Adenine nucleotide binding sites on beef heart F1-ATPase. Evidence for three exchangeable sites that are distinct from three noncatalytic sites

Elucidating Events within the Black Box of Enzyme Catalysis in Energy Metabolism: Insights into the Molecular Mechanism of ATP Hydrolysis by F1-ATPase

Oxygen exchange reactions occurring at β-catalytic sites of the FOF1-ATP synthase/F1-ATPase imprint a unique record of molecular events during the catalytic cycle of ATP synthesis/hydrolysis. This work presents a new theory of oxygen exchange and tests it on oxygen exchange data recorded on ATP hydrolysis by mitochondrial F1-ATPase (MF1). The apparent rate constant of oxygen exchange governing the intermediate Pi-HOH exchange accompanying ATP hydrolysis is determined by kinetic analysis over a ~50,000-fold range of substrate ATP concentration (0.1-5000 μM) and a corresponding ~200-fold range of reaction velocity (3.5-650 [moles of Pi/{moles of F1-ATPase}-1 s-1]). Isotopomer distributions of [18O]Pi species containing 0, 1, 2, and 3 labeled oxygen atoms predicted by the theory have been quantified and shown to be in perfect agreement with the experimental distributions over the entire range of medium ATP concentrations without employing adjustable parameters. A novel molecular mechanism of steady-state multisite ATP hydrolysis by the F1-ATPase has been proposed. Our results show that steady-state ATP hydrolysis by F1-ATPase occurs with all three sites occupied by Mg-nucleotide. The various implications arising from models of energy coupling in ATP synthesis/hydrolysis by the ATP synthase/F1-ATPase have been discussed. Current models of ATP hydrolysis by F1-ATPase, including those postulated from single-molecule data, are shown to be effectively bisite models that contradict the data. The trisite catalysis formulated by Nath's torsional mechanism of energy transduction and ATP synthesis/hydrolysis since its first appearance 25 years ago is shown to be in better accord with the experimental record. The total biochemical information on ATP hydrolysis is integrated into a consistent model by the torsional mechanism of ATP synthesis/hydrolysis and shown to elucidate the elementary chemical and mechanical events within the black box of enzyme catalysis in energy metabolism by F1-ATPase.

Beyond binding change: the molecular mechanism of ATP hydrolysis by F1-ATPase and its biochemical consequences

F1-ATPase is a universal multisubunit enzyme and the smallest-known motor that, fueled by the process of ATP hydrolysis, rotates in 120o steps. A central question is how the elementary chemical steps occurring in the three catalytic sites are coupled to the mechanical rotation. Here, we performed cold chase promotion experiments and measured the rates and extents of hydrolysis of preloaded bound ATP and promoter ATP bound in the catalytic sites. We found that rotation was caused by the electrostatic free energy change associated with the ATP cleavage reaction followed by Pi release. The combination of these two processes occurs sequentially in two different catalytic sites on the enzyme, thereby driving the two rotational sub-steps of the 120o rotation. The mechanistic implications of this finding are discussed based on the overall energy balance of the system. General principles of free energy transduction are formulated, and their important physical and biochemical consequences are analyzed. In particular, how exactly ATP performs useful external work in biomolecular systems is discussed. A molecular mechanism of steady-state, trisite ATP hydrolysis by F1-ATPase, consistent with physical laws and principles and the consolidated body of available biochemical information, is developed. Taken together with previous results, this mechanism essentially completes the coupling scheme. Discrete snapshots seen in high-resolution X-ray structures are assigned to specific intermediate stages in the 120o hydrolysis cycle, and reasons for the necessity of these conformations are readily understood. The major roles played by the "minor" subunits of ATP synthase in enabling physiological energy coupling and catalysis, first predicted by Nath's torsional mechanism of energy transduction and ATP synthesis 25 years ago, are now revealed with great clarity. The working of nine-stepped (bMF1, hMF1), six-stepped (TF1, EF1), and three-stepped (PdF1) F1 motors and of the α3β3γ subcomplex of F1 is explained by the same unified mechanism without invoking additional assumptions or postulating different mechanochemical coupling schemes. Some novel predictions of the unified theory on the mode of action of F1 inhibitors, such as sodium azide, of great pharmaceutical importance, and on more exotic artificial or hybrid/chimera F1 motors have been made and analyzed mathematically. The detailed ATP hydrolysis cycle for the enzyme as a whole is shown to provide a biochemical basis for a theory of "unisite" and steady-state multisite catalysis by F1-ATPase that had remained elusive for a very long time. The theory is supported by a probability-based calculation of enzyme species distributions and analysis of catalytic site occupancies by Mg-nucleotides and the activity of F1-ATPase. A new concept of energy coupling in ATP synthesis/hydrolysis based on fundamental ligand substitution chemistry has been advanced, which offers a deeper understanding, elucidates enzyme activation and catalysis in a better way, and provides a unified molecular explanation of elementary chemical events occurring at enzyme catalytic sites. As such, these developments take us beyond binding change mechanisms of ATP synthesis/hydrolysis proposed for oxidative phosphorylation and photophosphorylation in bioenergetics.

ADP-Inhibition of H+-FOF1-ATP Synthase

H+-F_OF₁-ATP synthase (F-ATPase, F-type ATPase, F_OF₁ complex) catalyzes ATP synthesis from ADP and inorganic phosphate in eubacteria, mitochondria, chloroplasts, and some archaea. ATP synthesis is powered by the transmembrane proton transport driven by the proton motive force (PMF) generated by the respiratory or photosynthetic electron transport chains. When the PMF is decreased or absent, ATP synthase catalyzes the reverse reaction, working as an ATP-dependent proton pump. The ATPase activity of the enzyme is regulated by several mechanisms, of which the most conserved is the non-competitive inhibition by the MgADP complex (ADP-inhibition). When ADP binds to the catalytic site without phosphate, the enzyme may undergo conformational changes that lock bound ADP, resulting in enzyme inactivation. PMF can induce release of inhibitory ADP and reactivate ATP synthase; the threshold PMF value required for enzyme reactivation might exceed the PMF for ATP synthesis. Moreover, membrane energization increases the catalytic site affinity to phosphate, thereby reducing the probability of ADP binding without phosphate and preventing enzyme transition to the ADP-inhibited state. Besides phosphate, oxyanions (e.g., sulfite and bicarbonate), alcohols, lauryldimethylamine oxide, and a number of other detergents can weaken ADP-inhibition and increase ATPase activity of the enzyme. In this paper, we review the data on ADP-inhibition of ATP synthases from different organisms and discuss the in vivo role of this phenomenon and its relationship with other regulatory mechanisms, such as ATPase activity inhibition by subunit ε and nucleotide binding in the noncatalytic sites of the enzyme. It should be noted that in Escherichia coli enzyme, ADP-inhibition is relatively weak and rather enhanced than prevented by phosphate.

