. The ADP-promoted GTP synthesis exhibited an "apparent" KGDPm = 4 microM and an "apparent" Vmax = 11 nmol of GTP (min.mg of protein)-1. These results were interpreted to mean that (a) micromolar [ADP] occupies sites I and II, allowing site III to bind and phosphorylate GDP, and (b) the KGDPm and Vmax calculated under these conditions represent values for the low Km-low Vmax mode of GTP synthesis, which in the absence of ADP is not detectable because of the positive cooperativity phase of GTP synthesis with the high KGDPII approximately 10(-4) M.

Studies on the mechanism of oxidative phosphorylation. Positive cooperativity in ATP synthesis

Kinetic and nucleotide binding studies have shown that submitochondrial particles from bovine heart possess three exchangeable binding sites for ADP or GDP. In order of decreasing affinity at neutral pH, these sites will be referred to as sites I, II, and III, and their respective dissociation constants as KI, KII, and KIII. In oxidative phosphorylation experiments in the presence of saturating amounts of inorganic phosphate, rapid ATP (or GTP) synthesis occurred only upon ADP (or GDP) binding to site III. The Eadie-Hofstee plots (v/[S] on the ordinate versus v on the abscissa) of the kinetics of ATP (or GTP) synthesis at variable ADP (or GDP) were, therefore, composed of an initial upward phase, indicating positive cooperativity with respect to substrate concentration, followed by a downward phase where rapid product formation took place. These data allowed calculation of KII from the upward phase and KIII (equivalent to apparent Km) from the downward phase. KI was estimated from Scatchard plots of binding data with radiolabeled ADP or GDP. Thus, together with our previous results, these findings have allowed characterization of the process of ATP or GTP synthesis by bovine-heart submitochondrial particles in terms of KI, KII, KIII, and kcat.

Uncoupling of oxidative phosphorylation: different effects of lipophilic weak acids and electrogenic ionophores on the kinetics of ATP synthesis

Previous studies from this laboratory have shown that the kinetics of ATP synthesis by bovine heart submitochondrial particles (SMP) are modulated by the coupled rate of respiration between two extremes of Vmax and apparent Km's for ADP and Pi [Matsuno-Yagi, A., & Hatefi, Y. (1986) J. Biol. Chem. 261, 14031-14038; Hekman, C., Matsuno-Yagi, A., & Hatefi, Y. (1988) Biochemistry 27, 7559-7565]. Thus, with ADP as the variable substrate, ATP synthesis occurred with Vmax = 200 nmol of ATP min-1 (mg of protein)-1 at 30 degrees C and an apparent KmADP = 2-4 microM at low rates of respiration, and with Vmax = 11,000 nmol of ATP min-1 (mg of protein)-1 at 30 degrees C and an apparent KmADP = 120-160 microM at high rates of respiration. At intermediate respiration rates, it was necessary to introduce a third intermediate KmADP for best fit of the kinetic data, indicating that transition from one kinetic extreme to the other is not abrupt and involves intermediate kinetic states of the ATP synthase complexes. The present paper shows that uncouplers affect the kinetics of ATP synthesis by SMP in two ways. When used at moderate concentrations, electrogenic ionophores such as gramicidin D or valinomycin plus nigericin decreased the Vmax for ATP synthesis without changing the contributions of the low, intermediate, and high KmADP to the overall rate of ATP synthesis. By contrast, potent lipophilic weak acid uncouplers, such as FCCP, CCCP, S-13, and SF6847, decreased Vmax and converted the kinetics of ATP synthesis toward high KmADP.(ABSTRACT TRUNCATED AT 250 WORDS)

Energy-induced modulation of the kinetics of oxidative phosphorylation and reverse electron transfer

