Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation

CHEMOMECHANICAL COUPLING AND STOCHASTIC THERMODYNAMICS OF THE F1-ATPase MOLECULAR MOTOR WITH AN APPLIED EXTERNAL TORQUE

The effects of external torque on the F 1-ATPase rotary molecular motor are studied from the viewpoint of recent advances in stochastic thermodynamics. This motor is modeled in terms of discrete-state and continuous-state stochastic processes. The dependence of the discrete-state description on external torque and friction is obtained by fitting its transition rates to a continuous-angle model based on Newtonian mechanics with Langevin fluctuating forces and reproducing experimental data on this motor. In this approach, the continuous-angle model is coarse-grained into discrete states separated by both mechanical and chemical transitions. The resulting discrete-state model allows us to identify the regime of tight chemomechanical coupling of the F 1 motor and to infer that its chemical and mechanical efficiencies may reach values close to the thermodynamically allowed maxima near the stalling torque. We also show that, under physiological conditions, the F 1 motor is functioning in a highly-nonlinear-response regime, providing a rotation rate a million times faster than would be possible in the linear-response regime of nonequilibrium thermodynamics. Furthermore, the counting statistics of fluctuations can be obtained in the tight-coupling regime thanks to the discrete-state stochastic process and we demonstrate that the so-called fluctuation theorem provides a useful method for measuring the thermodynamic forces driving the motor out of equilibrium.

Mechanical modulation of catalytic power on F1-ATPase

The conformational fluctuation of enzymes has a crucial role in reaction acceleration. However, the contribution to catalysis enhancement of individual substates with conformations far from the average conformation remains unclear. We studied the catalytic power of the rotary molecular motor F(1)-ATPase from thermophilic Bacillus PS3 as it was stalled in transient conformations far from a stable pausing angle. The rate constants of ATP binding and hydrolysis were determined as functions of the rotary angle. Both rates exponentially increase with rotation, revealing the molecular basis of positive cooperativity among three catalytic sites: elementary reaction steps are accelerated via the mechanical rotation driven by other reactions on neighboring catalytic sites. The rate enhancement induced by ATP binding upon rotation was greater than that brought about by hydrolysis, suggesting that the ATP binding step contributes more to torque generation than does the hydrolysis step. Additionally, 9% of the ATP-driven rotary step was supported by thermal diffusion, suggesting that acceleration of the ATP docking process occurs via thermally agitated conformational fluctuations.

Importance of water entropy in rotation mechanism of F1-ATPase

We briefly review our theoretical study on the rotation scheme of F1-ATPase. In the scheme, the key factor is the water entropy which has been shown to drive a variety of self-assembly processes in biological systems. We decompose the crystal structure of F1-ATPase into three sub-complexes each of which is composed of the γ subunit, one of the β subunits, and two α subunits adjacent to them. The βE, βTP, and βDP subunits are involved in the sub-complexes I, II, and III, respectively. We calculate the hydration entropy of each sub-complex using a hybrid of the integral equation theory for molecular liquids and the morphometric approach. It is found that the absolute value of the hydration entropy follows the order, sub-complex I > sub-complex II > sub-complex III. Moreover, the differences are quite large, which manifests highly asymmetrical packing of F1-ATPase. In our picture, this asymmetrical packing plays crucially important roles in the rotation of the γ subunit. We discuss how the rotation is induced by the water-entropy effect coupled with such chemical processes as ATP binding, ATP hydrolysis, and release of the products.

A change in the radius of rotation of F1-ATPase indicates a tilting motion of the central shaft

F(1)-ATPase is a water-soluble portion of F(o)F(1)-ATP synthase and rotary molecular motor that exhibits reversibility in chemical reactions. The rotational motion of the shaft subunit γ has been carefully scrutinized in previous studies, but a tilting motion of the shaft has never been explicitly postulated. Here we found a change in the radius of rotation of the probe attached to the shaft subunit γ between two different intermediate states in ATP hydrolysis: one waiting for ATP binding, and the other waiting for ATP hydrolysis and/or subsequent product release. Analysis of this radial difference indicates a ~4° outward tilting of the γ-subunit induced by ATP binding. The tilt angle is a new parameter, to our knowledge, representing the motion of the γ-subunit and provides a new constraint condition of the ATP-waiting conformation of F(1)-ATPase, which has not been determined as an atomic structure from x-ray crystallography.

