Comparison between single-molecule and X-ray crystallography data on yeast F1-ATPase

Conformational ensemble of yeast ATP synthase at low pH reveals unique intermediates and plasticity in F1-Fo coupling

Mitochondrial adenosine triphosphate (ATP) synthase uses the proton gradient across the inner mitochondrial membrane to synthesize ATP. Structural and single molecule studies conducted mostly at neutral or basic pH have provided details of the reaction mechanism of ATP synthesis. However, pH of the mitochondrial matrix is slightly acidic during hypoxia and pH-dependent conformational changes in the ATP synthase have been reported. Here we use single-particle cryo-EM to analyze the conformational ensemble of the yeast (Saccharomyces cerevisiae) ATP synthase at pH 6. Of the four conformations resolved in this study, three are reaction intermediates. In addition to canonical catalytic dwell and binding dwell structures, we identify two unique conformations with nearly identical positions of the central rotor but different catalytic site conformations. These structures provide new insights into the catalytic mechanism of the ATP synthase and highlight elastic coupling between the catalytic and proton translocating domains.

Angle-dependent rotation velocity consistent with ADP release in bacterial F1-ATPase

A model-based method is used to extract a short-lived state in the rotation kinetics of the F1-ATPase of a bacterial species, Paracoccus denitrificans (PdF1). Imaged as a single molecule, PdF1 takes large 120ø steps during it rotation. The apparent lack of further substeps in the trajectories not only renders the rotation of PdF1 unlike that of other F-ATPases, but also hinders the establishment of its mechano-chemical kinetic scheme. We addressed these challenges using the angular velocity extracted from the single-molecule trajectories and compare it with its theoretically calculated counterpart. The theory-experiment comparison indicate the presence of a 20μs lifetime state, 40o after ATP binding. We identify a kinetic cycle in which this state is a three-nucleotide occupancy state prior to ADP release from another site. A similar state was also reported in our earlier study of the Thermophilic bacillus F1-ATPase (lifetime ∼ 10 μ s), suggesting thereby a common mechanism for removing a nucleotide release bottleneck in the rotary mechanism.

Six states of Enterococcus hirae V-type ATPase reveals non-uniform rotor rotation during turnover

The vacuolar-type ATPase from Enterococcus hirae (EhV-ATPase) is a thus-far unique adaptation of V-ATPases, as it performs Na⁺ transport and demonstrates an off-axis rotor assembly. Recent single molecule studies of the isolated V₁ domain have indicated that there are subpauses within the three major states of the pseudo three-fold symmetric rotary enzyme. However, there was no structural evidence for these. Herein we activate the EhV-ATPase complex with ATP and identified multiple structures consisting of a total of six states of this complex by using cryo-electron microscopy. The orientations of the rotor complex during turnover, especially in the intermediates, are not as perfectly uniform as expected. The densities in the nucleotide binding pockets in the V₁ domain indicate the different catalytic conditions for the six conformations. The off-axis rotor and its' interactions with the stator a-subunit during rotation suggests that this non-uniform rotor rotation is performed through the entire complex.

Rotary properties of hybrid F1-ATPases consisting of subunits from different species

F₁-ATPase (F₁) is an ATP-driven rotary motor protein ubiquitously found in many species as the catalytic portion of F_oF₁-ATP synthase. Despite the highly conserved amino acid sequence of the catalytic core subunits: α and β, F₁ shows diversity in the maximum catalytic turnover rate V_max and the number of rotary steps per turn. To study the design principle of F₁, we prepared eight hybrid F₁s composed of subunits from two of three genuine F₁s: thermophilic Bacillus PS3 (TF₁), bovine mitochondria (bMF₁), and Paracoccus denitrificans (PdF₁), differing in the V_max and the number of rotary steps. The V_max of the hybrids can be well fitted by a quadratic model highlighting the dominant roles of β and the couplings between α-β. Although there exist no simple rules on which subunit dominantly determines the number of steps, our findings show that the stepping behavior is characterized by the combination of all subunits.