The Role of Light-Dark Regulation of the Chloroplast ATP Synthase

The chloroplast ATP synthase catalyzes the light-driven synthesis of ATP and is activated in the light and inactivated in the dark by redox-modulation through the thioredoxin system. It has been proposed that this down-regulation is important for preventing wasteful hydrolysis of ATP in the dark. To test this proposal, we compared the effects of extended dark exposure in Arabidopsis lines expressing the wild-type and mutant forms of ATP synthase that are redox regulated or constitutively active. In contrast to the predictions of the model, we observed that plants with wild-type redox regulation lost photosynthetic capacity rapidly in darkness, whereas those expressing redox-insensitive form were far more stable. To explain these results, we propose that in wild-type plants, down-regulation of ATP synthase inhibits ATP hydrolysis, leading to dissipation of thylakoid proton motive force (pmf) and subsequent inhibition of protein transport across the thylakoid through the twin arginine transporter (Tat)-dependent and Sec-dependent import pathways, resulting in the selective loss of specific protein complexes. By contrast, in mutants with a redox-insensitive ATP synthase, pmf is maintained by ATP hydrolysis, thus allowing protein transport to maintain photosynthetic activities for extended periods in the dark. Hence, a basal level of Tat-dependent, as well as, Sec-dependent import activity, in the dark helps replenishes certain components of the photosynthetic complexes and thereby aids in maintaining overall complex activity. However, the influence of a dark pmf on thylakoid protein import, by itself, could not explain all the effects we observed in this study. For example, we also observed in wild type plants a large transient buildup of thylakoid pmf and nonphotochemical exciton quenching upon sudden illumination of dark adapted plants. Therefore, we conclude that down-regulation of the ATP synthase is probably not related to preventing loss of ATP per se. Instead, ATP synthase redox regulation may be impacting a number of cellular processes such as (1) the accumulation of chloroplast proteins and/or ions or (2) the responses of photosynthesis to rapid changes in light intensity. A model highlighting the complex interplay between ATP synthase regulation and pmf in maintaining various chloroplast functions in the dark is presented. Significance Statement: We uncover an unexpected role for thioredoxin modulation of the chloroplast ATP synthase in regulating the dark-stability of the photosynthetic apparatus, most likely by controlling thylakoid membrane transport of proteins and ions.

ATP synthase

Oxygenic photosynthesis is the principal converter of sunlight into chemical energy. Cyanobacteria and plants provide aerobic life with oxygen, food, fuel, fibers, and platform chemicals. Four multisubunit membrane proteins are involved: photosystem I (PSI), photosystem II (PSII), cytochrome b6f (cyt b6f), and ATP synthase (FOF1). ATP synthase is likewise a key enzyme of cell respiration. Over three billion years, the basic machinery of oxygenic photosynthesis and respiration has been perfected to minimize wasteful reactions. The proton-driven ATP synthase is embedded in a proton tight-coupling membrane. It is composed of two rotary motors/generators, FO and F1, which do not slip against each other. The proton-driven FO and the ATP-synthesizing F1 are coupled via elastic torque transmission. Elastic transmission decouples the two motors in kinetic detail but keeps them perfectly coupled in thermodynamic equilibrium and (time-averaged) under steady turnover. Elastic transmission enables operation with different gear ratios in different organisms.

Light- and metabolism-related regulation of the chloroplast ATP synthase has distinct mechanisms and functions

The chloroplast CF0-CF1-ATP synthase (ATP synthase) is activated in the light and inactivated in the dark by thioredoxin-mediated redox modulation of a disulfide bridge on its γ subunit. The activity of the ATP synthase is also fine-tuned during steady-state photosynthesis in response to metabolic changes, e.g. altering CO2 levels to adjust the thylakoid proton gradient and thus the regulation of light harvesting and electron transfer. The mechanism of this fine-tuning is unknown. We test here the possibility that it also involves redox modulation. We found that modifying the Arabidopsis thaliana γ subunit by mutating three highly conserved acidic amino acids, D211V, E212L, and E226L, resulted in a mutant, termed mothra, in which ATP synthase which lacked light-dark regulation had relatively small effects on maximal activity in vivo. In situ equilibrium redox titrations and thiol redox-sensitive labeling studies showed that the γ subunit disulfide/sulfhydryl couple in the modified ATP synthase has a more reducing redox potential and thus remains predominantly oxidized under physiological conditions, implying that the highly conserved acidic residues in the γ subunit influence thiol redox potential. In contrast to its altered light-dark regulation, mothra retained wild-type fine-tuning of ATP synthase activity in response to changes in ambient CO2 concentrations, indicating that the light-dark- and metabolic-related regulation occur through different mechanisms, possibly via small molecule allosteric effectors or covalent modification.

Characteristics of protection by MgADP and MgATP of α3β3γ subcomplex of thermophilic Bacillus PS3 βY341W-mutant F1-ATPase from inhibition by 7-chloro-4-nitrobenz-2-oxa-1,3-diazole support a bi-site mechanism of catalysis

MgADP and MgATP binding to catalytic sites of βY341W-α(3)β(3)γ subcomplex of F(1)-ATPase from thermophilic Bacillus PS3 has been assessed using their effect on the enzyme inhibition by 7-chloro-4-nitrobenz-2-oxa-1,3-diazole (NBD-Cl). It was assumed that NBD-Cl can inhibit only when catalytic sites are empty, and inhibition is prevented if a catalytic site is occupied with a nucleotide. In the absence of an activator, MgADP and MgATP protect βY341W-α(3)β(3)γ subcomplex from inhibition by NBD-Cl by binding to two catalytic sites with an affinity of 37 µM and 12 mM, and 46 µM and 15 mM, respectively. In the presence of an activator lauryldimethylamine-N-oxide (LDAO), MgADP protects βY341W-α(3)β(3)γ subcomplex from inhibition by NBD-Cl by binding to a catalytic site with a K(d) of 12 mM. Nucleotide binding to a catalytic site with affinity in the millimolar range has not been previously revealed in the fluorescence quenching experiments with βY341W-α(3)β(3)γ subcomplex. In the presence of activators LDAO or selenite, MgATP protects βY341W-α(3)β(3)γ subcomplex from inhibition by NBD-Cl only partially, and the enzyme remains sensitive to inhibition by NBD-Cl even at MgATP concentrations that are saturating for ATPase activity. The results support a bi-site mechanism of catalysis by F(1)-ATPases.

Modulation of the mitochondrial permeability transition by cyclophilin D: moving closer to F(0)-F(1) ATP synthase?

Cyclophilin D was recently shown to mask an inhibitory site of the mitochondrial permeability transition pore (PTP) for phosphate, and to constitutively bind F(0)-F(1) ATP synthase resulting in the slowing of ATP synthesis and hydrolysis rates, thus regulating matrix adenine nucleotide levels. Here we review the striking similarities of the factors affecting the threshold for PTP induction, to those affecting binding of phosphate to formerly proposed sides on F(1)-ATPase affecting ATP hydrolytic activity, including critical arginine residues, matrix pH, [Mg(2+)], adenine nucleotides and proton motive force. Based on these similarities, we scrutinize the hypothesis that in depolarized mitochondria exhibiting reversal of F(0)-F(1) ATP synthase operation, the genetic ablation of cyclophilin D or its inhibition by cyclosporin A results in accelerated proton pumping by ATP hydrolysis, opposing a further decrease in membrane potential and promoting high matrix phosphate levels, both negatively affecting the probability of PTP opening.

