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Upper and lower limits of the charge translocation stoichiometry of cytochrome c oxidase.

The mechanistic stoichiometry of charge separation coupled to the flow of electrons through cytochrome c oxidase has remained a center of controversy since it was first demonstrated that cytochrome oxidase is an H+ pump. Currently the major dispute is whether the q+/O ratio for this segment is 4 or 6. One cause of the controversy is incomplete coupling between electron flow, electrogenic H+ ejection, and electrophoretic cation uptake, which is usually attributed to finite rates of H+ leakage and/or slippage of the H+ pumps. To minimize the uncertainty which incomplete coupling introduces into estimates of the mechanistic stoichiometry, a new approach (Beavis, A. D., and Lehninger, A. L. (1986) Eur. J. Biochem. 158, 307-314) has been used to determine the upper and lower limits of the mechanistic q+/O translocation stoichiometry of cytochrome oxidase. In this approach, the relationship between the rate of valinomycin-dependent K+ uptake, JK, and rate of O2 consumption, JO, is determined as the rates are modulated by two distinct means. When the rates are modulated by the rate of electron flow (i.e. rate of energy supply) the slope of JK versus JO must at all points be less than the mechanistic K+/O ratio. On the other hand, when the rates are modulated by varying the concentration of valinomycin (i.e. the rate of energy utilization) the slope of JK versus JO must at all points be greater than the mechanistic K+/O ratio. The results indicate that the q+/O ratio lies between 4.3 and 5.5. These data are inconsistent with both currently favored stoichiometries, and it is suggested that the true mechanistic stoichiometry of charge separation coupled to electron flow through cytochrome oxidase may be 5 q+/O.

Antimycin A↗

Stoichiometry of actin X S-1 cross-linked complex.

Mornet et al. ( Mornet , D., Bertrand , R., Pantel , P., Audemard , E., Kassab , R. (1981) Nature (Lond.) 292, 301-306) have shown that myosin subfragment 1 (S-1) can be covalently linked to F-actin by the zero-length cross-linker 1-ethyl-3-[3-(dimethylamino)-propyl]carbodiimide. Their results indicated that the stoichiometry of the cross-linked complex is one S-1 to two actin monomers. However, Sutoh ( Sutoh , K. (1983) Biochemistry 22, 1579-1585) reported that S-1 is cross-linked to only one actin monomer. In both of these measurements, the stoichiometry was determined by separating the cross-linked complex from free actin on sodium dodecyl sulfate-polyacrylamide gels and then determining the concentration of actin and S-1 in the complex. In this study, a new approach was used to determine the stoichiometry of actin to S-1 in the cross-linked complex. The cross-linked actin X S-1 preparation, which was composed of [14C]iodoacetamide-modified S-1 and [3H]N-ethylmaleimide-modified actin, was passed through several cycles of actin depolymerization and centrifugation. This had no effect on the ATPase activity of the cross-linked S-1, but it preferentially removed noncross-linked actin which in turn increased the ratio of S-1 to total actin from 1:5 to 1:2 in the recycled cross-linked preparation. The stoichiometry of the cross-linked complex could then be determined by measuring the amount of free actin in the 42-kDa band on sodium dodecyl sulfate-polyacrylamide gels. The amount of free actin in the 42-kDa band was equal to the amount of cross-linked S-1. This establishes that the stoichiometry of the cross-linked complex is one S-1/one F-actin monomer, in agreement with the results of Sutoh .

Actins↗

Dependence of trp repressor-operator affinity, stoichiometry, and apparent cooperativity on DNA sequence and size.