Torque generation in F1-ATPase devoid of the entire amino-terminal helix of the rotor that fills half of the stator orifice

F(1)-ATPase is an ATP-driven rotary molecular motor in which the central γ-subunit rotates inside a cylinder made of α(3)β(3) subunits. The amino and carboxyl termini of the γ rotor form a coiled coil of α-helices that penetrates the stator cylinder to serve as an axle. Crystal structures indicate that the axle is supported by the stator at two positions, at the orifice and by the hydrophobic sleeve surrounding the axle tip. The sleeve contacts are almost exclusively to the longer carboxyl-terminal helix, whereas nearly half the orifice contacts are to the amino-terminal helix. Here, we truncated the amino-terminal helix stepwise up to 50 residues, removing one half of the axle all the way up and far beyond the orifice. The half-sliced axle still rotated with an unloaded speed a quarter of the wild-type speed, with torque nearly half the wild-type torque. The truncations were made in a construct where the rotor tip was connected to a β-subunit via a short peptide linker. Linking alone did not change the rotational characteristics significantly. These and previous results show that nearly half the normal torque is generated if rotor-stator interactions either at the orifice or at the sleeve are preserved, suggesting that the make of the motor is quite robust.

Thermodynamic efficiency and mechanochemical coupling of F1-ATPase

F(1)-ATPase is a nanosized biological energy transducer working as part of F(o)F(1)-ATP synthase. Its rotary machinery transduces energy between chemical free energy and mechanical work and plays a central role in the cellular energy transduction by synthesizing most ATP in virtually all organisms. However, information about its energetics is limited compared to that of the reaction scheme. Actually, fundamental questions such as how efficiently F(1)-ATPase transduces free energy remain unanswered. Here, we demonstrated reversible rotations of isolated F(1)-ATPase in discrete 120° steps by precisely controlling both the external torque and the chemical potential of ATP hydrolysis as a model system of F(o)F(1)-ATP synthase. We found that the maximum work performed by F(1)-ATPase per 120° step is nearly equal to the thermodynamical maximum work that can be extracted from a single ATP hydrolysis under a broad range of conditions. Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F(1)-ATPase.

High-speed atomic force microscopy reveals rotary catalysis of rotorless F₁-ATPase

F(1) is an adenosine triphosphate (ATP)-driven motor in which three torque-generating β subunits in the α(3)β(3) stator ring sequentially undergo conformational changes upon ATP hydrolysis to rotate the central shaft γ unidirectionally. Although extensive experimental and theoretical work has been done, the structural basis of cooperative torque generation to realize the unidirectional rotation remains elusive. We used high-speed atomic force microscopy to show that the rotorless F(1) still "rotates"; in the isolated α(3)β(3) stator ring, the three β subunits cyclically propagate conformational states in the counterclockwise direction, similar to the rotary shaft rotation in F(1). The structural basis of unidirectionality is programmed in the stator ring. These findings have implications for cooperative interplay between subunits in other hexameric ATPases.

Structural comparison of F1-ATPase: interplay among enzyme structures, catalysis, and rotations

F(1)-ATPase, a rotary motor powered by adenosine triphosphate hydrolysis, has been extensively studied by various methods. Here, we performed a systematic comparison of 29 X-ray crystal structures of F(1)-complexes, finding fine interplay among enzyme structures, catalysis, and rotations. First, analyzing the 87 structures of enzymatic αβ-subunits, we confirmed that the two modes, the hinge motion of β-subunit and the loose/tight motion of the αβ-interface, dominate the variations. The structural ensemble was nearly contiguous bridging three clusters, αβ(TP), αβ(DP), and αβ(E). Second, the catalytic site analysis suggested the correlation between the phosphate binding and the tightening of the αβ-interface. Third, addressing correlations of enzymatic structures with the orientations of the central stalk γ, we found that the γ rotation highly correlates with loosening of αβ(E)-interface and β(DP) hinge motions. Finally, calculating the helix 6 angle of β, we identified the recently observed partially closed conformation being consistent with β(HC).

Resolving stepping rotation in Thermus thermophilus H(+)-ATPase/synthase with an essentially drag-free probe

Vacuole-type ATPases (V_oV₁) and F_oF₁ ATP synthases couple ATP hydrolysis/synthesis in the soluble V₁ or F₁ portion with proton (or Na⁺) flow in the membrane-embedded V_o or F_o portion through rotation of one common shaft. Here we show at submillisecond resolutions the ATP-driven rotation of isolated V₁ and the whole V_oV₁ from Thermus thermophilus, by attaching a 40-nm gold bead for which viscous drag is almost negligible. V₁ made 120° steps, commensurate with the presence of three catalytic sites. Dwells between the steps involved at least two events other than ATP binding, one likely to be ATP hydrolysis. V_oV₁ exhibited 12 dwell positions per revolution, consistent with the 12-fold symmetry of the V_o rotor in T. thermophilus. Unlike F₁ that undergoes 80°–40° substepping, chemo-mechanical checkpoints in isolated V₁ are all at the ATP-waiting position, and V_o adds further bumps through stator–rotor interactions outside and remote from V₁.

Rotary ATPases F_oF₁ and V_oV₁ couple ATP hydrolysis with proton flow. Furuike et al. observe ATP-driven rotation in V₁ and V_oV₁, at submillisecond resolution, and find that rate-limiting reactions in V₁ all occur at the same angle, and stator–rotor interactions in V_o introduce additional checkpoints.

