How azide inhibits ATP hydrolysis by the F-ATPases

Single molecule behavior of inhibited and active states of Escherichia coli ATP synthase F1 rotation

ATP hydrolysis-dependent rotation of the F(1) sector of the ATP synthase is a successive cycle of catalytic dwells (∼0.2 ms at 24 °C) and 120° rotation steps (∼0.6 ms) when observed under V(max) conditions using a low viscous drag 60-nm bead attached to the γ subunit (Sekiya, M., Nakamoto, R. K., Al-Shawi, M. K., Nakanishi-Matsui, M., and Futai, M. (2009) J. Biol. Chem. 284, 22401-22410). During the normal course of observation, the γ subunit pauses in a stochastic manner to a catalytically inhibited state that averages ∼1 s in duration. The rotation behavior with adenosine 5'-O-(3-thiotriphosphate) as the substrate or at a low ATP concentration (4 μM) indicates that the rotation is inhibited at the catalytic dwell when the bound ATP undergoes reversible hydrolysis/synthesis. The temperature dependence of rotation shows that F(1) requires ∼2-fold higher activation energy for the transition from the active to the inhibited state compared with that for normal steady-state rotation during the active state. Addition of superstoichiometric ε subunit, the inhibitor of F(1)-ATPase, decreases the rotation rate and at the same time increases the duration time of the inhibited state. Arrhenius analysis shows that the ε subunit has little effect on the transition between active and inhibited states. Rather, the ε subunit confers lower activation energy of steady-state rotation. These results suggest that the ε subunit plays a role in guiding the enzyme through the proper and efficient catalytic and transport rotational pathway but does not influence the transition to the inhibited state.

Phosphate release in F1-ATPase catalytic cycle follows ADP release

F(1)-ATPase is an ATP-driven rotary motor protein in which the γ-subunit rotates against the catalytic stator ring. Although the reaction scheme of F(1) has mostly been revealed, the timing of inorganic phosphate (P(i)) release remains controversial. Here we addressed this issue by verifying the reversibility of ATP hydrolysis on arrested F(1) with magnetic tweezers. ATP hydrolysis was found to be essentially reversible, implying that P(i) is released after the γ rotation and ADP release, although extremely slow P(i) release was found at the ATP hydrolysis angle as an uncoupling side reaction. On the basis of this finding, we deduced the chemomechanical coupling scheme of F(1). We found that the affinity for P(i) was strongly angle dependent, implying a large contribution by P(i) release to torque generation. These findings imply that under ATP synthesis conditions, P(i) binds to an empty catalytic site, preventing solution ATP (though not ADP) from binding. Thus, this supports the concept of selective ADP binding for efficient ATP synthesis.

Quantitative evaluation of the intrinsic uncoupling modulated by ADP and P(i) in the reconstituted ATP synthase of Escherichia coli

The ATP synthase from Escherichia coli was isolated and reconstituted into liposomes. The ATP hydrolysis by these proteoliposomes was coupled to proton pumping, and the ensuing inner volume acidification was measured by the fluorescent probe 9-amino-6-chloro-2-methoxyacridine (ACMA). The ACMA response was calibrated by acid-base transitions, and converted into internal pH values. The rates of internal acidification and of ATP hydrolysis were measured in parallel, as a function of P(i) or ADP concentration. Increasing P(i) monotonically inhibited the hydrolysis rate with a half-maximal effect at 510μM, whereas it stimulated the acidification rate up to 100-200μM, inhibiting it only at higher concentrations. The ADP concentration in the assay, due both to contaminant ADP in ATP and to the hydrolysis reaction, was progressively decreased by means of increasing pyruvate kinase activities. Decreasing ADP stimulated the hydrolysis rate, whereas it inhibited the internal acidification rate. The quantitative analysis showed that the relative number of translocated protons per hydrolyzed ATP, i.e. the relative coupling ratio, depended on the concentrations of P(i) and ADP with apparent K(d) values of 220μM and 27nM respectively. At the smallest ADP concentrations reached, and in the absence of P(i), the coupling ratio dropped down to 15% relative to the value observed at the highest ADP and P(i) concentrations tested. In addition, the data indicate the presence of two ADP and P(i) binding sites, of which only the highest affinity one is related to changes in the coupling ratio.

Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection

Crystals of biological macromolecules often exhibit considerable inter-crystal and intra-crystal variation in diffraction quality. This requires the evaluation of many samples prior to data collection, a practice that is already widespread in macromolecular crystallography. As structural biologists move towards tackling ever more ambitious projects, new automated methods of sample evaluation will become crucial to the success of many projects, as will the availability of synchrotron-based facilities optimized for high-throughput evaluation of the diffraction characteristics of samples. Here, two examples of the types of advanced sample evaluation that will be required are presented: searching within a sample-containing loop for microcrystals using an X-ray beam of 5 microm diameter and selecting the most ordered regions of relatively large crystals using X-ray beams of 5-50 microm in diameter. A graphical user interface developed to assist with these screening methods is also presented. For the case in which the diffraction quality of a relatively large crystal is probed using a microbeam, the usefulness and implications of mapping diffraction-quality heterogeneity (diffraction cartography) are discussed. The implementation of these techniques in the context of planned upgrades to the ESRF's structural biology beamlines is also presented.