The kinetics of ATP synthesis by bovine heart submitochondrial particles (SMP) are modulated by the rate of energy production by the respiratory chain between two fixed limits characterized by apparent KmADP = 2-4 microM and Vmax approximately 200 nmol of ATP min-1 (mg of SMP protein)-1 at low energy levels and apparent KmADP = 120-160 microM and Vmax = 11,000 nmol of ATP min-1 (mg of SMP protein)-1 at high energy levels. These data indicate that KmADP and Vmax increase approximately 50-fold each; therefore, there is essentially no change in the catalytic efficiency of the ATP synthase complex in going from one extreme to the other. At intermediate rates of energy production, the kinetic data required introduction of a third, intermediate KmADP. A KmADP of 10-15 microM fitted all the data reported here and previously [Matsuno-Yagi, A., & Hatefi, Y. (1986) J. Biol. Chem. 261, 14031-14038]. However, this is not meant to suggest that there is a fixed intermediate KmADP, as the transition from one fixed limit to the other may be fluid or involve more than one intermediate state. In addition, it has been shown that kinetic plots of SMP-catalyzed and ATP-driven reverse electron transfer from succinate to NAD are curvilinear and resolvable into a minimum of two apparent KmNAD values of about 20-30 and 200-300 microM. These results have been discussed in relation to the three potentially active catalytic sites of F1-ATPase and the structure of the NADH:ubiquinone oxidoreductase complex, the curvilinear kinetics of ATP hydrolysis, and changes in KmADP and KmPi in photophosphorylation as affected by the duration and intensity of light.

Role of energy in oxidative phosphorylation

This article reviews the current status of information regarding the role of energy in the process of oxidative phosphorylation by mitochondria. The available data suggest that in submitochondrial particles (SMP) energy is utilized for the binding of ADP and Pi and for the release of ATP bound at the catalytic sites of F1-ATPase. The process of ATP synthesis on the surface of F1 from F1-bound ADP and Pi appears to be associated with negligible free energy change. The rate of energy production by the respiratory chain modulates the kinetics of ATP synthesis between a low Km (for ADP and Pi)-low Vmax mode and a high Km-high Vmax mode. The Km extremes for ADP are 2-3 microM and 120-150 microM, and Vmax for ATP synthesis at high rates of energy production by bovine-heart SMP is about 440 S-1 (mole F1)-1 at 30 degrees C, which corresponds to 11 mumol ATP (min.mg of protein)-1. The interaction of dicyclohexylcarbodiimide (DCCD) or oligomycin at the proteolipid (subunit c) of the membrane sector (F0) of the ATP synthase complex alters the mode of ATP binding at the catalytic sites of F1, probably to one of lower affinity. It has been suggested that protonic energy might be conveyed to the catalytic sites of F1 in an analogous manner, i.e., via conformation changes in the ATP synthase complex initiated by proton-induced alterations in the structure of the DCCD-binding proteolipid. Finally, the relationship between the steady-state membrane potential (delta psi) and the rates of electron transfer and ATP synthesis has been discussed. It has been shown, in agreement with the delocalized chemiosmotic mechanism, that under appropriate conditions delta psi is exquisitely sensitive to changes in the rates of energy production and consumption.

Estimation of the turnover number of bovine heart F0F1 complexes for ATP synthesis

In mitochondria and submitochondrial particles (SMP), the rate of ATP synthesis is restricted by the rate of energy production by the respiratory chain. Fractional inactivation of the ATP synthase complexes (F0F1) of bovine heart SMP by covalent modifiers increased the rate of ATP synthesis per mole of active F0F1. Thus, by use of SMP containing fractionally inactivated F0F1 complexes, a synthetic rate of 420 mol of ATP (mol of F0F1.s)-1 was measured, which extrapolated to a Vmax of 440 s-1. At this extrapolated point, the turnover rate of F0F1 complexes was independent of the rate of energy production by the respiratory chain. These results have been discussed in relation to the effect of fractional inactivation of the F0F1 complexes of SMP on the steady-state free energy of the system. The above rate of ATP synthesis is comparable to the rate of ATP hydrolysis by SMP (400-520 s-1) in the absence of energy coupling constraints and control by the ATPase inhibitor protein. More interestingly, this rate is also comparable to the rate of ATP synthesis by chloroplast F0F1 under high light intensity (approximately 420 s-1). Under the conditions specified, bovine heart SMP and chloroplasts show similar apparent Km values for ADP. Thus, it appears that the mammalian and chloroplast ATP synthase complexes are similar not only in structure but also in catalytic efficiency for ATP synthesis.

