ATP-driven rotation of the gamma subunit in F(1)-ATPase

Structural Asymmetry and Kinetic Limping of Single Rotary F-ATP Synthases

F-ATP synthases use proton flow through the FO domain to synthesize ATP in the F₁ domain. In Escherichia coli, the enzyme consists of rotor subunits γεc10 and stator subunits (αβ)₃δab₂. Subunits c10 or (αβ)₃ alone are rotationally symmetric. However, symmetry is broken by the b₂ homodimer, which together with subunit δa, forms a single eccentric stalk connecting the membrane embedded FO domain with the soluble F₁ domain, and the central rotating and curved stalk composed of subunit γε. Although each of the three catalytic binding sites in (αβ)₃ catalyzes the same set of partial reactions in the time average, they might not be fully equivalent at any moment, because the structural symmetry is broken by contact with b₂δ in F₁ and with b₂a in FO. We monitored the enzyme's rotary progression during ATP hydrolysis by three single-molecule techniques: fluorescence video-microscopy with attached actin filaments, Förster resonance energy transfer between pairs of fluorescence probes, and a polarization assay using gold nanorods. We found that one dwell in the three-stepped rotary progression lasting longer than the other two by a factor of up to 1.6. This effect of the structural asymmetry is small due to the internal elastic coupling.

The rotary mechanism of the ATP synthase

The F0F1 ATP synthase is a large complex of at least 22 subunits, more than half of which are in the membranous F0 sector. This nearly ubiquitous transporter is responsible for the majority of ATP synthesis in oxidative and photo-phosphorylation, and its overall structure and mechanism have remained conserved throughout evolution. Most examples utilize the proton motive force to drive ATP synthesis except for a few bacteria, which use a sodium motive force. A remarkable feature of the complex is the rotary movement of an assembly of subunits that plays essential roles in both transport and catalytic mechanisms. This review addresses the role of rotation in catalysis of ATP synthesis/hydrolysis and the transport of protons or sodium.

Determination of the partial reactions of rotational catalysis in F1-ATPase

Steady-state ATP hydrolysis in the F1-ATPase of the F(O)F1 ATP synthase complex involves rotation of the central gamma subunit relative to the catalytic sites in the alpha3beta3 pseudo-hexamer. To understand the relationship between the catalytic mechanism and gamma subunit rotation, the pre-steady-state kinetics of Mg x ATP hydrolysis in the soluble F1-ATPase upon rapid filling of all three catalytic sites was determined. The experimentally accessible partial reactions leading up to the rate-limiting step and continuing through to the steady-state mode were obtained for the first time. The burst kinetics and steady-state hydrolysis for a range of Mg x ATP concentrations provide adequate constraints for a unique minimal kinetic model that can fit all the data and satisfy extensive sensitivity tests. Significantly, the fits show that the ratio of the rates of ATP hydrolysis and synthesis is close to unity even in the steady-state mode of hydrolysis. Furthermore, the rate of Pi binding in the absence of the membranous F(O) sector is insignificant; thus, productive Pi binding does not occur without the influence of a proton motive force. In addition to the minimal steps of ATP binding, reversible ATP hydrolysis/synthesis, and the release of product Pi and ADP, one additional rate-limiting step is required to fit the burst kinetics. On the basis of the testing of all possible minimal kinetic models, this step must follow hydrolysis and precede Pi release in order to explain burst kinetics. Consistent with the single molecule analysis of Yasuda et al. (Yasuda, R., Noji, H., Yoshida, M., Kinosita, K., and Itoh, H. (2001) Nature 410, 898-904), we propose that the rate-limiting step involves a partial rotation of the gamma subunit; hence, we name this step k(gamma). Moreover, the only model that is consistent with our data and many other observations in the literature suggests that reversible hydrolysis/synthesis can only occur in the active site of the beta(TP) conformer (Abrahams, J. P., Leslie, A. G. W., Lutter, R., and Walker, J. E. (1994) Nature 370, 621-628).