A series of chemically synthesized trp and mutant operator DNAs was employed to examine trp repressor binding. Although only a single repressor-operator complex was observed for most DNAs as reported previously, varying DNA sequence revealed two retarded complexes with an additional band of faster mobility. The relative intensity of the two retarded bands with varying repressor concentrations suggests that cooperative interactions between dimers may occur in the formation of the predominant repressor-operator complex. Direct stoichiometry measurements demonstrated that a 2:1 stoichiometry (two dimers per operator) is found in the primary repressor-operator complex band and that a 1:1 stoichiometry is observed, when present, for the minor repressor-operator complex band of faster mobility. Similar retardation patterns with a single complex of 2:1 stoichiometry were observed for 40-base pair (bp) trp operators corresponding to TrpEDCBA, aroH, and Trp-PL (a derivative of TrpEDCBA with increased symmetry) operator sequences as well as to hybrid operators containing a half-binding site from TrpEDCBA in conjunction with lac operator sequences, although the apparent affinity for the half-site DNAs was diminished by 10-fold. In contrast, the prominence of the 1:1 dimer-operator complex for Trp-PR, a different derivative of TrpEDCBA with increased symmetry, suggests that sequence context may diminish cooperativity between dimers. The stoichiometry observed was also dependent on the length of TrpEDCBA operator DNA used, shifting from primarily 2:1 for 40- and 33-bp TrpEDCBA DNA to primarily 1:1 for 29-, 26-, and 20-bp TrpEDCBA DNAs. In addition, the stability of the repressor-operator complex to electrophoresis is reduced for DNA lengths of 33, 29, and 26 bp. Based on the binding data and footprinting patterns for two hybrid 40-bp TrpEDCBA/lac half-binding site DNAs, it appears that repressor associates tightly to the specific trp half-site, whereas the nonspecific half of the DNA is more loosely bound. These results suggest that repressor dimer-dimer interaction may be an important feature in the trp repressor-operator interaction.

Allosteric Regulation↗

Study of binding stoichiometries of the human immunodeficiency virus type 1 reverse transcriptase by capillary electrophoresis and laser-induced fluorescence polarization using aptamers as probes.

Binding stoichiometries between four DNA aptamers (RT12, RT26, RTlt49, and ODN93) and the reverse transcriptase (RT) of the type 1 human immunodeficiency virus (HIV-1) were studied using affinity CE (ACE) coupled with LIF polarization and fluorescence polarization (FP). The ACE/LIF study showed evidence of two binding stoichiometries between the HIV-1 RT protein and aptamers RT12, RT26, and ODN93, suggesting that these aptamers can bind to both the p66 and p51 subunits of the HIV-1 RT. Only one binding stoichiometry for aptamer RTlt49 was found. The affinity complexes were easily separated from the unbound aptamers; however, the different stoichiometries were not well resolved. A complementary technique, FP, was able to provide additional information about the binding and supporting evidence for the ACE/LIF results. The ACE/LIFP study also revealed that the FP values of the 1:1 complexes of the HIV-1 RT protein with aptamers RT12, RT26, and ODN93 were always much greater than those of the 1:2 complexes. This was initially surprising because the larger molecular size of the 1:2 complexes was expected to result in higher FP values than the corresponding 1:1 complexes. This phenomenon was probably a result of fluorescence resonance energy transfer between the two fluorescent molecules bound to the HIV-1 RT protein.

Aptamers, Nucleotide↗

The use of HgCl2 to evaluate the cosubstrate: amino acid transport stoichiometry in Ehrlich ascites tumor cells.

Recent investigations have indicated that cellular rheogenic properties may interfere with the correct estimation of Na+ and amino transport stoichiometry. We have reevaluated the stoichiometry of Na+ and alpha-aminoisobutyric acid (alpha-AIB) cotransport in Ehrlich ascites tumor cells depleted of Na+ and ATP by incubation in Na+-free HEPES-buffered medium (pH 7.2) containing 160 mM K+ and 2.5 microM valinomycin. Transfer of the cells to a medium with 10 mM 22Na+, 10 mM 3H-AIB, and 150 mM K+ resulted in an enhancement of Na+ flux above basal levels, which represents 0.6 of the AIB uptake. Under these conditions the membrane potential, -7.0 +/- 0.1 mV (SEM), does not change with the addition of AIB, -7.3 +/- 0.6 mV (SEM). HgCl2 (10 microM) added to the medium inhibited AIB flux and AIB-stimulated Na+ flux by 45-50% but did not change the coupling ratio. HgCl2 (10 microM) does not inhibit the basal Na+ flux nor does it affect cellular Na+ or K+ content. In physiological medium cotransport is electrogenic. The membrane potential of Ehrlich cells in physiological medium is -22.3 +/- 0.8 mV (SEM) and depolarizes to -16.7 +/- 0.7 mV (SEM) upon addition of AIB. Under these conditions the coupling ratio was highly variable but the ratio of codepression is 0.90 +/- 0.02 (SEM) in the presence of HgCl2 (10 microM). These results are consistent with a model (Smith and Robinson, 1981) in which the stoichiometry is one cosubstrate molecule per molecule of alpha-AIB. We suggest that H+ provides the alternative cosubstrate in this low Na+ environment and that in high Na+ medium the Na+:AIB stoichiometry approaches 1:1.