Studies on the mechanism of oxidative phosphorylation. Flow-force relationships in mitochondrial energy-linked reactions

The relationship between the steady-state level of membrane potential (delta psi) and the rates of energy production and consumption has been studied in mitochondria and submitochondrial particles. The energy-linked reactions investigated were oxidative phosphorylation (with NADH, succinate, and beta-hydroxybutyrate as respiratory substrates) and nucleoside triphosphate-driven transhydrogenation from NADH to NADP and uphill electron transfer from succinate to NAD. Results have shown the following. 1) Attenuation of the rates of the energy-producing reactions results in a parallel change in the rates of the energy-consuming reactions with little or no change in the magnitude of steady-state delta psi. 2) At low rates of energy production and consumption, steady-state delta psi decreases. However, this is due largely to the energy leak of the system which lowers static-head delta psi when the rate of energy production is slow. 3) When the rate of energy production and static-head delta psi are held constant, and the rate of energy consumption is diminished by partial inhibition or the use of suboptimal conditions (e.g. subsaturating substrate concentrations), then even a small decrease in the rate of energy consumption results in an upward adjustment of the level of steady-state delta psi. The lower the rate of energy input, the greater the upward adjustment of steady-state delta psi upon suppression of the rate of energy consumption. 4) The above results have been discussed with regard to the role of bulk-phase delta mu H+ or delta psi in the mitochondrial energy transfer reactions.

Kinetic modalities of ATP synthesis. Regulation by the mitochondrial respiratory chain

Two interconvertible kinetic modes are described for ATP synthesis by bovine heart submitochondrial particles. One mode is characterized by low apparent Km values for ADP (6-10 microM) and Pi (less than or equal to 0.25 mM), and a limited capacity for ATP synthesis (apparent Vmax approximately 500 nmol ATP.min-1.mg of protein-1). ATP synthesis occurs predominantly in this mode when the coupled activity of the respiratory chain relative to the number of functional ATP synthase complexes is low. The second kinetic mode is characterized by high apparent Km values for ADP (50-100 microM) and Pi (approximately 2.0 mM) and a high capacity for ATP synthesis (Vmax greater than 1800 nmol ATP.min-1.mg of protein-1). This mode of ATP synthesis predominates when the available free energy relative to the number of functional ATP synthase units is high. These results suggest that energy pressure in mitochondria might regulate ATP synthesis such that at low levels of energy the ATP synthase operates economically (low substrate Km values, low turnover capacity for ATP synthesis), while at high levels of energy these kinetic constraints are relaxed (high substrate Km values, high turnover capacity for ATP synthesis). The implications of these findings are discussed in relation to the cooperative-type kinetics of ATP synthesis and hydrolysis, the differential effects of a number of F0-F1 inhibitors on the rates of ATP synthesis and hydrolysis, and the controversy as to whether protonic energy in mitochondria is localized or delocalized.

Studies on the mechanism of oxidative phosphorylation. Catalytic site cooperativity in ATP synthesis

Oxidative phosphorylation catalyzed by bovine heart submitochondrial particles appears to exhibit negative cooperativity with respect to [ADP] and positive cooperativity in catalysis. Eadie-Hofstee plots (v/[S]versus v) of the kinetics of oxidative phosphorylation at the variable ADP concentration range of 1-1200 microM were curvilinear and could be analyzed for two apparent KmADP values differing by one order of magnitude, and two apparent Vmax values. The KmADP values with either NADH or succinate as the respiratory substrate were in the ranges of 10 and 100 microM, and the Vmax values in nmol of ATP formed X min-1 (mg of protein)-1 were, respectively, 500 and 1840 when NADH was the oxidizable substrate, and 550 and 100 when succinate was the energy source. Site-site cooperativity of the ATP synthase, which is a central feature of current theories for the mechanism of oxidative phosphorylation, has been well-documented for ATP hydrolysis by isolated F1-ATPase, but never before demonstrated for mitochondrial ATP synthesis.