Probes of inhibition of Escherichia coli F(1)-ATPase by 7-chloro-4-nitrobenz-2-oxa-1,3-diazole in the presence of MgADP and MgATP support a bi-site mechanism of ATP hydrolysis by the enzyme

Binding of MgADP and MgATP to Escherichia coli F(1)-ATPase (EcF(1)) has been assessed by their effects on extent of the enzyme inhibition by 7-chloro-4-nitrobenz-2-oxa-1,3-diazole (NBD-Cl). MgADP at low concentrations (K(d) 1.3 microM) promotes the inhibition, whereas at higher concentrations (K(d) 0.7 mM) EcF(1) is protected from inhibition. The mutant betaY331W-EcF(1) requires much higher MgADP, K(d) of about 10 mM, for protection. Such MgADP binding was not revealed by fluorescence quenching measurements. MgATP partially protects EcF(1) from inactivation by NBD-Cl, but the enzyme remains sensitive to NBD-Cl in the presence of MgATP at concentrations as high as 10 mM. The activating anion selenite in the absence of MgATP partially protects EcF(1) from inhibition by NBD-Cl. A complete protection of EcF(1) from inhibition by NBD-Cl has been observed in the presence of both MgATP and selenite. The results support a bi-site catalytic mechanism for MgATP hydrolysis by F(1)-ATPases and suggest that stimulation of the enzyme activity by activating anions is due to the anion binding to a catalytic site that remains unoccupied at saturating substrate concentration.

ATP binding and hydrolysis steps of the uni-site catalysis by the mitochondrial F(1)-ATPase are affected by inorganic phosphate

The effect of inorganic phosphate (P(i)) on uni-site ATP binding and hydrolysis by the nucleotide-depleted F(1)-ATPase from beef heart mitochondria (ndMF(1)) has been investigated. It is shown for the first time that P(i) decreases the apparent rate constant of uni-site ATP binding by ndMF(1) 3-fold with the K(d) of 0.38+/-0.14mM. During uni-site ATP hydrolysis, P(i) also shifts equilibrium between bound ATP and ADP+P(i) in the direction of ATP synthesis with the K(d) of 0.17+/-0.03mM. However, 10mM P(i) does not significantly affect ATP binding during multi-site catalysis.

Nitration of specific tyrosines in FoF1 ATP synthase and activity loss in aging

It has been reported that C-nitration of proteins occurs under nitrative/oxidative stress; however, its role in pathophysiological situations is not fully understood. In this study, we determined that nitration of Tyr(345) and Tyr(368) in the beta-subunit of the mitochondrial F(o)F(1)-ATPase is a major target for nitrative stress in rat liver under in vivo conditions. The chemical characteristics of these Tyr make them suitable for a facilitated nitration (solvent accessibility, consensus sequence, and pK(a)). Moreover, beta-subunit nitration increased significantly with the age of the rats (from 4 to 80 weeks old) and correlated with decreased ATP hydrolysis and synthesis rates. Although its affinity for ATP binding was unchanged, maximal ATPase activity decreased between young and old rats by a factor of two. These changes directly impacted the available ATP concentration in vivo, and it was expected that they would affect multiple cellular ATP-dependent processes. For instance, at least 50% of available [ATP] in the liver of older rats would have to be committed to sustain maximal Na(+)-K(+)-ATPase activity, whereas only 30% would be required for young rats. If this requirement was not fulfilled, the osmoregulation and Na(+)-nutrient cotransport in liver of older rats would be compromised. On the basis of our studies, we propose that targeted nitration of the beta-subunit is an early marker for nitrative stress and aging.

Nitration of tyrosine residues 368 and 345 in the β-subunit elicits FoF1-ATPase activity loss

Tyrosine nitration is a covalent post-translational protein modification associated with various diseases related to oxidative/nitrative stress. A role for nitration of tyrosine in protein inactivation has been proposed; however, few studies have established a direct link between this modification and loss of protein function. In the present study, we determined the effect of nitration of Tyr345 and Tyr368 in the β-subunit of the F1-ATPase using site-directed mutagenesis. Nitration of the β-subunit, achieved by using TNM (tetranitromethane), resulted in 66% ATPase activity loss. This treatment resulted in the modification of several asparagine, methionine and tyrosine residues. However, nitrated tyrosine and ATPase inactivation were decreased in reconstituted F1 with Y368F (54%), Y345F (28%) and Y345,368F (1%) β-subunits, indicating a clear link between nitration at these positions and activity loss, regardless of the presence of other modifications. Kinetic studies indicated that an F1 with one nitrated tyrosine residue (Tyr345 or Tyr368) or two Tyr368 residues was sufficient to grant inactivation. Tyr368 was four times more reactive to nitration due to its lower pKa. Inactivation was attributed mainly to steric hindrance caused by adding a bulky residue more than the presence of a charged group or change in the phenolic pKa due to the introduction of a nitro group. Nitration at this residue would be more relevant under conditions of low nitrative stress. Conversely, at high nitrative stress conditions, both tyrosine residues would contribute equally to ATPase inactivation.

A bi-site mechanism for Escherichia coli F1-ATPase accounts for the observed positive catalytic cooperativity

Nucleotide binding to nucleotide-depleted F(1)-ATPase from Escherichia coli (EcF(1)) during MgATP hydrolysis in the presence of excess epsilon subunit has been studied using a combination of centrifugal filtration and column-centrifugation methods. The results show that nucleotide-binding properties of catalytic sites on EcF(1) are affected by the state of occupancy of noncatalytic sites. The ATP-concentration dependence of catalytic-site occupancy during MgATP hydrolysis demonstrates that a bi-site mechanism is responsible for the positive catalytic cooperativity observed during multi-site catalysis by EcF(1). The results suggest that a bi-site mechanism is a general feature of F(1) catalysis.

ATP synthase and the actions of inhibitors utilized to study its roles in human health, disease, and other scientific areas

ATP synthase, a double-motor enzyme, plays various roles in the cell, participating not only in ATP synthesis but in ATP hydrolysis-dependent processes and in the regulation of a proton gradient across some membrane-dependent systems. Recent studies of ATP synthase as a potential molecular target for the treatment of some human diseases have displayed promising results, and this enzyme is now emerging as an attractive molecular target for the development of new therapies for a variety of diseases. Significantly, ATP synthase, because of its complex structure, is inhibited by a number of different inhibitors and provides diverse possibilities in the development of new ATP synthase-directed agents. In this review, we classify over 250 natural and synthetic inhibitors of ATP synthase reported to date and present their inhibitory sites and their known or proposed modes of action. The rich source of ATP synthase inhibitors and their known or purported sites of action presented in this review should provide valuable insights into their applications as potential scaffolds for new therapeutics for human and animal diseases as well as for the discovery of new pesticides and herbicides to help protect the world's food supply. Finally, as ATP synthase is now known to consist of two unique nanomotors involved in making ATP from ADP and P(i), the information provided in this review may greatly assist those investigators entering the emerging field of nanotechnology.

