Robustness of the Rotary Catalysis Mechanism of F1-ATPase

F₁-ATPase (F₁) is the rotary motor protein fueled by ATP hydrolysis. Previous studies have suggested that three charged residues are indispensable for catalysis of F₁ as follows: the P-loop lysine in the phosphate-binding loop, GXXXXGK(T/S); a glutamic acid that activates water molecules for nucleophilic attack on the γ-phosphate of ATP (general base); and an arginine directly contacting the γ-phosphate (arginine finger). These residues are well conserved among P-loop NTPases. In this study, we investigated the role of these charged residues in catalysis and torque generation by analyzing alanine-substituted mutants in the single-molecule rotation assay. Surprisingly, all mutants continuously drove rotary motion, even though the rotational velocity was at least 100,000 times slower than that of wild type. Thus, although these charged residues contribute to highly efficient catalysis, they are not indispensable to chemo-mechanical energy coupling, and the rotary catalysis mechanism of F₁ is far more robust than previously thought.     

Steady-state rate of F1-ATPase turnover during ATP hydrolysis by the single catalytic site

Under the conditions of ATP regeneration and molar excess of nucleotide-depleted F1-ATPase the enzyme catalyses steady-state ATP hydrolysis by the single catalytic site. Values of Km = 10(-8) M and Vm = 0.05 s-1 for the single-site catalysis have been determined. ADP release limits single-site ATP hydrolysis under steady-state conditions. The equilibrium constant for ATP hydrolysis at the F1-ATPase catalytic site is less than or equal to 0.7.     

Mechanism of F1-ATPase studied by the genetic approach

E. coli F₁-ATPase has been studied mainly by the genetic approach. Mutations in either the or subunit modified the kinetics of multisite and uni-site hydrolysis of ATP. The mechanism of F₁-ATPase and the essential amino acid residues of subunits are discussed.Abbreviations used: P_i, inorganic phosphate; DCCD, dicyclohexylcarbodiimide.     

Torque Transmission Mechanism via DELSEED Loop of F1-ATPase

F₁-ATPase (F₁) is an ATP-driven rotary motor in which the three catalytic β subunits in the stator ring sequentially induce the unidirectional rotation of the rotary γ subunit. Many lines of evidence have revealed open-to-closed conformational transitions in the β subunit that swing the C-terminal domain inward. This conformational transition causes a C-terminal protruding loop with conserved sequence DELSEED to push the γ subunit. Previous work, where all residues of DELSEED were substituted with glycine to disrupt the specific interaction with γ and introduce conformational flexibility, showed that F₁ still rotated, but that the torque was halved, indicating a remarkable impact on torque transmission. In this study, we conducted a stall-and-release experiment on F₁ with a glycine-substituted DELSEED loop to investigate the impact of the glycine substitution on torque transmission upon ATP binding and ATP hydrolysis. The mutant F₁ showed a significantly reduced angle-dependent change in ATP affinity, whereas there was no change in the equilibrium for ATP hydrolysis. These findings indicate that the DELSEED loop is predominantly responsible for torque transmission upon ATP binding but not for that upon ATP hydrolysis.     

Torque Generation Mechanism of F1-ATPase upon NTP Binding

Molecular machines fueled by NTP play pivotal roles in a wide range of cellular activities. One common feature among NTP-driven molecular machines is that NTP binding is a major force-generating step among the elementary reaction steps comprising NTP hydrolysis. To understand the mechanism in detail,in this study, we conducted a single-molecule rotation assay of the ATP-driven rotary motor protein F₁-ATPase using uridine triphosphate (UTP) and a base-free nucleotide (ribose triphosphate) to investigate the impact of a pyrimidine base or base depletion on kinetics and force generation. Although the binding rates of UTP and ribose triphosphate were 10³ and 10⁶ times, respectively, slower than that of ATP, they supported rotation, generating torque comparable to that generated by ATP. Affinity change of F₁ to UTP coupled with rotation was determined, and the results again were comparable to those for ATP, suggesting that F₁ exerts torque upon the affinity change to UTP via rotation similar to ATP-driven rotation. Thus, the adenine-ring significantly enhances the binding rate, although it is not directly involved in force generation. Taking into account the findings from another study on F₁ with mutated phosphate-binding residues, it was proposed that progressive bond formation between the phosphate region and catalytic residues is responsible for the rotation-coupled change in affinity.     