Crystal structure of the Mg·ADP-inhibited state of the yeast F1c10-ATP synthase

The F(1)c(10) subcomplex of the yeast F(1)F(0)-ATP synthase includes the membrane rotor part c(10)-ring linked to a catalytic head, (αβ)(3), by a central stalk, γδε. The Saccharomyces cerevisiae yF(1)c(10)·ADP subcomplex was crystallized in the presence of Mg·ADP, dicyclohexylcarbodiimide (DCCD), and azide. The structure was solved by molecular replacement using a high resolution model of the yeast F(1) and a bacterial c-ring model with 10 copies of the c-subunit. The structure refined to 3.43-Å resolution displays new features compared with the original yF(1)c(10) and with the yF(1) inhibited by adenylyl imidodiphosphate (AMP-PNP) (yF(1)(I-III)). An ADP molecule was bound in both β(DP) and β(TP) catalytic sites. The α(DP)-β(DP) pair is slightly open and resembles the novel conformation identified in yF(1), whereas the α(TP)-β(TP) pair is very closed and resembles more a DP pair. yF(1)c(10)·ADP provides a model of a new Mg·ADP-inhibited state of the yeast F(1). As for the original yF(1) and yF(1)c(10) structures, the foot of the central stalk is rotated by ∼40 ° with respect to bovine structures. The assembly of the F(1) central stalk with the F(0) c-ring rotor is mainly provided by electrostatic interactions. On the rotor ring, the essential cGlu(59) carboxylate group is surrounded by hydrophobic residues and is not involved in hydrogen bonding.

Cytosolic action of phytochelatin synthase

Glutathionylation of compounds is an important reaction in the detoxification of electrophilic xenobiotics and in the biosynthesis of endogenous molecules. The glutathione conjugates (GS conjugates) are further processed by peptidic cleavage reactions. In animals and plants, gamma-glutamyl transpeptidases initiate the turnover by removal of the glutamate residue from the conjugate. Plants have a second route leading to the formation of gamma-glutamylcysteinyl (gamma-GluCys) conjugates. Phytochelatin synthase (PCS) is well known to mediate the synthesis of heavy metal-binding phytochelatins. In addition, the enzyme is also able to catabolize GS conjugates to the gamma-GluCys derivative. In this study, we addressed the cellular compartmentalization of PCS and its role in the plant-specific gamma-GluCys conjugate pathway in Arabidopsis (Arabidopsis thaliana). Localization studies of both Arabidopsis PCS revealed a ubiquitous presence of AtPCS1 in Arabidopsis seedlings, while AtPCS2 was only detected in the root tip. A functional AtPCS1:eGFP (enhanced green fluorescent protein) fusion protein was localized to the cytosolic compartment. Inhibition of the vacuolar import of GS-bimane conjugate via azide treatment resulted in both a strong accumulation of gamma-GluCys-bimane and a massive increase of the cellular cysteine to GS-bimane ratio, which was not observed in PCS-deficient lines. These findings support a cytosolic action of PCS. Analysis of a triple mutant deficient in both Arabidopsis PCS and vacuolar gamma-glutamyl transpeptidase GGT4 is consistent with earlier observations of an efficient sequestration of GS conjugates into the vacuole and the requirement of GGT4 for their turnover. Hence, PCS contributes specifically to the cytosolic turnover of GS conjugates, and AtPCS1 plays the prominent role. We discuss a potential function of PCS in the cytosolic turnover of GS conjugates.

Analysis of the open and closed conformations of the beta subunits in thermophilic F1-ATPase by solution NMR

F(1)-ATPase, composed of alpha, beta, gamma, delta, and epsilon subunits, is a unique enzyme in terms of its rotational catalytic activity. The smallest unit showing this function is the alpha(3)beta(3)gamma complex. We have investigated the alpha(3)beta(3)gamma epsilon(Delta C) (epsilon(Delta C), truncated epsilon) complex from thermophilic Bacillus PS3 (TF(1)', 360 kDa) in the solution state by using the combination of extensive deuteration, segmental-labeling, and CRINEPT (cross-correlated relaxation-enhanced polarization transfer) NMR. Well-resolved CRINEPT-HMQC (heteronuclear multiple-quantum correlation) spectra of partially (15)N-labeled TF(1)' were obtained for this huge and asymmetric protein complex. The spectrum of the C-terminal domain of the beta subunit revealed that the open form of the beta subunit in the TF(1)' complex is similar to that of the free beta monomer. The open beta subunit in the TF(1)' complex does not exhibit high affinity for nucleotides unlike the monomer, but this is in agreement with the results of single-molecule analysis of TF(1)alpha(3)beta(3)gamma. On the other hand, the closed form of the beta subunit in the TF(1)' complex was shown to be distinct from that of the nucleotide-bound beta monomer. This is consistent with a previous report that the closed form of the TF(1)beta monomer could be a catalytically activated state. The loop between the N-terminal beta-barrel and the central domain is highly flexible in the TF(1)' complex, in contrast to that in the alpha(3)beta(3) hexamer, suggesting that it is affected by the presence of the gamma subunit in this area.