Amino Acids↗

Nuclear magnetic resonance investigation of the stoichiometries in beta-cyclodextrin:steroid inclusion complexes.

Nuclear magnetic resonance at high field has been used to investigate the stoichiometries of pharmacologically important beta-cyclodextrin:steroid complexes. This technique provides evidence for the existence of true inclusion complexes and allows unequivocal determination of the stoichiometry for complexes obtained in the solid state, as well as in solution. The present data clarify previously published determinations of the stoichiometry of these complexes and show the influence of the nature and position of functional groups on the molecular ratio in the complex. The observed behavior can be rationalized using representative steroids and allows prediction of the strength of inclusion and the most probable stoichiometry.

Cyclodextrins↗

Determination of the stoichiometry of protein complexes using liquid chromatography with fluorescence and mass spectrometric detection of fluorescently labeled proteolytic peptides.

A method for the determination of the stoichiometry of protein complexes has been developed, which is based on proteolytic digestion of the complex, labeling with a fluorescent reagent, specific for amino or sulfhydryl groups, and separation by liquid chromatography with fluorescence and mass spectrometric detection. The intensity of the fluorescence signal of the labeled peptides resulting from different proteins is directly proportional to the stoichiometry of these proteins in the complex. The performance of the method was evaluated with standard peptides and proteins to ensure that accurate molar ratios can be obtained from the fluorescence chromatogram. Standard deviations of the measured molar ratio from the expected molar ratio were below 10% for both peptides and proteins. The method was finally employed for the determination of the stoichiometry of the 1:1 complex of sFc gamma RIII and hFc1. Using the described methodology, a stoichiometry of 1:1.1 was measured, which agrees well with a 1:1 complex.

Angiotensins↗

Energy transduction in tonoplast vesicles from red beet (Beta vulgaris L.) storage tissue: H+/substrate stoichiometries for the H(+)-ATPase and H(+)-PPase.

The H+/substrate stoichiometries of the tonoplast H(+)-ATPase and H(+)-PPase were determined by a kinetic approach. Using red beet (Beta vulgaris L.) tonoplast vesicles, rates of substrate-dependent H+ transport were estimated by (I) a mathematical model describing the time course of delta pH formation, (II) the rate of H+ leakage following H+ pump inhibition at a steady state delta pH, and (III) the initial rate of alkalinization of the external medium. When compared with rates of substrate hydrolysis measured under identical conditions, all three methods yielded an H+/ATP stoichiometry of 2 while the H+/PPi stoichiometry was determined to be 1 using methods I and II. Experimental limitations did not permit an analysis of the H+/PPi stoichiometry by method III. From these results and the estimated level of substrate and product typically found in the cytoplasm of plant cells, it is suggested that the H(+)-ATPase and H(+)-PPase as primary H(+)-pumps are poised toward net substrate hydrolysis under in vivo conditions thereby operating in parallel to generate a proton electrochemical gradient across the tonoplast.

Carbonyl Cyanide m-Chlorophenyl Hydrazone↗

Binding constants and stoichiometries of glyceraldehyde 3-phosphate dehydrogenase-tubulin complexes.