Influence of hydrogen bonds on charge distribution and conformation of L-arginine

The molecular recognition of adenosine-5'-triphosphate (ATP) with L-arginine (Arg) through hydrogen bonding interactions has been found using 1H NMR, H-H NOESY, acidity titration and fluorescence spectra techniques. The interactions could influence charge distribution in Arg and induce Arg conformational variation. It is realized that Arg conformation change from a partly folded state to an extended state through the rotation of CC single bonds of Arg side chain during the molecular recognition process.

Hydrogen bonds between the alpha and beta subunits of the F1-ATPase allow communication between the catalytic site and the interface of the beta catch loop and the gamma subunit

F(1)-ATPase mutations in Escherichia coli that changed the strength of hydrogen bonds between the alpha and beta subunits in a location that links the catalytic site to the interface between the beta catch loop and the gamma subunit were examined. Loss of the ability to form the hydrogen bonds involving alphaS337, betaD301, and alphaD335 lowered the k(cat) of ATPase and decreased its susceptibility to Mg(2+)-ADP-AlF(n) inhibition, while mutations that maintain or strengthen these bonds increased the susceptibility to Mg(2+)-ADP-AlF(n) inhibition and lowered the k(cat) of ATPase. These data suggest that hydrogen bonds connecting alphaS337 to betaD301 and betaR323 and connecting alphaD335 to alphaS337 are important to transition state stabilization and catalytic function that may result from the proper alignment of catalytic site residues betaR182 and alphaR376 through the VISIT sequence (alpha344-348). Mutations betaD301E, betaR323K, and alphaR282Q changed the rate-limiting step of the reaction as determined by an isokinetic plot. Hydrophobic mutations of betaR323 decreased the susceptibility to Mg(2+)-ADP-AlF(n)() inhibition and lowered the number of interactions required in the rate-limiting step yet did not affect the k(cat) of ATPase, suggesting that betaR323 is important to transition state formation. The decreased rate of ATP synthase-dependent growth and decreased level of lactate-dependent quenching observed with alphaD335, betaD301, and alphaE283 mutations suggest that these residues may be important to the formation of an alternative set of hydrogen bonds at the interface of the alpha and beta subunits that permits the release of intersubunit bonds upon the binding of ATP, allowing gamma rotation in the escapement mechanism.

Zooming in on ATP hydrolysis in F1

We summarize our current view of the reaction mechanism in F(1)-ATPase as it has emerged from experiment, theory, and computational studies over the last several years. ATP catalysis in the catalytic binding pockets of F(1) takes place without the release of any significant free energy and is efficiently driven by the combined action of two water molecules utilizing a so-called protein-relay mechanism. The chemical reaction itself is controlled by the spatial position of a key arginine residue.

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin

Rho is a hexameric RNA/DNA helicase/translocase that terminates transcription of select genes in bacteria. The naturally occurring antibiotic, bicyclomycin (BCM), acts as a noncompetitive inhibitor of ATP turnover to disrupt this process. We have determined three independent X-ray crystal structures of Rho complexed with BCM and two semisynthetic derivatives, 5a-(3-formylphenylsulfanyl)-dihydrobicyclomycin (FPDB) and 5a-formylbicyclomycin (FB) to 3.15, 3.05, and 3.15 A resolution, respectively. The structures show that BCM and its derivatives are nonnucleotide inhibitors that interact with Rho at a pocket adjacent to the ATP and RNA binding sites in the C-terminal half of the protein. BCM association prevents ATP turnover by an unexpected mechanism, occluding the binding of the nucleophilic water molecule required for ATP hydrolysis. Our data explain why only certain elements of BCM have been amenable to modification and serve as a template for the design of new inhibitors.