ATP hydrolysis in ATP synthases can be differently coupled to proton transport and modulated by ADP and phosphate: a structure based model of the mechanism

In the ATP synthases of Escherichia coli ADP and phosphate exert an apparent regulatory role on the efficiency of proton transport coupled to the hydrolysis of ATP. Both molecules induce clearly biphasic effects on hydrolysis and proton transfer. At intermediate concentrations (approximately 0.5-1 microM and higher) ADP inhibits hydrolysis and proton transfer; a quantitative analysis of the fluxes however proves that the coupling efficiency remains constant in this concentration range. On the other hand at nanomolar concentrations of ADP (a level obtainable only using an enzymatic ATP regenerating system) the efficiency of proton transport drops progressively, while the rate of hydrolysis remains high. Phosphate, at concentrations>or=0.1 mM, inhibits hydrolysis only if ADP is present at sufficiently high concentrations, keeping the coupling efficiency constant. At lower ADP levels phosphate is, however, necessary for an efficiently coupled catalytic cycle. We present a model for a catalytic cycle of ATP hydrolysis uncoupled from the transport of protons. The model is based on the available structures of bovine and yeast F1 and on the known binding affinities for ADP and Pi of the catalytic sites in their different functional states. The binding site related to the inhibitory effects of Pi (in association with ADP) is identified as the alphaHCbetaHC site, the pre-release site for the hydrolysis products. We suggest, moreover, that the high affinity site, associated with the operation of an efficient proton transport, could coincide with a conformational state intermediate between the alphaTPbetaTP and the alphaDPbetaDP (similar to the transition state of the hydrolysis/synthesis reaction) that does not strongly bind the ligands and can exchange them rather freely with the external medium. The emptying of this site can lead to an unproductive hydrolysis cycle that occurs without a net rotation of the central stalk and, consequently, does not translocate protons.

The first low microM SecA inhibitors

SecA ATPase is a critical member of the Sec family, which is important in the translocation of membrane and secreted polypeptides/proteins in bacteria. Small molecule inhibitors can be very useful research tools as well as leads for future antimicrobial agent development. Based on previous virtual screening work, we optimized the structures of two hit compounds and obtained SecA ATPase inhibitors with IC(50) in the single digit micromolar range. These represent the first low micromolar synthetic inhibitors of bacterial SecA and will be very useful for mechanistic studies.

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.

Normal-mode-based modeling of allosteric couplings that underlie cyclic conformational transition in F(1) ATPase

F(1) ATPase, a rotary motor comprised of a central stalk (gamma subunit) enclosed by three alpha and beta subunits alternately arranged in a hexamer, features highly cooperative binding and hydrolysis of ATP. Despite steady progress in biophysical, biochemical, and computational studies of this fascinating motor, the structural basis for cooperative ATPase involving its three catalytic sites remains not fully understood. To illuminate this key mechanistic puzzle, we have employed a coarse-grained elastic network model to probe the allosteric couplings underlying the cyclic conformational transition in F(1) ATPase at a residue level of detail. We will elucidate how ATP binding and product (ADP and phosphate) release at two catalytic sites are coupled with the rotation of gamma subunit via various domain motions in alpha(3)beta(3) hexamer (including intrasubunit hinge-bending motions in beta subunits and intersubunit rigid-body rotations between adjacent alpha and beta subunits). To this end, we have used a normal-mode-based correlation analysis to quantify the allosteric couplings of these domain motions to local motions at catalytic sites and the rotation of gamma subunit. We have then identified key amino acid residues involved in the above couplings, some of which have been validated against past studies of mutated and gamma-truncated F(1) ATPase. Our finding strongly supports a binding change mechanism where ATP binding to the empty catalytic site triggers a series of intra- and intersubunit domain motions leading to ATP hydrolysis and product release at the other two closed catalytic sites.

Essentials for ATP synthesis by F1F0 ATP synthases

The majority of cellular energy in the form of adenosine triphosphate (ATP) is synthesized by the ubiquitous F(1)F(0) ATP synthase. Power for ATP synthesis derives from an electrochemical proton (or Na(+)) gradient, which drives rotation of membranous F(0) motor components. Efficient rotation not only requires a significant driving force (DeltamuH(+)), consisting of membrane potential (Deltapsi) and proton concentration gradient (DeltapH), but also a high proton concentration at the source P side. In vivo this is maintained by dynamic proton movements across and along the surface of the membrane. The torque-generating unit consists of the interface of the rotating c ring and the stator a subunit. Ion translocation through this unit involves a sophisticated interplay between the c-ring binding sites, the stator arginine, and the coupling ions on both sides of the membrane. c-ring rotation is transmitted to the eccentric shaft gamma-subunit to elicit conformational changes in the catalytic sites of F(1), leading to ATP synthesis.

Structure of the c14 rotor ring of the proton translocating chloroplast ATP synthase

The structure of the membrane integral rotor ring of the proton translocating F(1)F(0) ATP synthase from spinach chloroplasts was determined to 3.8 A resolution by x-ray crystallography. The rotor ring consists of 14 identical protomers that are symmetrically arranged around a central pore. Comparisons with the c(11) rotor ring of the sodium translocating ATPase from Ilyobacter tartaricus show that the conserved carboxylates involved in proton or sodium transport, respectively, are 10.6-10.8 A apart in both c ring rotors. This finding suggests that both ATPases have the same gear distance despite their different stoichiometries. The putative proton-binding site at the conserved carboxylate Glu(61) in the chloroplast ATP synthase differs from the sodium-binding site in Ilyobacter. Residues adjacent to the conserved carboxylate show increased hydrophobicity and reduced hydrogen bonding. The crystal structure reflects the protonated form of the chloroplast c ring rotor. We propose that upon deprotonation, the conformation of Glu(61) is changed to another rotamer and becomes fully exposed to the periphery of the ring. Reprotonation of Glu(61) by a conserved arginine in the adjacent a subunit returns the carboxylate to its initial conformation.