Direct identification of the rotary angle of ATP cleavage in F1-ATPase from Bacillus PS3

F1-ATPase is the world's smallest biological rotary motor driven by ATP hydrolysis at three catalytic β subunits. The 120° rotational step of the central shaft γ consists of 80° substep driven by ATP binding and a subsequent 40° substep. In order to correlate timing of ATP cleavage at a specific catalytic site with a rotary angle, we designed a new F1-ATPase (F1) from thermophilic Bacillus PS3 carrying β(E190D/F414E/F420E) mutations, which cause extremely slow rates of both ATP cleavage and ATP binding. We produced an F1 molecule that consists of one mutant β and two wild-type βs (hybrid F1). As a result, the new hybrid F1 showed two pausing angles that are separated by 200°. They are attributable to two slowed reaction steps in the mutated β, thus providing the direct evidence that ATP cleavage occurs at 200° rather than 80° subsequent to ATP binding at 0°. This scenario resolves the long-standing unclarified issue in the chemomechanical coupling scheme and gives insights into the mechanism of driving unidirectional rotation.

How Does F1-ATPase Generate Torque?: Analysis From Cryo-Electron Microscopy and Rotational Catalysis of Thermophilic F1

The F₁-ATPase is a rotary motor fueled by ATP hydrolysis. Its rotational dynamics have been well characterized using single-molecule rotation assays. While F₁-ATPases from various species have been studied using rotation assays, the standard model for single-molecule studies has been the F₁-ATPase from thermophilic Bacillus sp. PS3, named TF₁. Single-molecule studies of TF₁ have revealed fundamental features of the F₁-ATPase, such as the principal stoichiometry of chemo-mechanical coupling (hydrolysis of 3 ATP per turn), torque (approximately 40 pN·nm), and work per hydrolysis reaction (80 pN·nm = 48 kJ/mol), which is nearly equivalent to the free energy of ATP hydrolysis. Rotation assays have also revealed that TF₁ exhibits two stable conformational states during turn: a binding dwell state and a catalytic dwell state. Although many structures of F₁ have been reported, most of them represent the catalytic dwell state or its related states, and the structure of the binding dwell state remained unknown. A recent cryo-EM study on TF₁ revealed the structure of the binding dwell state, providing insights into how F₁ generates torque coupled to ATP hydrolysis. In this review, we discuss the torque generation mechanism of F₁ based on the structure of the binding dwell state and single-molecule studies.

Structure of ATP synthase under strain during catalysis

ATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F₁ motor and a proton-translocation-driven F_O motor. The F₁ and F_O motors oppose each other’s action on a shared rotor subcomplex and are held stationary relative to each other by a peripheral stalk. Structures of resting mitochondrial ATP synthases revealed a left-handed curvature of the peripheral stalk even though rotation of the rotor, driven by either ATP hydrolysis in F₁ or proton translocation through F_O, would apply a right-handed bending force to the stalk. We used cryoEM to image yeast mitochondrial ATP synthase under strain during ATP-hydrolysis-driven rotary catalysis, revealing a large deformation of the peripheral stalk. The structures show how the peripheral stalk opposes the bending force and suggests that during ATP synthesis proton translocation causes accumulation of strain in the stalk, which relaxes by driving the relative rotation of the rotor through six sub-steps within F₁, leading to catalysis.

CryoEM of mitochondrial ATP synthase frozen during rotary catalysis reveals dramatic conformational changes in the peripheral stalk subcomplex, which enable the enzyme’s efficient synthesis of ATP.