The catalytic activity of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) decreased (almost linearly) as a function of increasing concentrations of tubulin; the total loss in activity was attained at a ratio of 1.2 to 1.8 tubulin dimer to GAPDH tetramer. Based on the inhibition data, a dissociation constant for the tubulin-GAPDH complex was calculated to be about 0.73 nM. The stoichiometry and the dissociation constants of the tubulin-GAPDH complex were found to be dependent upon the ionic strength of the assay media. Qualitatively similar results were obtained (i.e., inhibition and ionic strength effect) when the GAPDH-catalyzed reaction was measured in the presence of Sepharose-immobilized tubulin. The physical interaction between these two proteins, i.e., GAPDH and tubulin, was measured by the ability of one protein (immobilized on a Sepharose matrix) to copellet the other protein. By employing this copelleting technique, we measured the dissociation constant and stoichiometry of the immobilized tubulin-GAPDH complex to be about 6.4 nM and 0.91 tubulin dimer/GAPDH tetramer, respectively. The dissociation constant and stoichiometry thus obtained were found to be remarkably similar to those obtained by the tubulin-dependent GAPDH inhibition data. In contrast to these results, (soluble) tubulin had no effect on the catalytic activity of the immobilized GAPDH, albeit the soluble tubulin copelleted with the immobilized GAPDH. The dissociation constant and stoichiometry of immobilized GAPDH-tubulin complex were calculated to be 0.76 +/- 0.13 microM and 3.23 +/- 0.16 tubulin dimer/GAPDH tetramer, respectively. These data suggest that there are two classes of binding sites for tubulin on a tetrameric GAPDH; high-affinity and low-affinity sites. The enzyme is inhibited when tubulin binds at the high-affinity site while the catalytic function of the enzyme is unaffected when the tubulin binds at the low-affinity site. The latter site is suggested herein to be responsible for the cross-linking (bundling) of microtubules.

Animals↗

H+/PPi stoichiometry of membrane-bound pyrophosphatase of Rhodospirillum rubrum.

Two kinetic methods have been used to measure the H+/PPi stoichiometry in the chromatophores of the photosynthetic bacteria Rhodospirillum rubrum. In the first method, the fluorescent probe acridine orange was employed to infer the proton pump activity at the steady state of the delta pH generation. At this point the translocation of protons by the H(+)-PPiase in one direction is balanced exactly by the leak of protons in the opposite direction. Pyrophosphatase activity was then quickly stopped by adding EDTA, producing a relaxation of delta pH. From the initial rate of this relaxation and the rate of PPi hydrolysis measured under the same condition, the H+/PPi stoichiometry was obtained. In the second method, a mathematical model was used to describe the time course of delta pH formation. In the two methods an apparent H+/PPi stoichiometry of nearly 2 was obtained. The H+/ATP stoichiometry was determined also as an internal control, giving a value of nearly 3.6, which is in agreement with the value in different F-type H(+)-ATPases.

Adenosine Triphosphate↗

Stoichiometry of BkdR to substrate DNA in Pseudomonas putida.

BkdR is the transcriptional activator of the bkd operon of Pseudomonas putida, which encodes branched chain keto acid dehydrogenase. BkdR binds to a large region of DNA between its own structural gene and the first gene of the bkd operon. The object of the present studies was to determine the stoichiometry of binding as part of an effort to understand the action of BkdR in regulation of the bkd operon. [35S]BkdR was prepared and found to be essentially 100% active in the gel shift assay. Only one complex was formed under all the conditions used. The stoichiometry of BkdR binding to its specific substrate DNA was three tetramers per mold substrate DNA. L-valine did not affect the stoichiometry although this ligand was previously shown to affect the DNase I protection pattern. The addition of nonspecific DNA to the incubation mixture also did not affect this stoichiometry.

3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗

Kinetic analysis of a model of the sarcoplasmic reticulum Ca-ATPase, with variable stoichiometry, which enhances the amount and the rate of Ca transport.

The sarcoplasmic reticulum (SR) Ca-dependent adenosinetriphosphatase (Ca-ATPase) actively transports Ca2+ from the myoplasm to the SR lumen. Under optimal conditions a 2:1 stoichiometry of Ca transport/ATP hydrolysis has been observed, but lower stoichiometries have been reported under several circumstances. A lower stoichiometry under conditions of high Ca2+ load, although thermodynamically less efficient, could in theory increase the rate and the maximal amount of Ca uptake. We analysed, by computing simulation, the transient kinetics of a model of the SR Ca-ATPase with variable stoichiometry. The model is based on current experimental reports and includes the most relevant properties of the system. The results show an acceleration in the rate of Ca uptake, an increase in the net Ca transport, and an increase in the rate of [Ca2+] reduction in the medium, which might be physiologically useful to increase the rate of Ca pumping at high Ca load of the sarcoplasmic reticulum.

Adenosine Triphosphate↗

Ecological stoichiometry of ants in a New World rain forest.