Inhibition of ATP synthase by chlorinated adenosine analogue

8-Chloroadenosine (8-Cl-Ado) is a ribonucleoside analogue that is currently in clinical trial for chronic lymphocytic leukemia. Based on the decline in cellular ATP pool following 8-Cl-Ado treatment, we hypothesized that 8-Cl-ADP and 8-Cl-ATP may interfere with ATP synthase, a key enzyme in ATP production. Mitochondrial ATP synthase is composed of two major parts; F(O) intermembrane base and F1 domain, containing alpha and beta subunits. Crystal structures of both alpha and beta subunits that bind to the substrate, ADP, are known in tight binding (alpha(dp)beta(dp)) and loose binding (alpha(tp)beta(tp)) states. Molecular docking demonstrated that 8-Cl-ADP/8-Cl-ATP occupied similar binding modes as ADP/ATP in the tight and loose binding sites of ATP synthase, respectively, suggesting that the chlorinated nucleotide metabolites may be functional substrates and inhibitors of the enzyme. The computational predictions were consistent with our whole cell biochemical results. Oligomycin, an established pharmacological inhibitor of ATP synthase, decreased both ATP and 8-Cl-ATP formation from exogenous substrates, however, did not affect pyrimidine nucleoside analogue triphosphate accumulation. Synthesis of ATP from ADP was inhibited in cells loaded with 8-Cl-ATP. These biochemical studies are in consent with the computational modeling; in the alpha(tp)beta(tp) state 8-Cl-ATP occupies similar binding as ANP, a non-hydrolyzable ATP mimic that is a known inhibitor. Similarly, in the substrate binding site (alpha(dp)beta(dp)) 8-Cl-ATP occupies a similar position as ATP mimic ADP-BeF(3)(-). Collectively, our current work suggests that 8-Cl-ADP may serve as a substrate and the 8-Cl-ATP may be an inhibitor of ATP synthase.

Characterization of Streptococcus gordonii SecA2 as a paralogue of SecA

The accessory Sec system of Streptococcus gordonii is essential for transport of the glycoprotein GspB to the bacterial cell surface. A key component of this dedicated transport system is SecA2. The SecA2 proteins of streptococci and staphylococci are paralogues of SecA and are presumed to have an analogous role in protein transport, but they may be specifically adapted for the transport of large, serine-rich glycoproteins. We used a combination of genetic and biochemical methods to assess whether the S. gordonii SecA2 functions similarly to SecA. Although mutational analyses demonstrated that conserved amino acids are essential for the function of SecA2, replacing such residues in one of two nucleotide binding folds had only minor effects on SecA2 function. SecA2-mediated transport is highly sensitive to azide, as is SecA-mediated transport. Comparison of the S. gordonii SecA and SecA2 proteins in vitro revealed that SecA2 can hydrolyze ATP at a rate similar to that of SecA and is comparably sensitive to azide but that the biochemical properties of these enzymes are subtly different. That is, SecA2 has a lower solubility in aqueous solutions and requires higher Mg(2+) concentrations for maximal activity. In spite of the high degree of similarity between the S. gordonii paralogues, analysis of SecA-SecA2 chimeras indicates that the domains are not readily interchangeable. This suggests that specific, unique contacts between SecA2 and other components of the accessory Sec system may preclude cross-functioning with the canonical Sec system.

Role of {alpha}-subunit VISIT-DG sequence residues Ser-347 and Gly-351 in the catalytic sites of Escherichia coli ATP synthase

This paper describes the role of alpha-subunit VISIT-DG sequence residues alphaSer-347 and alphaGly-351 in catalytic sites of Escherichia coli F(1)F(o) ATP synthase. X-ray structures show the very highly conserved alpha-subunit VISIT-DG sequence in close proximity to the conserved phosphate-binding residues alphaArg-376, betaArg-182, betaLys-155, and betaArg-246 in the phosphate-binding subdomain. Mutations alphaS347Q and alphaG351Q caused loss of oxidative phosphorylation and reduced ATPase activity of F(1)F(o) in membranes by 100- and 150-fold, respectively, whereas alphaS347A mutation showed only a 13-fold loss of activity and also retained some oxidative phosphorylation activity. The ATPase of alphaS347Q mutant was not inhibited, and the alphaS347A mutant was slightly inhibited by MgADP-azide, MgADP-fluoroaluminate, or MgADP-fluoroscandium, in contrast to wild type and alphaG351Q mutant. Whereas 7-chloro-4-nitrobenzo-2-oxa-1, 3-diazole (NBD-Cl) inhibited wild type and alphaG351Q mutant ATPase essentially completely, ATPase in alphaS347A or alphaS347Q mutant was inhibited maximally by approximately 80-90%, although reaction still occurred at residue betaTyr-297, proximal to the alpha-subunit VISIT-DG sequence, near the phosphate-binding pocket. Inhibition characteristics supported the conclusion that NBD-Cl reacts inbetaE (empty) catalytic sites, as shown previously by x-ray structure analysis. Phosphate protected against NBD-Cl inhibition in wild type and alphaG351Q mutant but not in alphaS347Q or alphaS347A mutant. The results demonstrate that alphaSer-347 is an additional residue involved in phosphate-binding and transition state stabilization in ATP synthase catalytic sites. In contrast, alphaGly-351, although strongly conserved and clearly important for function, appears not to play a direct role.