Regulatory mechanisms of proton-translocating F(O)F (1)-ATP synthase

H(+)-F(O)F(1)-ATP synthase catalyzes synthesis of ATP from ADP and inorganic phosphate using the energy of transmembrane electrochemical potential difference of proton (deltamu(H)(+). The enzyme can also generate this potential difference by working as an ATP-driven proton pump. Several regulatory mechanisms are known to suppress the ATPase activity of F(O)F(1): 1. Non-competitive inhibition by MgADP, a feature shared by F(O)F(1) from bacteria, chloroplasts and mitochondria 2. Inhibition by subunit epsilon in chloroplast and bacterial enzyme 3. Inhibition upon oxidation of two cysteines in subunit gamma in chloroplast F(O)F(1) 4. Inhibition by an additional regulatory protein (IF(1)) in mitochondrial enzyme In this review we summarize the information available on these regulatory mechanisms and discuss possible interplay between them.

Studies of nucleotide binding to the catalytic sites of Escherichia coli betaY331W-F1-ATPase using fluorescence quenching

Most studies of nucleotide binding to catalytic sites of Escherichia coli betaY331W-F(1)-ATPase by the quenching of the betaY331W fluorescence have been conducted in the presence of approximately 20 mM sulfate. We find that, in the absence of sulfate, the nucleotide concentration dependence of fluorescence quenching induced by ADP, ATP, and MgADP is biphasic, revealing two classes of binding sites, each contributing about equally to the overall extent of quenching. For the high-affinity catalytic site, the K(d) values for MgADP, ADP, and ATP equal 10, 43, and 185 nM, respectively. For the second class of sites, the K(d) values for these ligands are approximately 1,000x larger at 8.1, 37, and 200 microM, respectively. The presence of sulfate or phosphate during assay results in a marked increase in the apparent K(d) values for the high-affinity catalytic site. The results show, contrary to earlier reports, that Mg(2+) is not required for expression of different affinities for a nucleotide by the three catalytic sites. In addition, they demonstrate that the fluorescence of the introduced tryptophans is nearly completely quenched when only two sites bind nucleotide. Binding of ADP to the third site with a K(d) near mM gives little fluorescence change. Many previous results of fluorescence quenching of introduced tryptophans appear to require reinterpretation. Our findings support a bi-site catalytic mechanism for F(1)-ATPase.

Light-dependent incorporation of adenine nucleotide into noncatalytic sites of chloroplast ATP synthase

The binding of ADP and ATP to noncatalytic sites of dithiothreitol-modified chloroplast ATP synthase was studied. Selective binding of nucleotides to noncatalytic sites was provided by preliminary light incubation of thylakoid membranes with [14C]ADP followed by its dissociation from catalytic sites during dark ATP hydrolysis stimulated by bisulfite ions ("cold chase"). Incorporation of labeled nucleotides increased with increasing light intensity. Concentration-dependent equilibrium between free and bound nucleotides was achieved within 2-10 min with the following characteristic parameters: the maximal value of nucleotide incorporation was 1.5 nmol/mg of chlorophyll, and the dissociation constant was 1.5 microM. The dependence of nucleotide incorporation on Mg2+ concentration was slight and changed insignificantly upon substituting Ca2+ for Mg2+. Dissociation of nucleotide from noncatalytic sites was illumination-dependent. The dissociation kinetics suggested the existence of at least two nucleotide-binding sites with different dissociation rate constants.

ADP and ATP binding to noncatalytic sites of thiol-modulated chloroplast ATP synthase

A modified 'cold chase' technique was used to study tight [(14)C]ADP and [(14)C]ATP binding to noncatalytic sites of chloroplast ATP synthase (CF(0)F(1)). The binding was very low in the dark and sharply increased with light intensity. Dissociation of labeled nucleotides incorporated into noncatalytic sites of CF(0)F(1 )or CF(1) reconstituted with EDTA-treated thylakoid membranes was also found to be light-dependent. Time dependence of nucleotide dissociation is described by the first order equation with a k (d) of about 5 min(-1). The exposure of thylakoid membranes to 0.7-24.8 muM nucleotides leads to filling of up to two noncatalytic sites of CF(0)F(1). The sites differ in their specificity: one preferentially binds ADP, whereas the other - ATP. A much higher ATP/ADP ratio of nucleotides bound at noncatalytic sites of isolated CF(1) dramatically decreases upon its reconstitution with EDTA-treated thylakoid membranes. It is suggested that the decrease is caused by conformational changes in one of the alpha subunits induced by its interaction with the delta subunit and/or subunit I-II when CF(1) becomes bound to a thylakoid membrane.

The translocation mechanism of P-glycoprotein

Multidrug transporters are involved in mediating the failure of chemotherapy in treating several serious diseases. The archetypal multidrug transporter P-glycoprotein (P-gp) confers resistance to a large number of chemically and functionally unrelated anti-cancer drugs by mediating efflux from cancer cells. The ability to efflux such a large number of drugs remains a biological enigma and the lack of mechanistic understanding of the translocation pathway used by P-gp prevents rational design of compounds to inhibit its function. The translocation pathway is critically dependent on ATP hydrolysis and drug interaction with P-gp is possible at one of a multitude of allosterically linked binding sites. However, aspects such as coupling stoichiometry, molecular properties of binding sites and the nature of conformational changes remain unresolved or the centre of considerable controversy. The present review attempts to utilise the available data to generate a detailed sequence of events in the translocation pathway for this dexterous protein.

Rapid hydrolysis of ATP by mitochondrial F1-ATPase correlates with the filling of the second of three catalytic sites

Strong positive catalytic cooperativity is a central feature of the binding change mechanism for F1-ATPases. However, a detail of the mechanism that remains controversial is whether the kinetic enhancement derived from using substrate-binding energy at one catalytic site to promote product release from another site occurs upon the filling of the second or third of three catalytic sites on F1. To address this question, we compare the ATP concentration dependence of the rate of ATP hydrolysis by F1 from beef heart mitochondria to the ATP concentration dependence of the level of occupancy of catalytic sites during steady-state catalysis as measured by a centrifuge filtration assay. A single Km(ATP) is observed at 77 +/- 6 microM. Analysis of the nucleotide-binding data shows that half-maximal occupancy of a second catalytic site occurs at 78 +/- 18 microM ATP. We conclude that ATP binding to a second catalytic site is sufficient to support rapid rates of catalysis.