High hydrostatic pressure perturbs the interactions between CF(0)F(1) subunits and induces a dual effect on activity

Chloroplast ATP-synthase is an H(+)/ATP-driven rotary motor in which a hydrophobic multi-subunit assemblage rotates within a hydrophilic stator, and subunit interactions dictate alternate-site catalysis. To explore the relevance of these interactions for catalysis we use hydrostatic pressure to induce conformational changes and/or subunit dissociation, and the resulting changes in the ATPase activity and oligomer structure are evaluated. Under moderate hydrostatic pressure (up to 60-80 MPa), ATPase activity is increased by 1.5-fold. This is not related to an increase in the affinity for ATP, but seems to correlate with an enhanced turnover induced by pressure, and an activation volume for the ATPase reaction of -23.7 ml/mol. Higher pressure (up to 200 MPa) leads to dissociation of the enzyme, as shown by enzyme inactivation, increased binding of 8-anilinonaphthalene-1-sulfonate (ANS) to hydrophobic regions, and labeling of specific Cys residues on the beta and alpha subunits by N-iodoacetyl-N'-(5-sulfo-1-naphthyl)ethylene-4-diamine (IAEDANS). Compression-decompression cycles (between 0.1 and 200 MPa) inactivate CF(0)F(1) in a concentration-dependent manner, although after decompression no enzyme subunit is retained on a Sephadex-G-50 centrifuge column or is further labeled by IAEDANS. It is proposed that moderate hydrostatic pressures induce elastic compression of CF(0)F(1), leading to enhanced turnover. High pressure dissociation impairs the contacts needed for rotational catalysis.

ATP hydrolysis in the betaTP and betaDP catalytic sites of F1-ATPase

The enzyme F1-adenosine triphosphatase (ATPase) is a molecular motor that converts the chemical energy stored in the molecule adenosine triphosphate (ATP) into mechanical rotation of its gamma-subunit. During steady-state catalysis, the three catalytic sites of F1 operate in a cooperative fashion such that at every instant each site is in a different conformation corresponding to a different stage along the catalytic cycle. Notwithstanding a large amount of biochemical and, recently, structural data, we still lack an understanding of how ATP hydrolysis in F1 is coupled to mechanical motion and how the catalytic sites achieve cooperativity during rotatory catalysis. In this publication, we report combined quantum mechanical/molecular mechanical simulations of ATP hydrolysis in the betaTP and betaDP catalytic sites of F1-ATPase. Our simulations reveal a dramatic change in the reaction energetics from strongly endothermic in betaTP to approximately equienergetic in betaDP. The simulations identify the responsible protein residues, the arginine finger alphaR373 being the most important one. Similar to our earlier study of betaTP, we find a multicenter proton relay mechanism to be the energetically most favorable hydrolysis pathway. The results elucidate how cooperativity between catalytic sites might be achieved by this remarkable molecular motor.

On the mechanism of ATP hydrolysis in F1-ATPase

Most of the cellular ATP in living organisms is synthesized by the enzyme F(1)F(o)-ATP synthase. The water soluble F(1) part of the enzyme can also work in reverse and utilize the chemical energy released during ATP hydrolysis to generate mechanical motion. Despite the availability of a large amount of biochemical data and several x-ray crystallographic structures of F(1), there still remains a considerable lack of understanding as to how this protein efficiently converts the chemical energy released during the reaction ATP + H(2)O --> ADP + P(i) into mechanical motion of the stalk. We report here an ab initio QM/MM study of ATP hydrolysis in the beta(TP) catalytic site of F(1). Our simulations provide an atomic level description of the reaction path, its energetics, and the interaction of the nucleotide with the protein environment during catalysis. The simulations suggest that the reaction path with the lowest potential energy barrier proceeds via nucleophilic attack on the gamma-phosphate involving two water molecules. Furthermore, the ATP hydrolysis reaction in beta(TP) is found to be endothermic, demonstrating that the catalytic site is able to support the synthesis of ATP and does not promote ATP hydrolysis in the particular conformation studied.

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.