Correlation between the conformational states of F1-ATPase as determined from its crystal structure and single-molecule rotation

F(1)-ATPase is a rotary molecular motor driven by ATP hydrolysis that rotates the gamma-subunit against the alpha(3)beta(3) ring. The crystal structures of F(1), which provide the structural basis for the catalysis mechanism, have shown essentially 1 stable conformational state. In contrast, single-molecule studies have revealed that F(1) has 2 stable conformational states: ATP-binding dwell state and catalytic dwell state. Although structural and single-molecule studies are crucial for the understanding of the molecular mechanism of F(1), it remains unclear as to which catalytic state the crystal structure represents. To address this issue, we introduced cysteine residues at betaE391 and gammaR84 of F(1) from thermophilic Bacillus PS3. In the crystal structures of the mitochondrial F(1), the corresponding residues in the ADP-bound beta (beta(DP)) and gamma were in direct contact. The betaE190D mutation was additionally introduced into the beta to slow ATP hydrolysis. By incorporating a single copy of the mutant beta-subunit, the chimera F(1), alpha(3)beta(2)beta(E190D/E391C)gamma(R84C), was prepared. In single-molecule rotation assay, chimera F(1) showed a catalytic dwell pause in every turn because of the slowed ATP hydrolysis of beta(E190D/E391C). When the mutant beta and gamma were cross-linked through a disulfide bond between betaE391C and gammaR84C, F(1) paused the rotation at the catalytic dwell angle of beta(E190D/E391C), indicating that the crystal structure represents the catalytic dwell state and that beta(DP) is the catalytically active form. The former point was again confirmed in experiments where F(1) rotation was inhibited by adenosine-5'-(beta,gamma-imino)-triphosphate and/or azide, the most commonly used inhibitors for the crystallization of F(1).

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.

Functional halt positions of rotary FOF1-ATPase correlated with crystal structures

The F(O)F(1)-ATPase is a rotary molecular motor. Driven by ATP-hydrolysis, its central shaft rotates in 80 degrees and 40 degrees steps, interrupted by catalytic and ATP-waiting dwells. We recorded rotations and halts by means of microvideography in laboratory coordinates. A correlation with molecular coordinates was established by using an engineered pair of cysteines that, under oxidizing conditions, formed zero-length cross-links between the rotor and the stator in an orientation as found in crystals. The fixed orientation coincided with that of the catalytic dwell, whereas the ATP waiting dwell was displaced from it by +40 degrees . In crystals, the convex side of the cranked central shaft faces an empty nucleotide binding site, as if holding it open for arriving ATP. Functional studies suggest that three sites are occupied during a catalytic dwell. Our data imply that the convex side faces a nucleotide-occupied rather than an empty site. The enzyme conformation in crystals seems to differ from the conformation during either dwell of the active enzyme. A revision of current schemes of the mechanism is proposed.

Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles

BACKGROUND

In plant organelles, specific messenger RNAs (mRNAs) are subjected to conversion editing, a process that often converts the first or second nucleotide of a codon and hence the encoded amino acid. No systematic patterns in converted sites were found on mRNAs, and the converted sites rarely encoded residues located at the active sites of proteins. The role and origin of RNA editing in plant organelles remain to be elucidated.

RESULTS

Here we study the relationship between amino acid residues encoded by edited codons and the structural characteristics of these residues within proteins, e.g., in protein-protein interfaces, elements of secondary structure, or protein structural cores. We find that the residues encoded by edited codons are significantly biased toward involvement in helices and protein structural cores. RNA editing can convert codons for hydrophilic to hydrophobic amino acids. Hence, only the edited form of an mRNA can be translated into a polypeptide with helix-preferring and core-forming residues at the appropriate positions, which is often required for a protein to form a functional three-dimensional (3D) structure.

CONCLUSION

We have performed a novel analysis of the location of residues affected by RNA editing in proteins in plant organelles. This study documents that RNA editing sites are often found in positions important for 3D structure formation. Without RNA editing, protein folding will not occur properly, thus affecting gene expression. We suggest that RNA editing may have conferring evolutionary advantage by acting as a mechanism to reduce susceptibility to DNA damage by allowing the increase in GC content in DNA while maintaining RNA codons essential to encode residues required for protein folding and activity.