Nature's design of nanomotors

The need for movement is an essential concept of all living organisms. On a macroscopic scale, animals and microbes have to be able to move towards food and away from poison and predators. Plants turn their leaves toward their energy source, the sunlight. But even on a molecular scale, movement is essential for life. It has been known for a long time that enzymes and proteins undergo large conformational changes while performing their biological tasks. The catalytically active regions of enzymes need to sequentially open to bind their respective substrates and close to allow the specific chemical reaction to occur in a defined chemical environment. The active sites finally open up again up to allow the product to be released. Molecular motors are proteins and protein complexes that have evolved in living cells to carry out a variety of functions essential for survival, reproduction and differentiation of the cells and organisms. They use chemical, electrochemical or potential energy and transduce that energy into physical, chemical or mechanical force. In this paper we review some of the molecular motors that were designed by nature to either perform physical work or that contain motor-like movements as part of their catalytic mechanism.

Trigger Factor from Thermus thermophilus Is a Zn2+-dependent Chaperone

The ribosome-associated chaperone trigger factor (TF) of Escherichia coli interacts with a variety of newly synthesized polypeptides to assist their correct folding. Here, we report that the TF of thermophilic eubacterium, Thermus thermophilus, arrested spontaneous folding of green fluorescent protein by forming a 1:1 binary complex. The complex was isolable by gel-filtration but was shown to be dynamic because green fluorescent protein was released by alpha-casein in large excess. Unexpectedly, EDTA completely abolished the folding-arrest activity of TF, and analysis revealed that the TF from our preparation contained approximately 0.5 mol Zn2+/mol TF. The folding-arrest activity of TF that was saturated with Zn2+ (approximately 1 mol/mol TF) was twice as efficient as that of untreated TF. Thus, chaperone activity of thermophilic TF is Zn2+-dependent.

Interaction of oxyanions with thioredoxin-activated chloroplast coupling factor 1

Interaction between F(1)-ATPase activity stimulating oxyanions and noncatalytic sites of coupling factor CF(1) was studied. Carbonate, borate and sulfite anions were shown to inhibit tight binding of [14C]ATP and [14C]ADP to CF(1) noncatalytic sites. The demonstrated change of their inhibitory efficiency in carbonate-borate-sulfite order coincides with the previously found change in efficiency of these anions as stimulators of CF(1)-ATPase activity [Biochemistry (Mosc.) 43 (1978) 1206-1211]. Inhibition of tight nucleotide binding to noncatalytic sites was accompanied by stimulation of nucleotide binding to catalytic sites. This suggests that stimulation of CF(1)-ATPase activity is caused by interaction between oxyanions and noncatalytic sites. A most efficient stimulator of CF(1)-ATPase activity, sulfite oxyanion, appeared to be a competitive inhibitor with respect to ATP and a partial noncompetitive inhibitor with respect to ADP. The inhibition weakened with increasing time of CF(1) incubation with sulfite and nucleotides. Sulfite is believed to inhibit fast reversible interaction between nucleotides and noncatalytic sites and to produce no effect on subsequent tight binding of nucleotides. A possible mechanism of the oxyanion-stimulating effect is discussed.

ATP synthesis driven by proton transport in F1F0-ATP synthase

Topical questions in ATP synthase research are: (1) how do protons cause subunit rotation and how does rotation generate ATP synthesis from ADP+Pi? (2) How does hydrolysis of ATP generate subunit rotation and how does rotation bring about uphill transport of protons? The finding that ATP synthase is not just an enzyme but rather a unique nanomotor is attracting a diverse group of researchers keen to find answers. Here we review the most recent work on rapidly developing areas within the field and present proposals for enzymatic and mechanoenzymatic mechanisms.

Properties of noncatalytic sites of thioredoxin-activated chloroplast coupling factor 1

Nucleotide binding properties of two vacant noncatalytic sites of thioredoxin-activated chloroplast coupling factor 1 (CF(1)) were studied. Kinetics of nucleotide binding to noncatalytic sites is described by the first-order equation that allows for two nucleotide binding sites that differ in kinetic features. Dependence of the nucleotide binding rate on nucleotide concentration suggests that tight nucleotide binding is preceded by rapid reversible binding of nucleotides. ADP binding is cooperative. The preincubation of CF(1) with Mg(2+) produces only slight effect on the rate of ADP binding and decreases the ATP binding rate. The ATP and ADP dissociation from noncatalytic sites is described by the first-order equation for similar sites with dissociation rate constants k(-2)(ADP)=1.5 x 10(-1) min(-1) and k(-2)(ATP) congruent with 10(-3) min(-1), respectively. As follows from the study, the noncatalytic sites of CF(1) are not homogeneous. One of them retains the major part of endogenous ADP after CF(1) precipitation with ammonium sulfate. Its other two sites can bind both ADP and ATP but have different kinetic parameters and different affinity for nucleotides.

The role of the Mg2+ cation in ATPsynthase studied by electron paramagnetic resonance using VO2+ and Mn2+ paramagnetic probes

The electron paramagnetic resonance (EPR), electron spin echo envelope modulation (ESEEM) and hyperfine sublevel correlation (HYSCORE) spectra of Mg2+-depleted chloroplast F1-ATPase substituted with stoichiometric VO2+ are reported. The ESEEM and HYSCORE spectra of the complex are dominated by the hyperfine and quadrupole interactions between the VO2+ paramagnet and two different nitrogen ligands with isotropic hyperfine couplings /A1/ = 4.11 MHz and /A2/ = 6.46 MHz and nuclear quadrupole couplings e2qQ1 approximately 3.89-4.49 MHz and e2qQ2 approximately 1.91-2.20 MHz, respectively. Aminoacid functional groups compatible with these magnetic couplings include a histidine imidazole, the epsilon-NH2 of a lysine residue, and the guanidinium group of an arginine. Consistent with this interpretation, very characteristic correlations are detected in the HYSCORE spectra between the 14N deltaM1 = 2 transitions in the negative quadrant, and also between some of the deltaM1 = 1 transitions in the positive quadrant. The interaction of the substrate and product ADP and ATP nucleotides with the enzyme has been studied in protein complexes where Mg2+ is substituted for Mn2+. Stoichiometric complexes of Mn x ADP and Mn x ATP with the whole enzyme show distinct and specific hyperfine couplings with the 31P atoms of the bonding phosphates in the HYSCORE (ADP, A(31Pbeta) = 5.20 MHz: ATP, A(31Pbeta) = 4.60 MHz and A(31Pgamma) = 5.90 MHz) demonstrating the role of the enzyme active site in positioning the di- or triphosphate chain of the nucleotide for efficient catalysis. When the complexes are formed with the isolated alpha or beta subunits of the enzyme, the HYSCORE spectra are substantially modified, suggesting that in these cases the nucleotide binding site is only partially structured.