The 3 × 120° rotary mechanism of Paracoccus denitrificans F1-ATPase is different from that of the bacterial and mitochondrial F1-ATPases

The rotation of Paracoccus denitrificans F₁-ATPase (PdF₁) was studied using single-molecule microscopy. At all concentrations of adenosine triphosphate (ATP) or a slowly hydrolyzable ATP analog (ATPγS), above or below K _m, PdF₁ showed three dwells per turn, each separated by 120°. Analysis of dwell time between steps showed that PdF₁ executes binding, hydrolysis, and probably product release at the same dwell. The comparison of ATP binding and catalytic pauses in single PdF₁ molecules suggested that PdF₁ executes both elementary events at the same rotary position. This point was confirmed in an inhibition experiment with a nonhydrolyzable ATP analog (AMP-PNP). Rotation assays in the presence of adenosine diphosphate (ADP) or inorganic phosphate at physiological concentrations did not reveal any obvious substeps. Although the possibility of the existence of substeps remains, all of the datasets show that PdF₁ is principally a three-stepping motor similar to bacterial vacuolar (V₁)-ATPase from Thermus thermophilus This contrasts with all other known F₁-ATPases that show six or nine dwells per turn, conducting ATP binding and hydrolysis at different dwells. Pauses by persistent Mg-ADP inhibition or the inhibitory ζ-subunit were also found at the same angular position of the rotation dwell, supporting the simplified chemomechanical scheme of PdF₁ Comprehensive analysis of rotary catalysis of F₁ from different species, including PdF₁, suggests a clear trend in the correlation between the numbers of rotary steps of F₁ and F_o domains of F-ATP synthase. F₁ motors with more distinctive steps are coupled with proton-conducting F_o rings with fewer proteolipid subunits, giving insight into the design principle the F₁F_o of ATP synthase.

Correlation between the numbers of rotation steps in the ATPase and proton-conducting domains of F- and V-ATPases

This letter reports the correlation in the number of distinct rotation steps between the F₁/V₁ and F_o/V_o domains that constitute common rotary F- and V-ATP synthases/ATPases. Recent single-molecule studies on the F₁-ATPase revealed differences in the number of discrete steps in rotary catalysis between different organisms—6 steps per turn in bacterial types and mitochondrial F₁ from yeast, and 9 steps in the mammalian mitochondrial F₁ domains. The number of rotational steps that F_o domain makes is thought to correspond to that of proteolipid subunits within the rotating c-ring present in F_o. Structural studies on F_o and in the whole ATP synthase complex have shown a large diversity in the number of proteolipid subunits. Interestingly, 6 steps in F₁ are always paired with 10 steps in F_o, whereas 9 steps in F₁ are paired with 8 steps in F_o. The correlation in the number of steps has also been revealed for two types of V-ATPases: one having 6 steps in V₁ paired with 10 steps in V_o, and the other one having 3 steps in V₁ paired with 12 steps in V_o. Although the abovementioned correlations await further confirmation, the results suggest a clear trend; ATPase motors with more steps have proton-conducting motors with less steps. In addition, ATPases with 6 steps are always paired with proton-conducting domains with 10 steps.

Rotary catalysis of bovine mitochondrial F1-ATPase studied by single-molecule experiments

The reaction scheme of rotary catalysis and the torque generation mechanism of bovine mitochondrial F₁ (bMF₁) were studied in single-molecule experiments. Under ATP-saturated concentrations, high-speed imaging of a single 40-nm gold bead attached to the γ subunit of bMF₁ showed 2 types of intervening pauses during the rotation that were discriminated by short dwell and long dwell. Using ATPγS as a slowly hydrolyzing ATP derivative as well as using a functional mutant βE188D with slowed ATP hydrolysis, the 2 pausing events were distinctively identified. Buffer-exchange experiments with a nonhydrolyzable analog (AMP-PNP) revealed that the long dwell corresponds to the catalytic dwell, that is, the waiting state for hydrolysis, while it remains elusive which catalytic state short pause represents. The angular position of catalytic dwell was determined to be at +80° from the ATP-binding angle, mostly consistent with other F₁s. The position of short dwell was found at 50 to 60° from catalytic dwell, that is, +10 to 20° from the ATP-binding angle. This is a distinct difference from human mitochondrial F₁, which also shows intervening dwell that probably corresponds to the short dwell of bMF₁, at +65° from the binding pause. Furthermore, we conducted "stall-and-release" experiments with magnetic tweezers to reveal how the binding affinity and hydrolysis equilibrium are modulated by the γ rotation. Similar to thermophilic F₁, bMF₁ showed a strong exponential increase in ATP affinity, while the hydrolysis equilibrium did not change significantly. This indicates that the ATP binding process generates larger torque than the hydrolysis process.