Studies on the mechanism of oxidative phosphorylation: effects of specific F0 modifiers on ligand-induced conformation changes of F1

Aurovertin is a fluorescent antibiotic that binds to the catalytic beta subunits of the mitochondrial F1-ATPase and inhibits ATP synthesis and hydrolysis. ATP, ADP, and membrane energization in submitochondrial particles (SMP) alter the fluorescence of F1-bound aurovertin. These fluorescence changes are considered to be in response to the conformation changes of F1-ATPase. This paper shows that the ATP-induced fluorescence change of aurovertin bound to SMP or complex V (purified ATP synthase complex F0-F1) is inhibited when these preparations are pretreated with oligomycin or N,N'-dicyclohexylcarbodiimide (DCCD). This inhibition is not seen with isolated F1-ATPase. These and other results have suggested that modifications of the DCCD-binding protein in the membrane sector (F0) of the ATP synthase complex are communicated to F1, thereby altering the binding characteristics of ATP to the beta subunits. By analogy, it is proposed that modifications (e.g., protonation/deprotonation) of the DCCD-binding protein effected by protonic energy alter the conformation of F1 and bring about the substrate/product binding changes that appear to be essential features of the mechanism and regulation of oxidative phosphorylation.

Six unidentified reading frames of human mitochondrial DNA encode components of the respiratory-chain NADH dehydrogenase

The products of six unidentified reading frames of human mitochondrial DNA are precipitated from a mitochondrial lysate by antibodies against highly purified native beef heart NADH-ubiquinone oxidoreductase (complex I). These products are enriched greatly in a human submitochondrial fraction enriched in NADH-Q1 and NADH-K3Fe(CN)6 oxidoreductase activities. We conclude that the six reading frames encode components of the respiratory-chain NADH dehydrogenase.

Kinetics of ATP hydrolysis by F1-ATPase and the effects of anion activation, removal of tightly bound nucleotides, and partial inhibition of the ATPase by covalent modification

Eadie-Hofstee plots (v/[S] vs. v) of the kinetics of ATP hydrolysis by purified bovine heart mitochondrial F1-ATPase (MF1) over a substrate (MgATP) concentration range of 1-5000 microM were curvilinear, indicating negative cooperativity with respect to [MgATP] as originally shown by Ebel & Lardy (1975) [Ebel, R. E., & Lardy, H. A. (1975) J. Biol. Chem. 250, 191-196]. The data were computer analyzed for the best fit of the least number of straight lines, each representing a different apparent Km and Vmax. The best fits for MF1 and TF1 from the thermophilic bacterium PS3 were three lines in each case. The upper limits of the apparent Km values for MF1 were of the order of 10(-6), 10(-4), and 10(-3) M, and the corresponding apparent Vmax values (per minute per milligram of protein) were in the range of micromoles or less for the lowest Km line and decamicromoles for the other two. The results for TF1 were very similar. The presence of an activating anion (10 mM KHCO3) in the MF1 assay medium increased the overall Vmax by about 50% and eliminated the high Km but had essentially no effect on the intermediate and low Km's, indicating retention of negative cooperativity in the corresponding substrate concentration range. Kinetic data for MgITP as substrate also yielded two Km values (in the absence of KHCO3) differing by about 10(4)-fold. The relationship between [14C]dicyclohexylcarbodiimide [( 14C]-DCCD) binding to MF1 and activity inhibition was linear up to approximately 1 mol of DCCD bound/mol of MF1. At this point, the degree of inhibition was about 95%.(ABSTRACT TRUNCATED AT 250 WORDS)