C:N stoichiometry was investigated in relation to diet (delta(15)N), N-deprivation, and worker body size for a diverse assemblage of tropical Amazonian ants. Relative nitrogen (N) deprivation was assayed for 54 species as an exchange ratio (ER), defined as SUCmin/AAmin, or the minimum sucrose concentration, divided by the minimum amino acid concentration, accepted as food by >/=50% of tested workers. On average, N-deprivation (ER) was almost fivefold greater for N-omnivorous and N-herbivorous (N-OH) taxa than for N-carnivores. In two-way ANOVAs at three taxonomic levels (species and species groups, genera, and tribes), higher ER was associated with small body size and (marginally) with less carnivorous diets. ERs did not differ systematically between trophobiont-tending and "leaf-foraging" functional groups, but specialized wound-feeders and coccid-tenders were prominent among high ER taxa. Paradoxically, some high ER taxa were among the most predatory members of their genera or subfamilies. Biomass % N was lower in N-OH taxa than in carnivores and varied inversely with N-deprivation (log ER) in the former taxa only. In an expanded data set, N-content increased allometrically in N-OHs, N-carnivores, and all ants combined, and with carnivory in large-bodied ants only. Exceptional taxa included small-bodied and predaceous Wasmannia, with high % N despite high ER, and Linepithema, with the lowest % N despite high delta(15)N. Patterns in C:N stoichiometry are explained largely at the genus level and above by elemental composition of alarm/defensive/offensive chemical weaponry and, perhaps in some cases, by reduced N investment in cuticle in taxa with high surface:volume ratios. Several consequences of C:N stoichiometry identify Azteca, and possibly Crematogaster, as taxa preadapted for their roles as prominent associates of myrmecophytes. C:N stoichiometry of ants should be incorporated into models of strategic colony design and examined in a phylogenetic context as opportunities permit.

Analysis of Variance↗

H+/ATP stoichiometry of proton pumps from Neurospora crassa and Escherichia coli.

A kinetic method has been used to measure the apparent stoichiometry of H+ ions translocated per ATP split by membrane-bound [H+]-ATPases. In this method, membrane vesicles are suspended in well-buffered medium, ATP is added, and a fluorescent probe of delta pH (acridine orange) is used to detect the formation of a steady-state pH gradient. At the steady state, it is assumed that proton pumping in one direction is exactly balanced by the leak of protons in the opposite direction. The pump is then rapidly turned off by the addition of an appropriate inhibitor, and the initial rate of relaxation of delta pH is used to infer the pump rate. This rate is divided by the rate of ATP hydrolysis, measured under the same condition, to give the apparent H+/ATP stoichiometry. The method has been applied to two different [H+]-ATPases, the plasma-membrane ATPase of Neurospora (a Mr = 100,000 integral membrane protein) and the ATPase of Escherichia coli (which belongs to the F0F1 group). The Neurospora ATPase displayed an apparent stoichiometry close to 1 H+/ATP (0.82-1.23), in agreement with previous estimates from electrophysiological measurements on whole cells. In contrast, the E. coli ATPase yielded an apparent stoichiometry close to 2 H+/ATP (1.90), consistent with several published values obtained by both kinetic and thermodynamic methods for bacterial, mitochondrial, and chloroplast ATPases.

Acridine Orange↗

Photorespiration stoichiometry in leaves estimated by combined physical and stereochemical methods: allowance for isomerase-catalyzed 3H losses in ribulose bisphosphate regeneration.