A model of stepping kinetics for rotary enzymes. Application to the F1-ATPase

Our simple kinetic model, based on the classic “binding change mechanism”, describes the stepping kinetics for the rotary enzyme motors. The model shows that the cooperative interactions between active sites in the motor enzyme F1-ATPase induce the stepping product release. This phenomenon results from non-harmonic oscillations in the enzyme forms. The found rate constants, corresponding to the stepping phenomenon, are close to the rate constants known for the F1-ATPase. The duration of dwells during the product release is shown to depend on the ATP concentration in accordance with the known experimental data.     

Steady-state kinetic properties of FoF1-ATPase: the pH effect.

1. The kinetic properties of FoF1-ATPase from submitochondrial particles isolated from rat heart were studied, with emphasis to the pH effect. The velocity data were treated according to the Hill equation, and the results were discussed on the basis of the knowledge on the soluble F1-ATPase properties. 2. Three kinetic phases were observed in the range of pH 6.0-8.5, with apparent dissociation constant values (K0.5) of 0.001, 0.04 and 1.5 mM (respectively sites I, II and III) at pH 7.0. Their contribution to the total activity of the enzyme were pH-dependent on the range of 6.0-7.0, but not from 7.0 to 8.5, where the maximal velocity (V) for site III was some 4-fold larger than for site II, and the total V of sites II and III was some 40-fold larger than V assumed for site I. Therefore, two catalytic sites seem to participate significantly in the catalysis at steady-state condition. 3. Azide increased the sites II and III K0.5 values as well as decreased the site III V. In the presence of bicarbonate these two sites were not distinguishable, and the kinetic parameters at pH 7.0 were similar to those for sites II and III combined. Both azide and bicarbonate did not have a significant effect on site I, and this behavior was not pH-dependent. 4. The studies on the effect of pH on the kinetic parameters showed the following results: (1) the optimum pH for V was around 8.5; (2) decrease in the K0.5 values at pH below 7.0 for site II, and increase at pH over 7.0 for sites II and III; (3) in the pH range of 6.0-8.5 the Hill coefficient increased for site II, decreased for site III, and an intermediary effect was observed for the sites II and III combined, with a Michaelis-Menten behavior in the highest affinity pH, which was found in the physiological range.     

Cold lability of membrane-bound F1-ATPase.

1. Preincubation of MgATP submitochondrial particles with EDTA or Tris.HCl liberated a measurable amount of ATPase inhibitor that could be rapidly purified using only trichloroacetic acid precipitation and heat treatment. 2. In spite of the emergence of high ATPase activity, a considerable amount of ATPase inhibitor was left in the particles. Comparative analysis of other submitochondrial preparations indicated that only AS-particles were effectively depleted. 3. The high ATPase activity of inhibitor-deficient particles, was labile at low temperature provided that the exposure to cold was done in the presence of MgATP. Other nucleotides could not substitute for ATP. Glycerol inhibited and salts enhanced the cold inactivation of membrane-bound F1-ATPase. Isolation of F1-ATPase from cold-inactivated particles yielded a soluble preparation of correspondingly lower activity. 4. It is concluded that together with the increase of ATPase activity, the ATP-dependent cold lability of membrane-bound F1-ATPase and the dislocation of ATPase inhibitor at non operative sites reveal the extent of ATPase complex disorganization.     