The mechanism of ATP hydrolysis at the noncatalytic sites of the transcription termination factor Rho

Escherichia coli transcription termination factor rho is a hexamer with three catalytic subunits that turnover ATP at a fast rate and three noncatalytic subunits that turnover ATP at a relatively slow rate. The mechanism of the ATPase reaction at the noncatalytic sites was determined and was compared with the ATPase mechanism at the catalytic sites. A sequential mechanism for ATP binding or hydrolysis that was proposed for the catalytic sites was not observed at the noncatalytic sites. Pre-steady-state pulse-chase experiments showed that three ATPs were tightly bound to the noncatalytic sites and these were simultaneously hydrolyzed at a rate of 1.8 s(-1) at 18 degrees C. The apparent bimolecular rate constant for ATP binding was determined as 5.4 x 10(5) M(-1) s(-1) in the presence of poly(C) RNA. The ATP hydrolysis products dissociated from the noncatalytic sites at 0.02 s(-1). The hydrolysis of ATP at the noncatalytic sites was at least 130 times slower, and the overall ATPase turnover was 1500 times slower than that at the catalytic sites. These results from studies of the rho protein are likely to be general to hexameric helicases. We propose that the ATPase activity at the noncatalytic site is too slow to drive translocation of the protein on the nucleic acid or to provide energy for nucleic acid unwinding.

One of the non-exchangeable nucleotides of the mitochondrial F1-ATPase is bound at a beta-subunit: evidence for a non-rotatory two-site catalytic mechanism

In active MF1, one of the two non-exchangeable tightly bound adenine nucleotides is an ATP, while the other is an ADP. The respective sites are called the T-site and the D-site. The activity of the enzyme correlates linearly with the amount of bound ATP, ADP at the T-site being inhibitory. When MF1 is stored at room temperature in 50% glycerol and 100 mM Tris-HCl (pH 7.3) after slow passage through a Sephadex column, the tightly bound ATP is slowly dephosphorylated to ADP which is subsequently released, without effect on activity. When enzyme with about one residual ADP left (at the D-site) was incubated at pH 7.3, after dilution of the glycerol, with 400 &mgr;M [14C]ATP under varying conditions, the amount of tightly bound nucleotide triphosphate again correlated well with activity, the residual ADP being bound at the D-site. Optimal results were obtained when the incubation was performed in the presence of a regenerating system. Binding of 2-azido-ATP instead of ATP to the T-site as a triphosphate, as indicated by the specific activity of the enzyme, appeared to be optimal when the binding was performed at pH 6.4 in the absence of Mg2+ and with high concentrations of the nucleotide. Under such conditions, 3 mol 2-azido-AXP per mol F1 remained tightly bound after ammonium sulfate precipitation and column centrifugation, in addition to about one residual ADP at the D-site. After a 2-min period of turnover with ATP/Mg2+ as substrate two mol 2-azido-AXP were left on the enzyme, of which one was bound at a beta-site. These results show that one of the non-catalytic nucleotide binding sites that contain tightly bound nucleotides, is a beta-site, in conflict with the requirements for a rotatory tri-site mechanism for ATP hydrolysis. This beta-site can further be identified with the T-site. The validity of these conclusions for F1 from other sources and for catalysis by membrane-bound enzyme is discussed.

Transcription termination factor Rho contains three noncatalytic nucleotide binding sites

The active form of transcription termination factor rho from Escherichia coli is a homohexamer, but several studies suggest that the six subunits of the hexamer are not functionally identical. Rho has three tight and three weak ATP binding sites. Based on our findings, we propose that the tight nucleotide binding sites are noncatalytic and the weak sites are catalytic. In the presence of RNA, the rho-catalyzed ATPase rate is fast, close to 30 s-1. However, under these conditions the three tightly bound nucleotides dissociate from the rho hexamer at a slow rate of 0.02 s-1, indicating that the three tight nucleotide binding sites of rho do not participate in the fast ATPase turnover. These slowly exchanging nucleotide binding sites of rho are capable of hydrolyzing ATP, but the resulting products (ADP and Pi) bind tightly and dissociate from rho about 1500 times slower than the fast ATPase turnover. Both RNA and excess ATP in solution are necessary for stabilizing nucleotide binding at these sites. In the absence of RNA, or when solution ATP is hydrolyzed to ADP, a faster dissociation of nucleotides was observed. Based on these results, we propose that the rho hexamer is similar to the F1-ATPase and T7 DNA helicase-containing noncatalytic sites that do not participate in the fast ATPase turnover. We propose that the three tight sites on rho are the noncatalytic sites and the three weak sites are the catalytic sites.

Contraction transitions of F1-F0 ATPase during catalytic turnover

Strong acoustic pressure was applied to submitochondrial particles (SMP) from bovine heart in order to drive ATP synthesis by F1-F0 complex for the account of sound waves. We observed a net ATP production at two narrow frequency ranges, about 170 Hz and about 340 Hz, that corresponds to the resonance oscillations of experimental cuvette when the acoustic pressure had a magnitude of 100 kPa. The results can be explained quantitatively by contractive conformational changes of F1-F0 complex during catalytic turnover. Negative staining electron microscopy of SMP preparations was used to visualize the ADP(Mg2+)-induced conformational changes of F1-F0 complex. In the particles with high ATPase activity in the presence of phosphate the factors F1 and F0 formed a congregated domain plunged into the membrane without any observable stalk in between. The presence of ADP(Mg2+) caused a structural rearrangement of F1-F0 to the essentially different conformation: the domains F1 and F0 were dislodged distinctly from each other and connected by a long thin stalk. The latter conformation resembled well the usual bipartite profile of ATPase. The data indicate that besides rotation, the catalytic turnover of ATP synthase is also accompanied by stretch transitions of F1-F0 complex.

Nucleotide and Mg2+ dependency of the thermal denaturation of mitochondrial F1-ATPase

The influence of adenine nucleotides and Mg2+ on the thermal denaturation of mitochondrial F1-ATPase (MF1) was analyzed. Differential scanning calorimetry in combination with ATPase activity experiments revealed the thermal unfolding of MF1 as an irreversible and kinetically controlled process. Three significant elements were analyzed during the thermal denaturation process: the endothermic calorimetric transition, the loss of ATP hydrolysis activity, and the release of tightly bound nucleotides. All three processes occur in the same temperature range, over a wide variety of conditions. The purified F1-ATPase, which contains three tightly bound nucleotides, denatures at a transition temperature (Tm) of 55 degrees C. The nucleotide and Mg2+ content of MF1 strongly influence the thermal denaturation process. First, further binding of nucleotides and/or Mg2+ to MF1 increases the thermal denaturation temperature, whereas the thermal stability of the enzyme is decreased upon removal of the endogenous nucleotides. Second, the stabilizing effect induced by nucleotides is smaller after hydrolysis of ATP (i.e., in the presence of ADP . Mg2+) than under nonhydrolytical conditions (i.e., absence of Mg2+ or using the nonhydrolyzable analog 5'-adenylyl-imidodiphosphate). Third, whereas the thermal denaturation of MF1 fully loaded with nucleotides follows an apparent two-state kinetic process, denaturation of MF1 with a low nucleotide content follows more complex kinetics. Nucleotide content is therefore an important factor in determining the thermal stability of the MF1 complex, probably by strengthening existing intersubunit interactions or by establishing new ones.