Inhibitory chemical modifications of F1-ATPase: effects on the kinetics of adenosine 5'-triphosphate synthesis and hydrolysis in reconstituted systems

The purified, soluble F1-ATPase was modified by several covalently reacting inhibitors, either known or considered to bind to the active site bearing beta-subunit, to cause partial inhibition up to 99%. The modified enzyme was then reconstituted in the presence of OSCP (oligomycin sensitivity conferring protein) with submitochondrial particles (SMP) almost completely (greater than 99%) denuded of active F1-ATPase and was assayed for oligomycin-sensitive ATPase and oxidative phosphorylation activities. The inhibitors used were 1-fluoro-2,4-dinitrobenzene (FDNB), N-(ethoxycarbonyl)-2-ethoxy-1,2-dihydroquinoline (EEDQ), 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCD), quinacrine mustard (QM), 5-(dimethylamino)-naphthalene-1-sulfonyl chloride (dansyl-Cl), 5'-[p-(fluoro-sulfonyl)benzoyl]adenosine (FSBA), and N,N'-dicyclohexylcarbodiimide (DCCD). The SMP reconstituted with unmodified F1 exhibited oxidative phosphorylation and oligomycin-sensitive ATPase (in the presence of uncouplers) activities as high as 500 nmol min-1 mg-1 and 8 mumol min-1 mg-1, respectively. The systems reconstituted with F1 modified to cause various degrees of inhibition with FDNB, EEDQ, CMCD, QM, and dansyl-Cl exhibited the same degree of inhibition of oxidative phosphorylation and oligomycin-sensitive ATPase activities as the inhibition of the ATPase activity of the modified F1 before reconstitution. The systems reconstituted with FSBA-modified F1 showed the following relative degrees of inhibition: oxidative phosphorylation greater than oligomycin-sensitive ATPase of particles greater than ATPase of soluble F1. In contrast, the systems reconstituted with DCCD-modified F1 showed much greater inhibition of oligomycin-sensitive ATPase than of oxidative phosphorylation activity.(ABSTRACT TRUNCATED AT 250 WORDS)

Modulation of the kinetics and the steady-state level of intermediates of mitochondrial coupled reactions by inhibitors and uncouplers

In oxidative phosphorylation and ATP-driven uphill electron transfer from succinate to NAD, double-reciprocal plots of rates vs. substrate concentrations of the energy-driven reactions are a family of parallel lines at several fixed subsaturating concentrations of the substrates or at several moderate concentrations of the inhibitors of the energy-yielding reactions. Thus, as shown elsewhere [Hatefi, Y., Yagi, T., Phelps, D. C., Wong, S.-Y., Vik, S. B., & Galante, Y. M. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 1756-1760], partial uncoupling decreases the Vappmax and increases the Kappm of the substrates of the energy-driven reactions, resulting in a decrease of Vmax/Km as a function of increased uncoupling. However, partial limitation of the flow rates of the energy-yielding reactions decreases both the Vappmax and the Kappm of the substrates of the energy-driven reactions, resulting in no change in Vmax/Km. This is true as long as the rate limitation is moderate (e.g., less than 60%), under which conditions the steady-state membrane potential (delta psi) remains essentially unchanged. At high inhibition of the energy-yielding reactions, or at moderate inhibition in the presence of low levels of an uncoupler to cause partial uncoupling, then the family of double-reciprocal plots is no longer parallel and tends to converge toward the left. Under these conditions, steady-state delta psi and Vmax/Km also decrease as inhibition is increased. The relationship between the magnitude of steady-state delta psi and the rate of the energy-driven reaction was studied in oxidative phosphorylation, ATP-driven electron transfer from succinate to NAD, and respiration-driven uniport calcium transport by intact mitochondria.(ABSTRACT TRUNCATED AT 250 WORDS)