Chaperones of F1-ATPase

Mitochondrial F₁-ATPase contains a hexamer of alternating α and β subunits. The assembly of this structure requires two specialized chaperones, Atp11p and Atp12p, that bind transiently to β and α. In the absence of Atp11p and Atp12p, the hexamer is not formed, and α and β precipitate as large insoluble aggregates. An early model for the mechanism of chaperone-mediated F₁ assembly (Wang, Z. G., Sheluho, D., Gatti, D. L., and Ackerman, S. H. (2000) EMBO J. 19, 1486–1493) hypothesized that the chaperones themselves look very much like the α and β subunits, and proposed an exchange of Atp11p for α and of Atp12p for β; the driving force for the exchange was expected to be a higher affinity of α and β for each other than for the respective chaperone partners. One important feature of this model was the prediction that as long as Atp11p is bound to β and Atp12p is bound to α, the two F₁ subunits cannot interact at either the catalytic site or the noncatalytic site interface. Here we present the structures of Atp11p from Candida glabrata and Atp12p from Paracoccus denitrificans, and we show that some features of the Wang model are correct, namely that binding of the chaperones to α and β prevents further interactions between these F₁ subunits. However, Atp11p and Atp12p do not resemble α or β, and it is instead the F₁ γ subunit that initiates the release of the chaperones from α and β and their further assembly into the mature complex.Mitochondrial F₁-ATPase consists of three α and three β subunits occupying alternate positions in a hexamer that surrounds a rod-like element containing one each of γ, δ, and ϵ subunits (1–3). Three nucleotide-binding catalytic sites (CS)⁴ and three noncatalytic sites (NCS) alternate at the six α/β interfaces. Early work with respiratory-deficient strains of Saccharomyces cerevisiae (4) revealed that two additional mitochondrial proteins, Atp11p and Atp12p, which are not integral subunits of the enzyme, are nonetheless necessary for the assembly of F₁-ATPase. Besides their failure to assemble F₁, a particularly interesting feature of atp11 and atp12 mutants is that they accumulate α and β subunits as high molecular weight aggregates (4) that can be recognized as densely stained inclusion bodies in the mitochondrial matrix (5). Subsequent studies in yeast have shown that Atp12p binds to F₁ α (6) and that Atp11p binds to β (7); these interactions include binding determinants in the nucleotide binding domains (NBD) of the two F₁ subunits. On this basis, it is now recognized that Atp11p and Atp12p are members of two new families of molecular chaperones, pfam06644 and pfam07542 (8), which are required for the assembly of mitochondrial ATP synthase in all eukaryotes. In fact, the first nuclear genetic lesion associated to a defect of mitochondrial ATP synthase in humans was identified in the locus ATPAF2 for Atp12p and was responsible for the death of a 14-month-old infant (9). Atp12p is also present in the α subdivision of Proteobacteria, consistent with the proposed origin of mitochondria from this ancestral line (10).The nature of the interactions between the F₁ subunits and Atp11p and Atp12p has remained elusive because of the lack of structural information for these chaperones. As α and β aggregate in the absence of Atp11p and Atp12p, it is usually assumed that the F₁ subunits are themselves poorly soluble, and that the two chaperones maintain them in a dispersed state until they are incorporated in the mature enzyme. Based on the analysis of the distribution of hydrophilic and hydrophobic areas on the surface of the α and β subunits of F₁, and on the interaction energies between these subunits at the interfaces that provide the CS and NCS sites, Wang et al. (6) have proposed a model of F₁ assembly in which Atp11p binds at the region of the β subunit that contributes to the CS site, and Atp12p binds at the region of the α subunit that contributes to the NCS site. One consequence of this particular binding of Atp11p and Atp12p to the F₁ subunits is that as long as Atp11p is bound to β and Atp12p is bound to α, the two F₁ subunits cannot interact at either the CS or the NCS interface. Since no other modulators of chaperone release are known, the Wang model requires an exchange of Atp11p for α and of Atp12p for β. Implied in this model is that the chaperones must themselves look very much like the α and β subunits, and that the driving force for the exchange must simply be a higher affinity of α and β for each other than for the respective chaperone partners. Here we present the structures of Atp11p from Candida glabrata and Atp12p from Paracoccus denitrificans, and we show that some features of the Wang model are correct, namely that binding of the chaperones to α and β prevents further interactions between these F₁ subunits. However, Atp11p and Atp12p do not resemble α or β, and it is instead the F₁ γ subunit that initiates the release of the chaperones from α and β and their further assembly into mature complex.     

F1-ATPase from different submitochondrial particles.

1. F1-ATPase has been extracted by the diphosphatidylglycerol procedure from mitochondrial ATPase complexes that differ in ATPase activity, cold stability, ATPase inhibitor and magnesium content. 2. The ATPase activity of the isolated enzymes was dependent upon the activity of the original particles. In this respect, F1-ATPase extracted from submitochondrial particles prepared in ammonia (pH 9.2) and filtered through Sephadex G-50 was comparable to the enzyme purified by conventional procedures (Horstman, L.L. and Racker, E. (1970) J. Biol. Chem. 245, 1336--1344), whereas F1-ATPase extracted from submitochondrial particles prepared in the presence of magnesium and ATP at neutral pH was similar to factor A (Andreoli, T.E., Lam, K.W. and Sanadi, D.R. (1965) J. Biol. Chem. 240, 2644--2653). 3. No systematic relationship has been found in these F1-ATPase preparations between their ATPase inhibitor content and ATPase activity. Rather, a relationship has been observed between this activity and the efficiency of the ATPase inhibitor-F1-ATPase association within the membrane. 4. It is concluded that the ATPase activity of isolated F1-ATPase reflects the properties of original ATPase complex provided a rapid and not denaturing procedure of isolation is employed.     

Steady-state kinetics of smooth muscle myosin.