A functionally important hydrogen-bonding network at the betaDP/alphaDP interface of ATP synthase

ATP synthase uses a unique rotary mechanism to couple ATP synthesis and hydrolysis to transmembrane proton translocation. The F1 subcomplex has three catalytic nucleotide binding sites, one on each beta subunit, at the interface to the adjacent alpha subunit. In the x-ray structure of F1 (Abrahams, J. P., Leslie, A. G. W., Lutter, R., and Walker, J. E. (1994) Nature 370, 621-628), the three catalytic beta/alpha interfaces differ in the extent of inter-subunit interactions between the C termini of the beta and alpha subunits. At the closed betaDP/alphaDP interface, a hydrogen-bonding network is formed between both subunits, which is absent at the more open betaTP/alphaTP interface and at the wide open betaE/alphaE interface. The hydrogen-bonding network reaches from betaL328 (Escherichia coli numbering) and betaQ441 via alphaQ399, betaR398, and alphaE402 to betaR394, and ends in a cation/pi interaction between betaR394 and alphaF406. Using mutational analysis in E. coli ATP synthase, the functional importance of the betaDP/alphaDP hydrogen-bonding network is demonstrated. Its elimination results in a severely impaired enzyme but has no pronounced effect on the binding affinities of the catalytic sites. A possible role for the hydrogen-bonding network in coupling of ATP synthesis/hydrolysis and rotation will be discussed.

Molecular processes of inhibition and stimulation of ATP synthase caused by the phytotoxin tentoxin

F1-ATPase is the smallest mechanical motor known. Tentoxin, a cyclic peptide produced by phytopathogenic fungi, inactivates the F1 motor in sensitive plants at nanomolar to micromolar concentrations, whereas higher concentrations surpass the natural activity of the enzyme. Single molecule studies now have clarified the molecular steps involved in both processes. Inactivation delays the dwell time of a single step in the complete 360 degrees turn and results in an asymmetric rotation of the central rotor subunit. In contrast, rotation in the stimulated F1 particle is smooth and accompanied by strongly reduced ADP inhibition. Our study provides for the first time the direct observation of a noncompetitively inhibited state of the enzyme and directly visualizes the regulation of the molecular motor by an external natural compound. In addition, the ADP release step during catalysis was revealed by analysis of the single molecule rotation behavior. Hence, tentoxin is a sophisticated molecular tool to mark and control certain catalytic steps within the reaction pathway of the molecular F1 motor.

The concerted nature between three catalytic subunits driving the F1 rotary motor

F(1), a rotational molecular motor, shows strong cooperativity during ATP catalysis when driving the rotation of the central gamma subunit surrounded by the alpha(3)beta(3) subunits. To understand how the three catalytic beta subunits cooperate to drive rotation, we made a hybrid F(1) containing one or two mutant beta subunits with altered catalytic kinetics and observed its rotations. Analysis of the asymmetric stepwise rotations elucidated a concerted nature inside the F(1) complex where all three beta subunits participate to rotate the gamma subunit with a 120 degrees phase. In addition, observing hybrid F(1) rotations at various solution conditions, such as ADP, P(i) and the ATPase inhibitor 2,3-butanedione 2-monoxime (BDM) provides additional information for each elementary event. This novel experimental system, which combines single molecule observations and biochemical methods, enables us to dynamically visualize the catalytic coordination inside active enzymes and shed light on how biological machines provide unidirectional functions and rectify information from stochastic reactions.

Structure of the cytosolic part of the subunit b-dimer of Escherichia coli F0F1-ATP synthase

The structure of the external stalk and its function in the catalytic mechanism of the F(0)F(1)-ATP synthase remains one of the important questions in bioenergetics. The external stalk has been proposed to be either a rigid stator that binds F(1) or an elastic structural element that transmits energy from the small rotational steps of subunits c to the F(1) sector during catalysis. We employed proteomics, sequence-based structure prediction, molecular modeling, and electron spin resonance spectroscopy using site-directed spin labeling to understand the structure and interfacial packing of the Escherichia coli b-subunit homodimer external stalk. Comparisons of bacterial, cyanobacterial, and plant b-subunits demonstrated little sequence similarity. Supersecondary structure predictions, however, show that all compared b-sequences have extensive heptad repeats, suggesting that the proteins all are capable of packing as left-handed coiled-coils. Molecular modeling subsequently indicated that b(2) from the E. coli ATP synthase could pack into stable left-handed coiled-coils. Thirty-eight substitutions to cysteine in soluble b-constructs allowed the introduction of spin labels and the determination of intersubunit distances by ESR. These distances correlated well with molecular modeling results and strongly suggest that the E. coli subunit b-dimer can stably exist as a left-handed coiled-coil.

Role of alphaPhe-291 residue in the phosphate-binding subdomain of catalytic sites of Escherichia coli ATP synthase

The role of alphaPhe-291 residue in phosphate binding by Escherichia coli F1F0-ATP synthase was examined. X-ray structures of bovine mitochondrial enzyme suggest that this residue resides in close proximity to the conserved betaR246 residue. Herein, we show that mutations alphaF291D and alphaF291E in E. coli reduce the ATPase activity of F1F0 membranes by 350-fold. Yet, significant oxidative phosphorylation activity is retained. In contrast to wild-type, ATPase activities of mutants were not inhibited by MgADP-azide, MgADP-fluoroaluminate, or MgADP-fluoroscandium. Whereas, 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) inhibited wild-type ATPase essentially completely, ATPase in mutants was inhibited maximally by approximately 75%, although reaction still occurred at residue betaTyr-297, proximal to alphaPhe-291 in the phosphate-binding pocket. Inhibition characteristics supported the conclusion that NBD-Cl reacts in betaE (empty) catalytic sites, as shown previously by X-ray structure analysis. Phosphate protected against NBD-Cl inhibition in wild-type but not in mutants. In addition, our data suggest that the interaction of alphaPhe-291 with phosphate during ATP hydrolysis or synthesis may be distinct.