We showed previously [K.R. Hanson and R.B. Peterson (1986) Arch. Biochem. Biophys. 246, 332-346] that under steady-state photosynthetic conditions the fraction of ribulose bisphosphate oxidized and the fraction of glycolate carbon photorespired (the stoichiometry of photorespiration) may be estimated in leaves by a combination of physical and stereochemical methods. The calculations assumed that when (3R)-D-[3-3H1,3-14C]glyceric acid is supplied to illuminated leaf discs the only loss of 3H from the combined photosynthetic and photorespiratory system is the result of glycolate oxidase action; i.e., the isomerase-catalyzed losses in the regeneration of ribulose bisphosphate are negligible. The present study of tobacco leaf discs under zero-photorespiration conditions (low O2 and high CO2 concentrations), and also of maize leaf discs, shows that some 3H losses occur (between 8 and 13% of the 3H at C-1 of ribulose 5-phosphate). The calculated loss varied moderately with temperature but did not vary when the flux of ribulose bisphosphate formation was altered by changing the irradiance. The calculated loss under zero-photorespiration conditions, therefore, may be used to calculate ribulose bisphosphate and glycolate partitioning under other conditions. Earlier experiments on the influence of O2 and CO2 concentrations of temperature on the partitioning of ribulose bisphosphate and glycolate have been reexamined. The loss corrections decreased all values for the fraction of ribulose bisphosphate oxidized and increased all values for the stoichiometry of photorespiration. Essentially all stoichiometry values were above the theoretical lower limit of 25%. The previous conclusion that the stoichiometry of photorespiration substantially exceeds 25% at higher O2 concentrations and higher temperatures is unchanged. The results with maize leaf discs implied that there is very little oxidation of ribulose 1,5-bisphosphate under normal-air conditions; i.e., photorespiration is indeed suppressed, not merely hidden, by efficient refixation of CO2.

Carbon Dioxide↗

Protonmotive stoichiometry of rat liver cytochrome c oxidase: determination by a new rate/pulse method.

The stoichoimetry of vectorial H+ ejection coupled to electron flow through the cytochrome c oxidase (EC 1.9.3.1) of rat liver mitochondria was determined by a new rate/pulse method. This is a modification of the oxygen-pulse method. Electron flow through the oxidase is initiated by adding oxygen to suspensions of anaerobic mitochondria at a known and constant rate. Cytochrome c oxidase was examined directly or in combination with cytochrome c reductase (ubiquinol:ferricytochrome c oxidoreductase). In both cases the----H0+/2e- ratio was found to be constant during the time-course of oxygen reduction, and thus independent of delta pH. The stoichiometries observed were consistent with mechanistic stoichiometries of 2 and 6 for cytochrome c oxidase alone and cytochrome c oxidase together with cytochrome c reductase, respectively. The stoichiometry of cytochrome c reductase alone was also examined, by using ferricyanide in place of oxygen. The results obtained were consistent with the accepted mechanistic stoichiometry of 4 for this enzyme.

Animals↗

Pigment stoichiometry of a newly isolated D1-D2-Cyt b559 complex from the higher plant Beta vulgaris L.

Two D1-D2-Cyt b559 complexes with different pigment stoichiometry were isolated from the higher plant B. vulgaris. The procedures for isolating both complexes only differed in the washing time of the DEAE column with 50 mM Tris-HCl, pH 7.2, 0.05% Triton X-100 and 30 mM NaCl. When the column was washed until the eluate had an absorbance of 0.01 at 670 nm, the isolated D1-D2-Cyt b559 complex presented a pigment stoichiometry of 6 chlorophyll a, 2 beta-carotene, and 1 cytochrome b559 per 2 pheophytin a. In contrast, when the column was exhaustively washed until the eluate reached an absorbance of 0.005 at 670 nm, the complex had a stoichiometry of 4 chlorophyll a, 1 beta-carotene, and 1 cytochrome b559 per 2 pheophytin a. We think that the former stoichiometry corresponds to that of the native D1-D2-Cyt b559 complex. Moreover, both preparations showed 2 mol of pheophytin a per 1 mol of reaction center protein.

Carotenoids↗

Regulation of the H+/e- stoichiometry of cytochrome c oxidase from bovine heart by intramitochondrial ATP/ADP ratios.

This paper describes the effect of intramitochondrial ATP/ADP ratios on the H+/e- stoichiometry of reconstituted cytochrome c oxidase (COX) from bovine heart. At 100% intraliposomal ATP the H+/e- stoichiometry of the reconstituted enzyme is decreased to half of the value measured below 98% intraliposomal ATP (above 2% ADP), while it remains constant up to 100% ADP. The decrease is obtained with different COX preparations, independent of the absolute value of the H+/e- stoichiometry. Decrease of H+/e- stoichiometry is prevented by preincubation of the enzyme with a tissue-specific monoclonal antibody to subunit VIa-H (heart type). Tissue-specific regulation of the efficiency of energy transduction in COX of muscle mitochondria could have a physiological function in maintaining the body temperature at rest or sleep, i.e. at low ATP expenditure.

Adenosine Diphosphate↗