Bovine F1-ATPase covalently inhibited with 4-chloro-7-nitrobenzofurazan: the structure provides further support for a rotary catalytic mechanism

BACKGROUND

F1-ATPase is the globular domain of F1F0-ATP synthase that catalyses the hydrolysis of ATP to ADP and phosphate. The crystal structure of bovine F1-ATPase has been determined previously to 2.8 A resolution. The enzyme comprises five different subunits in the stoichiometry alpha 3 beta 3 gamma delta epsilon; the three catalytic beta subunits alternate with the three alpha subunits around the centrally located single gamma subunit. To understand more about the catalytic mechanisms, F1-ATPase was inhibited by reaction with 4-chloro-7-nitrobenzofurazan (NBD-Cl) and the structure of the inhibited complex (F1-NBD) determined by X-ray crystallography.

RESULTS

In the structure the three beta subunits adopt a different conformation with different nucleotide occupancy. NBD-Cl reacts with the phenolic oxygen of Tyr311 of the beta E subunit, which contains no bound nucleotide. The two other catalytic subunits beta TP and beta DP contain bound adenylyl-imidodiphosphate (AMP-PNP) and ADP, respectively. The binding site of the NBD moiety does not overlap with the regions of beta E that form the nucleotide-binding pocket in subunits beta TP and beta DP nor does it occlude the nucleotide-binding site. Catalysis appears to be inhibited because neither beta TP nor beta DP can accommodate a Tyr311 residue bearing an NBD group.

CONCLUSIONS

The results presented here are consistent with a rotary catalytic mechanism of ATP synthesis and hydrolysis, which requires the sequential and concerted participation of all three catalytic sites. NBD-Cl inhibits the enzyme by preventing the modified subunit from adopting a conformation that is essential for catalysis to proceed.

Catalytic mechanism of F1-ATPase

The structure of the core catalytic unit of ATP synthase, alpha 3 beta 3 gamma, has been determined by X-ray crystallography, revealing a roughly symmetrical arrangement of alternating alpha and beta subunits around a central cavity in which helical portions of gamma are found. A low-resolution structural model of F0, based on electron spectroscopic imaging, locates subunit a and the two copies of subunit b outside of a subunit c oligomer. The structures of individual subunits epsilon and c (largely) have been solved by NMR spectroscopy, but the oligomeric structure of c is still unknown. The structures of subunits a and delta remain undefined, that of b has not yet been defined but biochemical evidence indicates a credible model. Subunits gamma, epsilon, b, and delta are at the interface between F1 and F0; gamma epsilon complex forms one element of the stalk, interacting with c at the base and alpha and beta at the top. The locations of b and delta are less clear. Elucidation of the structure F0, of the stalk, and of the entire F1F0 remains a challenging goal.

ATP synthase. Conditions under which all catalytic sites of the F1 moiety are kinetically equivalent in hydrolyzing ATP

Conditions have been reported under which the F1 moiety of bovine heart ATP synthase catalyzes the hydrolysis of ATP by an apparently cooperative mechanism in which the slow rate of hydrolysis at a single catalytic site (unisite catalysis) is enhanced more than 10(6)-fold when ATP is added in excess to occupy one or both of the other two catalytic sites (multisite catalysis) (Cross, R. L., Grubmeyer, C., and Penefsky, H. S. (1982) J. Biol. Chem. 257, 12101-12105). In the novel studies reported here, and in contrast to the earlier report, we have (a) monitored the kinetics of ATP hydrolysis of F1 by using nucleotide-depleted preparations and a highly sensitive chemiluminescent assay; (b) followed the reaction immediately upon addition of F1 to ATP, rather than after prior incubation with ATP; and (c) used a reaction medium with Pi as the only buffer. The following observations were noted. First, regardless of the source of enzyme, bovine or rat, and catalytic conditions (unisite or multisite), the rates of hydrolysis depend on ATP concentration to the first power. Second, the first order rate constant for ATP hydrolysis remains relatively constant under both unisite and multisite conditions declining only slightly at high ATP concentration. Third, the initial rates of ATP hydrolysis exhibit Michaelis-Menten kinetic behavior with a single Vmax exceeding 100 micromol of ATP hydrolyzed per min/mg of F1 (turnover number = 635 s-1) and a single Km for ATP of about 57 microM. Finally, the reaction is inhibited markedly by low concentrations of ADP. It is concluded that, under the conditions described here, all catalytic sites that participate in the hydrolysis of ATP within the F1 moiety of mitochondrial ATP synthase function in a kinetically equivalent manner.

The bound adenine nucleotides of purified bovine mitochondrial ATP synthase

The experiments in this study were directed towards defining the nucleotide content of purified beef-heart mitochondrial F1F0 ATP synthase during binding and hydrolysis of ATP. The purified, soluble synthase as prepared contained 2 mol ATP and 2 mol ADP/mol enzyme. Three of these four nucleotides were exchangeable on incubation with radiolabelled MgATP. Passage of the ATP synthase through a column of Sephadex G-50 readily removed 1 mol ADP/mol. The remaining bound nucleotides were not displaced by incubation with 1 mM GTP or 5 mM sodium sulfite, the latter an activator of the ATPase activity of the synthase. Incubation of the synthase with 250 microM MgATP in the presence of 3 mM sodium azide, an inhibitor of the ATPase, resulted in the transitory formation of a form of the enzyme in which 5-6 nucleotide-binding sites were loaded with ATP and/or ADP, thus showing that the ATP synthase, like the soluble F1 ATPase, contained a minimum of six nucleotide-binding sites. The presence of an ATP-regenerating system during incubation with MgATP resulted in the loading of 5-6 sites to yield a form of the enzyme containing 3-4 mol ATP and 2 mol ADP/mol synthase even after passage through a centrifuged column. Following hydrolysis of the medium MgATP, the enzyme reached a stable form containing 2 mol ATP and 2 mol ADP/mol synthase. Like the form of the enzyme originally prepared, 1 mol ADP/mol synthase was readily released. However, this ADP remained bound to the synthase in the presence of GTP if azide was present. These results are discussed in the context of current ideas about nucleotide-binding sites on the F1 ATPase portion of the F1F0 ATP synthase. It is concluded that the properties of the sites on the F1F0 synthase show some differences from those on the F1 ATPase.

Catalytic activities of alpha3beta3gamma complexes of F1-ATPase with 1, 2, or 3 incompetent catalytic sites

In order to know how many functional catalytic sites are necessary for ATPase activity of F1-ATPase from a thermophilic Bacillus PS3, a new method of isolating homogeneous preparations of the alpha3beta3gamma complex with 1, 2, or 3 incompetent catalytic sites was developed. Ten glutamic acids (Glu.Tag) were linked to the C terminus of the catalytically incompetent beta(E190Q) subunit. The Glu.Tag itself did not affect ATPase activity of the complexes. Two kinds of alpha3beta3gamma complexes, one containing beta(wild-type) and the other Glu.Tag-linked beta(E190Q), were mixed, urea-denatured, and dialyzed, and alpha3beta3gamma complexes were reconstituted. Each of the complexes containing a different number of Glu.Tag-linked beta(E190Q) was separated by anion-exchange chromatography and analyzed. The results were as follows. 1) Normal steady-state ATPase activity requires three intact catalytic sites. 2) Chase-acceleration, a catalytic cooperativity, requires at least two intact catalytic sites. 3) Single-site catalysis can be mediated by a single intact catalytic site alone. Rescrambling of subunits between complexes could occur when the complex was aged under certain conditions, and this might be one of the reasons for previous contradictory results (Miwa, K., Ohtsubo, M., Denda, K., Hisabori, T., Date, T., and Yoshida, M.(1989) J. Biochem. (Tokyo) 106, 730-734).