Metal dependency for transcription factor rho activation

The Escherichia coli rho transcription termination factor terminates select transcripts and rho activity requires Mg(2+). We investigated whether divalent metal ions other than Mg(2+) catalyze rho-dependent ATP hydrolysis to ADP and P(i) in vitro. The effects of 11 divalent metal ions (Be(2+), Ca(2+), Cd(2+), Co(2+), Cu(2+), Hg(2+), Mn(2+), Ni(2+), Sr(2+), VO(2+), Zn(2+)) on ATPase activity were determined in the absence and presence of MgCl(2). Without MgCl(2), Ca(2+), Cd(2+), Co(2+), Cu(2+), Hg(2+), Mn(2+), Ni(2+), VO(2+), and Zn(2+) activated ATP hydrolysis with either hyberbolic (Ca(2+), Co(2+), Cu(2+), Hg(2+), VO(2+)), peak velocity (Cd(2+), Mn(2+), Zn(2+)), or sigmoidal (Ni(2+)) rate acceleration curves. Sr(2+) was found to be a nonactivator and Be(2+) an inhibitor of rho-dependent ATPase activity. The metals' effects were compared with Mg(2+) and gave different rank orders when either the velocity (V(max), V(peak)) or the efficiency (V(max)/K(M), V(peak)/K(M)) of ATP hydrolysis was used as the determinant (V: Mg(2+) approximately Mn(2+) > Zn(2+) > Co(2+) > Ni(2+) approximately Cd(2+) > Ca(2+) > Cu(2+) > Hg(2+) approximately VO(2+); V/K(M): Mg(2+) > Mn(2+) > Ca(2+) > Co(2+) > Zn(2+) > Cu(2+) > Ni(2+) > Hg(2+) > Cd(2+)). Mg(2+) proved to be the most effective divalent metal. We observed that the metal-dependent rates were affected by metal ion interactions with rho, RNA, and the buffer constituents. Significantly, replacement of the octahedral Mg(2+) ion by metals that typically prefer coordination spheres less than six (Cd(2+), Co(2+), Ni(2+), VO(2+), Zn(2+)) led to ATPase activity, suggesting that the putative Mg x ATP(2-) coordination sphere in rho does not need to remain fully intact for ATP hydrolysis.

The Mg2+ requirements for rho transcription termination factor: catalysis and bicyclomycin inhibition

Kinetic studies document that the essential Escherichia coli transcription termination factor rho utilizes Mg(2+) and ATP as a substrate and requires a second Mg(2+) ion for maximum poly(C)-dependent ATP hydrolysis activity. The velocity curves show a classic nonessential Mg(2+) activation pattern in which Mg(2+) augments hydrolysis by 39% and gives a K(1)' for MgATP of 9.5 microM in the presence of excess Mg(2+) and a K(1) for MgATP of 21.2 microM under limiting Mg(2+) concentrations. Bicyclomycin (1), a commercial antibiotic that inhibits rho, weakened Mg(2+) binding at the nonessential site and disrupted the nonessential Mg(2+) activation pathway for poly(C)-dependent ATP hydrolysis. The K(i) values for 1 were 23 microM and 35 microM under excess and limiting Mg(2+) conditions, respectively, while the K(Mg(app)) for nonessential Mg(2+) increased with increasing 1 concentrations. These findings, when combined with reported mechanistic studies, provide an emerging picture of key catalytic and substrate binding sites that are necessary for rho function and that are proximal to the 1 binding site.

Quantitative determination of binding affinity of delta-subunit in Escherichia coli F1-ATPase: effects of mutation, Mg2+, and pH on Kd