Single-molecule analysis reveals rotational substeps and chemo-mechanical coupling scheme of Enterococcus hirae V1-ATPase

V₁-ATPase (V₁), the catalytic domain of an ion-pumping V-ATPase, is a molecular motor that converts ATP hydrolysis-derived chemical energy into rotation. Here, using a gold nanoparticle probe, we directly observed rotation of V₁ from the pathogen Enterococcus hirae (EhV₁). We found that 120° steps in each ATP hydrolysis event are divided into 40 and 80° substeps. In the main pause before the 40° substep and at low ATP concentration ([ATP]), the time constant was inversely proportional to [ATP], indicating that ATP binds during the main pause with a rate constant of 1.0 × 10⁷ m^-1 s^-1 At high [ATP], we observed two [ATP]-independent time constants (0.5 and 0.7 ms). One of two time constants was prolonged (144 ms) in a rotation driven by slowly hydrolyzable ATPγS, indicating that ATP is cleaved during the main pause. In another subpause before the 80° substep, we noted an [ATP]-independent time constant (2.5 ms). Furthermore, in an ATP-driven rotation of an arginine-finger mutant in the presence of ADP, -80 and -40° backward steps were observed. The time constants of the pauses before -80° backward and +40° recovery steps were inversely proportional to [ADP] and [ATP], respectively, indicating that ADP- and ATP-binding events trigger these steps. Assuming that backward steps are reverse reactions, we conclude that 40 and 80° substeps are triggered by ATP binding and ADP release, respectively, and that the remaining time constant in the main pause represents phosphate release. We propose a chemo-mechanical coupling scheme of EhV₁, including substeps largely different from those of F₁-ATPases.

Kinetic analysis methods applied to single motor protein trajectories

Molecular motors convert chemical or electrical energy into mechanical displacement, either linear or rotary. Under ideal circumstances, single-molecule measurements can spatially and temporally resolve individual steps of the motor, revealing important properties of the underlying mechanochemical process. Unfortunately, steps are often hard to resolve, as they are masked by thermal noise. In such cases, details of the mechanochemistry can nonetheless be recovered by analyzing the fluctuations in the recorded traces. Here, we expand upon existing statistical analysis methods, providing two new avenues to extract the motor step size, the effective number of rate-limiting chemical states per translocation step, and the compliance of the link between the motor and the probe particle. We first demonstrate the power and limitations of these methods using simulated molecular motor trajectories, and we then apply these methods to experimental data of kinesin, the bacterial flagellar motor, and F1-ATPase.

Understanding structure, function, and mutations in the mitochondrial ATP synthase

The mitochondrial ATP synthase is a multimeric enzyme complex with an overall molecular weight of about 600,000 Da. The ATP synthase is a molecular motor composed of two separable parts: F₁ and F_o. The F₁ portion contains the catalytic sites for ATP synthesis and protrudes into the mitochondrial matrix. F_o forms a proton turbine that is embedded in the inner membrane and connected to the rotor of F₁. The flux of protons flowing down a potential gradient powers the rotation of the rotor driving the synthesis of ATP. Thus, the flow of protons though F_o is coupled to the synthesis of ATP. This review will discuss the structure/function relationship in the ATP synthase as determined by biochemical, crystallographic, and genetic studies. An emphasis will be placed on linking the structure/function relationship with understanding how disease causing mutations or putative single nucleotide polymorphisms (SNPs) in genes encoding the subunits of the ATP synthase, will affect the function of the enzyme and the health of the individual. The review will start by summarizing the current understanding of the subunit composition of the enzyme and the role of the subunits followed by a discussion on known mutations and their effect on the activity of the ATP synthase. The review will conclude with a summary of mutations in genes encoding subunits of the ATP synthase that are known to be responsible for human disease, and a brief discussion on SNPs.