How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase

F(o)F(1)-ATP synthase manufactures the energy "currency," ATP, of living cells. The soluble F(1) portion, called F(1)-ATPase, can act as a rotary motor, with ATP binding, hydrolysis, and product release, inducing a torque on the gamma-subunit. A coarse-grained plastic network model is used to show at a residue level of detail how the conformational changes of the catalytic beta-subunits act on the gamma-subunit through repulsive van der Waals interactions to generate a torque that drives unidirectional rotation, as observed experimentally. The simulations suggest that the calculated 85 degrees substep rotation is driven primarily by ATP binding and that the subsequent 35 degrees substep rotation is produced by product release from one beta-subunit and a concomitant binding pocket expansion of another beta-subunit. The results of the simulation agree with single-molecule experiments [see, for example, Adachi K, et al. (2007) Cell 130:309-321] and support a tri-site rotary mechanism for F(1)-ATPase under physiological condition.

The structure and function of mitochondrial F1F0-ATP synthases

We review recent advances in understanding of the structure of the F(1)F(0)-ATP synthase of the mitochondrial inner membrane (mtATPase). A significant achievement has been the determination of the structure of the principal peripheral or stator stalk components bringing us closer to achieving the Holy Grail of a complete 3D structure for the complex. A major focus of the field in recent years has been to understand the physiological significance of dimers or other oligomer forms of mtATPase recoverable from membranes and their relationship to the structure of the cristae of the inner mitochondrial membrane. In addition, the association of mtATPase with other membrane proteins has been described and suggests that further levels of functional organization need to be considered. Many reports in recent years have concerned the location and function of ATP synthase complexes or its component subunits on the external surface of the plasma membrane. We consider whether the evidence supports complete complexes being located on the cell surface, the biogenesis of such complexes, and aspects of function especially related to the structure of mtATPase.

Identification of the betaTP site in the x-ray structure of F1-ATPase as the high-affinity catalytic site

ATP synthase uses a unique rotary mechanism to couple ATP synthesis and hydrolysis to transmembrane proton translocation. The F(1) subcomplex has three catalytic nucleotide binding sites, one on each beta subunit, with widely differing affinities for MgATP or MgADP. During rotational catalysis, the sites switch their affinities. The affinity of each site is determined by the position of the central gamma subunit. The site with the highest nucleotide binding affinity is catalytically active. From the available x-ray structures, it is not possible to discern the high-affinity site. Using fluorescence resonance energy transfer between tryptophan residues engineered into gamma and trinitrophenyl nucleotide analogs on the catalytic sites, we were able to determine that the high-affinity site is close to the C-terminal helix of gamma, but at considerable distance from its N terminus. Thus, the beta(TP) site in the x-ray structure [Abrahams JP, Leslie AGW, Lutter R, Walker JE (1994) Nature 370:621-628] is the high-affinity site, in agreement with the prediction of Yang et al. [Yang W, Gao YQ, Cui Q, Ma J, Karplus M (2003) Proc Natl Acad Sci USA 100:874-879]. Taking into account the known direction of rotation, the findings establish the sequence of affinities through which each catalytic site cycles during MgATP hydrolysis as low --> high --> medium --> low.

How the regulatory protein, IF(1), inhibits F(1)-ATPase from bovine mitochondria

The structure of bovine F(1)-ATPase inhibited by a monomeric form of the inhibitor protein, IF(1), known as I1-60His, lacking most of the dimerization region, has been determined at 2.1-A resolution. The resolved region of the inhibitor from residues 8-50 consists of an extended structure from residues 8-13, followed by two alpha-helices from residues 14-18 and residues 21-50 linked by a turn. The binding site in the beta(DP)-alpha(DP) catalytic interface is complex with contributions from five different subunits of F(1)-ATPase. The longer helix extends from the external surface of F(1) via a deep groove made from helices and loops in the C-terminal domains of subunits beta(DP), alpha(DP), beta(TP), and alpha(TP) to the internal cavity surrounding the central stalk. The linker and shorter helix interact with the gamma-subunit in the central stalk, and the N-terminal region extends across the central cavity to interact with the nucleotide binding domain of the alpha(E) subunit. To form these complex interactions and penetrate into the core of the enzyme, it is likely that the initial interaction of the inhibitor with F(1) forms via the open conformation of the beta(E) subunit. Then, as two ATP molecules are hydrolyzed, the beta(E)-alpha(E) interface converts to the beta(DP)-alpha(DP) interface via the beta(TP)-alpha(TP) interface, trapping the inhibitor progressively in its binding site and a nucleotide in the catalytic site of subunit beta(DP). The inhibition probably arises by IF(1) imposing the structure and properties of the beta(TP)-alpha(TP) interface on the beta(DP)-alpha(DP) interface, thereby preventing it from hydrolyzing the bound ATP.