To study the stator function in ATP synthase, a fluorimetric assay has been devised for quantitative determination of binding affinity of delta-subunit to Escherichia coli F(1)-ATPase. The signal used is that of the natural tryptophan at residue delta28, which is enhanced by 50% upon binding of delta-subunit to alpha(3)beta(3)gammaepsilon complex. K(d) for delta binding is 1.4 nm, which is energetically equivalent (50.2 kJ/mol) to that required to resist the rotor strain. Only one site for delta binding was detected. The deltaW28L mutation increased K(d) to 4.6 nm, equivalent to a loss of 2.9 kJ/mol binding energy. While this was insufficient to cause detectable functional impairment, it did facilitate preparation of delta-depleted F(1). The alphaG29D mutation reduced K(d) to 26 nm, equivalent to a loss of 7.2 kJ/mol binding energy. This mutation did cause serious functional impairment, referable to interruption of binding of delta to F(1). Results with the two mutants illuminate how finely balanced is the stator resistance function. delta' fragment, consisting of residues delta1-134, bound with the same K(d) as intact delta, showing that, at least in absence of F(o) subunits, the C-terminal domain of delta contributes zero binding energy. Mg(2+) ions had a strong effect on increasing delta binding affinity, supporting the possibility of bridging metal ion involvement in stator function. High pH environment greatly reduced delta binding affinity, suggesting the involvement of protonatable side-chains in the binding site.

Chromatophore vesicles of Rhodobacter capsulatus contain on average one F(O)F(1)-ATP synthase each

ATP synthase is a unique rotary machine that uses the transmembrane electrochemical potential difference of proton (Delta(H(+))) to synthesize ATP from ADP and inorganic phosphate. Charge translocation by the enzyme can be most conveniently followed in chromatophores of phototrophic bacteria (vesicles derived from invaginations of the cytoplasmic membrane). Excitation of chromatophores by a short flash of light generates a step of the proton-motive force, and the charge transfer, which is coupled to ATP synthesis, can be spectrophotometrically monitored by electrochromic absorption transients of intrinsic carotenoids in the coupling membrane. We assessed the average number of functional enzyme molecules per chromatophore vesicle. Kinetic analysis of the electrochromic transients plus/minus specific ATP synthase inhibitors (efrapeptin and venturicidin) showed that the extent of the enzyme-related proton transfer dropped as a function of the inhibitor concentration, whereas the time constant of the proton transfer changed only marginally. Statistical analysis of the kinetic data revealed that the average number of proton-conducting F(O)F(1)-molecules per chromatophore was approximately one. Thereby chromatophores of Rhodobacter capsulatus provide a system where the coupling of proton transfer to ATP synthesis can be studied in a single enzyme/single vesicle mode.

The molecular mechanism of ATP synthesis by F1F0-ATP synthase

ATP synthesis by oxidative phosphorylation and photophosphorylation, catalyzed by F1F0-ATP synthase, is the fundamental means of cell energy production. Earlier mutagenesis studies had gone some way to describing the mechanism. More recently, several X-ray structures at atomic resolution have pictured the catalytic sites, and real-time video recordings of subunit rotation have left no doubt of the nature of energy coupling between the transmembrane proton gradient and the catalytic sites in this extraordinary molecular motor. Nonetheless, the molecular events that are required to accomplish the chemical synthesis of ATP remain undefined. In this review we summarize current state of knowledge and present a hypothesis for the molecular mechanism of ATP synthesis.

Bi-site catalysis in F1-ATPase: does it exist?

The mechanism of action of F(1)F(0)-ATP synthase is controversial. Some favor a tri-site mechanism, where substrate must fill all three catalytic sites for activity, others a bi-site mechanism, where one of the three sites is always unoccupied. New approaches were applied to examine this question. First, ITP was used as hydrolysis substrate; lower binding affinities of ITP versus ATP enable more accurate assessment of sites occupancy. Second, distributions of all eight possible enzyme species (with zero, one, two or three sites filled) as fraction of total enzyme population at each ITP concentration were calculated, and compared with measured ITPase activity. Confirming data were obtained with ATP as substrate. Third, we performed a theoretical analysis of possible bi-site mechanisms. The results argue convincingly that bi-site hydrolysis activity is negligible, and may not even exist. Effectively, tri-site hydrolysis is the only mechanism. We argue that only tri-site hydrolysis drives subunit rotation. Theoretical analyses of possible bi-site mechanisms reveal serious flaws, not previously recognized. One is that, in bi-site catalysis, the predicted direction of subunit rotation is the same for both ATP synthesis and hydrolysis; a second is that infrequently occurring enzyme species are required.