F1F0-ATP synthase: development of direct optical probes of the catalytic mechanism

Using strategically-placed tryptophan (Trp) residues as optical probes to monitor nucleotide binding and hydrolysis, we demonstrate that all three catalytic nucleotide binding sites in F1-ATPase must be filled to obtain physiological (Vmax) MgATP hydrolysis rates. At Vmax hydrolysis rates, the predominant enzyme species has one of the three catalytic sites filled with unhydrolyzed substrate MgATP, the other two sites are filled with product MgADP. A specifically-inserted Trp probe was also developed to characterize nucleotide binding to the noncatalytic sites, and a model to explain the specificity of these sites is shown. These sites appear to play no role in ATP hydrolysis.

3'-O-(4-Benzoyl)benzoyladenosine 5'-triphosphate inhibits activity of the vacuolar (H+)-ATPase from bovine brain clathrin-coated vesicles by modification of a rapidly exchangeable, noncatalytic nucleotide binding site on the B subunit

It was previously observed that the B subunit of the tonoplast V-ATPase is modified by the photoactivated nucleotide analog 3'-O-(4-benzoyl)benzoyladenosine 5'-triphosphate (BzATP) (Manolson, M. F., Rea, P. A., and Poole, R. J. (1985) J. Biol. Chem. 260, 12273-12279). We have further characterized the nucleotide binding sites on the V-ATPase and the interaction between BzATP and the B subunit. We observe that the V-ATPase isolated from bovine clathrin-coated vesicles possesses approximately 1 mol of endogenous, tightly bound ATP/mol of V-ATPase complex. BzATP is not a substrate for the V-ATPase, but does act as a noncovalent inhibitor in the absence of irradiation, changing the kinetic characteristics of ATP hydrolysis. Irradiation of the V-ATPase in the presence of [3H]BzATP results primarily in modification of the 58-kDa B subunit, with complete inhibition of V-ATPase activity occurring upon modification of one B subunit per V-ATPase complex. Inhibition occurs as the result of modification of a rapidly (t1/2 < 2 min) exchangeable site, and yet this site does not correspond to a catalytic site, as indicated by the effects of cysteine-modifying reagents which react with Cys254 located at the catalytic sites on the A subunit. Thus, the noncatalytic nucleotide binding site modified by BzATP appears to be rapidly exchangeable. The site of [3H]BzATP modification of the B subunit was localized to the region Ile164 to Gln171, which from the x-ray crystal structure of the homologous F-ATPase alpha subunit, is within 10 A of the ribose ring of ATP bound to the noncatalytic nucleotide binding site. Thus, despite the absence of a glycine-rich loop region in the B subunit, these data are consistent with a similar overall folding pattern for the V-ATPase B subunit and the F-ATPase alpha subunit.

2,8-Diazido-ATP--a short-length bifunctional photoaffinity label for photoaffinity cross-linking of a stable F1 in ATP synthase (from thermophilic bacteria PS3)

To demonstrate the direct interfacial position of nucleotide binding sites between subunits of proteins we have synthesized the bifunctional photoaffinity label 2,8-diazidoadenosine 5'-triphosphate (2,8-DiN3ATP). UV irradiation of the F1-ATPase (TF1) from the thermophilic bacterium PS3 in the presence of 2,8-DiN3ATP results in a nucleotide-dependent inactivation of the enzyme and in a nucleotide-dependent formation of alpha-beta crosslinks. The results confirm an interfacial localization of all the nucleotide binding sites on TF1.

Conformational changes of the mitochondrial F1-ATPase epsilon-subunit induced by nucleotide binding as observed by phosphorescence spectroscopy

Changes in conformation of the epsilon-subunit of the bovine heart mitochondrial F1-ATPase complex as a result of nucleotide binding have been demonstrated from the phosphorescence emission of tryptophan. The triplet state lifetime shows that whereas nucleoside triphosphate binding to the enzyme in the presence of Mg2+ increases the flexibility of the protein structure surrounding the chromophore, nucleoside diphosphate acts in an opposite manner, enhancing the rigidity of this region of the macromolecule. Such changes in dynamic structure of the epsilon-subunit are evident at high ligand concentration added to both the nucleotide-depleted F1 (Nd-F1) and the F1 preparation containing the three tightly bound nucleotides (F1(2,1)). Since the effects observed are similar in both the F1 forms, the binding to the low affinity sites must be responsible for the conformational changes induced in the epsilon-subunit. This is partially supported by the observation that the Trp lifetime is not significantly affected by adding an equimolar concentration of adenine nucleotide to Nd-F1. The effects on protein structure of nucleotide binding to either catalytic or noncatalytic sites have been distinguished by studying the phosphorescence emission of the F1 complex prepared with the three noncatalytic sites filled and the three catalytic sites vacant (F1(3,0)). Phosphorescence lifetime measurements on this F1 form demonstrate that the binding of Mg-NTP to catalytic sites induces a slight enhancement of the rigidity of the epsilon-subunit. This implies that the binding to the vacant noncatalytic site of F1(2,1) must exert the opposite and larger effect of enhancing the flexibility of the protein structure observed in both Nd-F1 and F1(2,1). The observation that enhanced flexibility of the protein occurs upon addition of adenine nucleotides to F1(2,1) in the absence of Mg2+ provides direct support for this suggestion. The connection between changes in structure and the possible functional role of the epsilon-subunit is discussed.

ATP synthesis catalyzed by the mitochondrial F1-F0 ATP synthase is not a reversal of its ATPase activity

The ADP(Mg2+)-deactivated oligomycin-sensitive F1-F0 ATPase of coupled submitochondrial particles treated with the substoichiometric amount of oligomycin was studied to test whether ATP synthesis and hydrolysis proceed in either direction through the same intermediates. The initial rates of ATP hydrolysis, oxidative phosphorylation, ATP-dependent, succinate-supported NAD+ reduction, and ATP-induced delta microH+ generation were measured using deactivated ATPase trapped by azide [Biochem. J. (1982) 202, 15-23]. Three ATP consuming reactions were strongly inhibited when azide was present in the assay mixtures, whereas ATP synthesis was not altered by azide. The unidirectional effect of azide is not consistent with three alternating binding sites mechanism operating in ATP synthesis and support our hypothesis on the existence of nucleotide(Mg2+)-controlled 'synthase' and 'hydrolase' states of the mitochondrial F1-F0 ATPase.