F1-ATPase rotates by an asymmetric, sequential mechanism using all three catalytic subunits

F1-ATPase, the catalytic part of FoF1-ATP synthase, rotates the central gamma subunit within the alpha3beta3 cylinder in 120 degrees steps, each step consuming a single ATP molecule. However, how the catalytic activity of each beta subunit is coordinated with the other two beta subunits to drive rotation remains unknown. Here we show that hybrid F1 containing one or two mutant beta subunits with altered catalytic kinetics rotates in an asymmetric stepwise fashion. Analysis of the rotations reveals that for any given beta subunit, the subunit binds ATP at 0 degrees, cleaves ATP at approximately 200 degrees and carries out a third catalytic event at approximately 320 degrees. This demonstrates the concerted nature of the F1 complex activity, where all three beta subunits participate to drive each 120 degrees rotation of the gamma subunit with a 120 degrees phase difference, a process we describe as a 'sequential three-site mechanism'.

Mechanism of inhibition of bovine F1-ATPase by resveratrol and related polyphenols

The structures of F(1)-ATPase from bovine heart mitochondria inhibited with the dietary phytopolyphenol, resveratrol, and with the related polyphenols quercetin and piceatannol have been determined at 2.3-, 2.4- and 2.7-A resolution, respectively. The inhibitors bind to a common site in the inside surface of an annulus made from loops in the three alpha- and three beta-subunits beneath the "crown" of beta-strands in their N-terminal domains. This region of F(1)-ATPase forms a bearing to allow the rotation of the tip of the gamma-subunit inside the annulus during catalysis. The binding site is a hydrophobic pocket between the C-terminal tip of the gamma-subunit and the beta(TP) subunit, and the inhibitors are bound via H-bonds mostly to their hydroxyl moieties mediated by bound water molecules and by hydrophobic interactions. There are no equivalent sites between the gamma-subunit and either the beta(DP) or the beta(E) subunit. The inhibitors probably prevent both the synthetic and hydrolytic activities of the enzyme by blocking both senses of rotation of the gamma-subunit. The beneficial effects of dietary resveratrol may derive in part by preventing mitochondrial ATP synthesis in tumor cells, thereby inducing apoptosis.

Met23Lys mutation in subunit gamma of F(O)F(1)-ATP synthase from Rhodobacter capsulatus impairs the activation of ATP hydrolysis by protonmotive force

H(+)-F(O)F(1)-ATP synthase couples proton flow through its membrane portion, F(O), to the synthesis of ATP in its headpiece, F(1). Upon reversal of the reaction the enzyme functions as a proton pumping ATPase. Even in the simplest bacterial enzyme the ATPase activity is regulated by several mechanisms, involving inhibition by MgADP, conformational transitions of the epsilon subunit, and activation by protonmotive force. Here we report that the Met23Lys mutation in the gamma subunit of the Rhodobacter capsulatus ATP synthase significantly impaired the activation of ATP hydrolysis by protonmotive force. The impairment in the mutant was due to faster enzyme deactivation that was particularly evident at low ATP/ADP ratio. We suggest that the electrostatic interaction of the introduced gammaLys23 with the DELSEED region of subunit beta stabilized the ADP-inhibited state of the enzyme by hindering the rotation of subunit gamma rotation which is necessary for the activation.

Ground state structure of F1-ATPase from bovine heart mitochondria at 1.9 A resolution

The structure of bovine F(1)-ATPase, crystallized in the presence of AMP-PNP and ADP, but in the absence of azide, has been determined at 1.9A resolution. This structure has been compared with the previously described structure of bovine F(1)-ATPase determined at 1.95A resolution with crystals grown under the same conditions but in the presence of azide. The two structures are extremely similar, but they differ in the nucleotides that are bound to the catalytic site in the beta(DP)-subunit. In the present structure, the nucleotide binding sites in the beta(DP)- and beta(TP)-subunits are both occupied by AMP-PNP, whereas in the earlier structure, the beta(TP) site was occupied by AMP-PNP and the beta(DP) site by ADP, where its binding is enhanced by a bound azide ion. Also, the conformation of the side chain of the catalytically important residue, alphaArg-373 differs in the beta(DP)- and beta(TP)-subunits. Thus, the structure with bound azide represents the ADP inhibited state of the enzyme, and the new structure represents a ground state intermediate in the active catalytic cycle of ATP hydrolysis.

Inhibitors of the catalytic domain of mitochondrial ATP synthase

An understanding of the mechanism of ATP synthase requires an explanation of how inhibitors act. The catalytic F1-ATPase domain of the enzyme has been studied extensively by X-ray crystallography in a variety of inhibited states. Four independent inhibitory sites have been identified by high-resolution structural studies. They are the catalytic site, and the binding sites for the antibiotics aurovertin and efrapeptin and for the natural inhibitor protein, IF1.

Novel features of the rotary catalytic mechanism revealed in the structure of yeast F1 ATPase

The crystal structure of yeast mitochondrial F(1) ATPase contains three independent copies of the complex, two of which have similar conformations while the third differs in the position of the central stalk relative to the alpha(3)beta(3) sub-assembly. All three copies display very similar asymmetric features to those observed for the bovine enzyme, but the yeast F(1) ATPase structures provide novel information. In particular, the active site that binds ADP in bovine F(1) ATPase has an ATP analog bound and therefore this structure does not represent the ADP-inhibited form. In addition, one of the complexes binds phosphate in the nucleotide-free catalytic site, and comparison with other structures provides a picture of the movement of the phosphate group during initial binding and subsequent catalysis. The shifts in position of the central stalk between two of the three copies of yeast F(1) ATPase and when these structures are compared to those of the bovine enzyme give new insight into the conformational changes that take place during rotational catalysis.