The kinetic properties of purified smooth muscle myosin, free of actin, have been examined. Analysis of the steady-state kinetic data revealed an intermediary plateau region on the substrate saturation curves. In addition, these data, when analyzed by Hill and Lineweaver and Burk plots, indicate both positive and negative cooperativity, suggesting at least four substrate binding sites. The plateau region was abolished when the kinetic measurements were made at pH 5.5 and 9.0. Both positive and negative cooperative effects were absent at pH 9.0 and hyperbolic kinetics was observed. In contrast, at pH 5.5, although the plateau region was abolished, the enzyme exhibited positive cooperativity of substrate binding. When either heated or urea treated enzyme was used for kinetic measurements: (i) the plateau region shifted toward higher substrate concentration range; (ii) the cooperativity of binding sites was lost at low substrate concentrations but was instead seen at higher concentrations; and (iii) the Vmax was doubled. These data have been interpreted as due to ligand-induced conformational changes in the enzyme according to J. Teipel and D. E. Koshland, Jr. (1969).     

Chemomechanical coupling in F1-ATPase revealed by simultaneous observation of nucleotide kinetics and rotation

F(1)-ATPase is a rotary molecular motor in which unidirectional rotation of the central gamma subunit is powered by ATP hydrolysis in three catalytic sites arranged 120 degrees apart around gamma. To study how hydrolysis reactions produce mechanical rotation, we observed rotation under an optical microscope to see which of the three sites bound and released a fluorescent ATP analog. Assuming that the analog mimics authentic ATP, the following scheme emerges: (i) in the ATP-waiting state, one site, dictated by the orientation of gamma, is empty, whereas the other two bind a nucleotide; (ii) ATP binding to the empty site drives an approximately 80 degrees rotation of gamma; (iii) this triggers a reaction(s), hydrolysis and/or phosphate release, but not ADP release in the site that bound ATP one step earlier; (iv) completion of this reaction induces further approximately 40 degrees rotation.     

Investigations on the kinetic mechanism of octopine dehydrogenase. 1. Steady-state kinetics.

The kinetic mechanism of action of octopine dehydrogenase was investigated. This enzyme catalyses the reversible dehydrogenation of D-octopine to L-arginine and pyruvate, in the presence of nicotinamide-adenine dinucleotide. Initial velocity and product inhibition studies were carried out in both directions. Most of the results are consistent with a bi-ter sequential mechanism where NAD+ binds first to the enzyme followed by D-octopine, and the products are released in the order L-arginine, pyruvate and NADH. Various kinetic parameters were determined for each reactant at 33 degrees C, at pH 9.6 for NAD reduction, at pH 6.6 for NADH oxidation.     

Study of the yeast Saccharomyces cerevisiae F1F0-ATPase epsilon-subunit.

The yeast Saccharomyces cerevisiae F1F0-ATPase epsilon-subunit (61 residues) was synthesized by the solid-phase peptide approach under both acidic and basic strategies. Only the latter strategy allowed us to obtain a pure epsilon-subunit. The strong propensity of the protein to produce few soluble dimeric species depending on pH has been proved by size-exclusion chromatography, electrophoresis and mass spectrometry. A circular dichroism study showed that an aqueous solution containing 30% trifluoroethanol or 200 mM sodium dodecyl sulphate is required for helical folding. In both solvents at acidic pH, the epsilon-subunit is soluble and monomeric.     

Steady state kinetics of proton translocation catalyzed by thermophilic F0F1-ATPase reconstituted in planar bilayer membranes

The proton-translocating ATPase of the thermophilic bacterium PS3 was reconstituted into planar phospholipid bilayers by the previously reported method (Hirata, H., Ohno, K., Sone, N., Kagawa, Y., and Hamamoto, T. (1986) J. Biol. Chem. 261, 9839-9843), and the relationship between the electric current induced by ATP and the concentration of ATP was examined. The magnitude of the electric current generated upon addition of ATP followed simple Michaelis-Menten type kinetics, and the Michaelis constant was found to be 0.14 mM under our conditions. This value is close to the values reported for F1- or F0F1-ATPase in its steady state catalytic cycle, indicating that the proton translocation is coupled to the steady state ATPase reaction. The relationship between the Km value and the membrane potential was also examined under the voltage-clamped condition, and we found that there was no apparent dependence of the Km on membrane voltage. These results together with the previous data suggest that the voltage dependence residues in some step that defines the apparent Vmax rather than Km in the reaction cycle, and proton translocation is not directly coupled to this ATP binding step.     

Rotation of Escherichia coli F(1)-ATPase.

By applying the same method used for F(1)-ATPase (TF(1)) from thermophilic Bacillus PS3 (Noji, H., Yasuda, R., Yoshida, M., and Kinosita, K., Jr. (1997) Nature 386, 299-302), we observed ATP-driven rotation of a fluorescent actin filament attached to the gamma subunit in Escherichia coli F(1)-ATPase. The torque value and the direction of the rotation were the same as those observed for TF(1). F(1)-ATPases seem to share common properties of rotation irrespective of the sources.