Efficient ATP synthesis by thermophilic Bacillus FoF1-ATP synthase

F(o)F(1)-ATP synthase (F(o)F(1)) synthesizes ATP in the F(1) portion when protons flow through F(o) to rotate the shaft common to F(1) and F(o). Rotary synthesis in isolated F(1) alone has been shown by applying external torque to F(1) of thermophilic origin. Proton-driven ATP synthesis by thermophilic Bacillus PS3 F(o)F(1) (TF(o)F(1)), however, has so far been poor in vitro, of the order of 1 s(-1) or less, hampering reliable characterization. Here, by using a mutant TF(o)F(1) lacking an inhibitory segment of the ε-subunit, we have developed highly reproducible, simple procedures for the preparation of active proteoliposomes and for kinetic analysis of ATP synthesis, which was driven by acid-base transition and K(+)-diffusion potential. The synthesis activity reached ∼ 16 s(-1) at 30 °C with a Q(10) temperature coefficient of 3-4 between 10 and 30 °C, suggesting a high level of activity at the physiological temperature of ∼ 60 °C. The Michaelis-Menten constants for the substrates ADP and inorganic phosphate were 13 μM and 0.55 mM, respectively, which are an order of magnitude lower than previous estimates and are suited to efficient ATP synthesis.

Monte Carlo simulation from proton slip to "coupled" proton flow in ATP synthase based on the bi-site mechanism

ATP synthase couples proton flow to ATP synthesis, but is leaky to protons at very low nucleotide concentration. Based on the bi-site mechanism, we simulated the proton conduction from proton slip to "coupled" proton flow in ATP synthase using the Monte Carlo method. Good agreement is obtained between the simulated and available experimental results. Our model provides deeper insight into the nucleotide dependence of ATP catalysis, and the kinetic cooperativity in three catalysis subunits. The results of simulation support the bi-site mechanism in ATP synthesis.

Rotation and structure of FoF1-ATP synthase

F(o)F(1)-ATP synthase is one of the most ubiquitous enzymes; it is found widely in the biological world, including the plasma membrane of bacteria, inner membrane of mitochondria and thylakoid membrane of chloroplasts. However, this enzyme has a unique mechanism of action: it is composed of two mechanical rotary motors, each driven by ATP hydrolysis or proton flux down the membrane potential of protons. The two molecular motors interconvert the chemical energy of ATP hydrolysis and proton electrochemical potential via the mechanical rotation of the rotary shaft. This unique energy transmission mechanism is not found in other biological systems. Although there are other similar man-made systems like hydroelectric generators, F(o)F(1)-ATP synthase operates on the nanometre scale and works with extremely high efficiency. Therefore, this enzyme has attracted significant attention in a wide variety of fields from bioenergetics and biophysics to chemistry, physics and nanoscience. This review summarizes the latest findings about the two motors of F(o)F(1)-ATP synthase as well as a brief historical background.

Double-lock ratchet mechanism revealing the role of alphaSER-344 in FoF1 ATP synthase

In a majority of living organisms, FoF1 ATP synthase performs the fundamental process of ATP synthesis. Despite the simple net reaction formula, ADP+Pi→ATP+H2O, the detailed step-by-step mechanism of the reaction yet remains to be resolved owing to the complexity of this multisubunit enzyme. Based on quantum mechanical computations using recent high resolution X-ray structures, we propose that during ATP synthesis the enzyme first prepares the inorganic phosphate for the γP-OADP bond-forming step via a double-proton transfer. At this step, the highly conserved αS344 side chain plays a catalytic role. The reaction thereafter progresses through another transition state (TS) having a planar ion configuration to finally form ATP. These two TSs are concluded crucial for ATP synthesis. Using stepwise scans and several models of the nucleotide-bound active site, some of the most important conformational changes were traced toward direction of synthesis. Interestingly, as the active site geometry progresses toward the ATP-favoring tight binding site, at both of these TSs, a dramatic increase in barrier heights is observed for the reverse direction, i.e., hydrolysis of ATP. This change could indicate a "ratchet" mechanism for the enzyme to ensure efficacy of ATP synthesis by shifting residue conformation and thus locking access to the crucial TSs.

Soft magnetic tweezers: a proof of principle

We present here the principle of soft magnetic tweezers which improve the traditional magnetic tweezers allowing the simultaneous application and measurement of an arbitrary torque to a deoxyribonucleic acid (DNA) molecule. They take advantage of a nonlinear coupling regime that appears when a fast rotating magnetic field is applied to a superparamagnetic bead immersed in a viscous fluid. In this work, we present the development of the technique and we compare it with other techniques capable of measuring the torque applied to the DNA molecule. In this proof of principle, we use standard electromagnets to achieve our experiments. Despite technical difficulties related to the present implementation of these electromagnets, the agreement of measurements with previous experiments is remarkable. Finally, we propose a simple way to modify the experimental design of electromagnets that should bring the performances of the device to a competitive level.

Characterization of the relationship between ADP- and epsilon-induced inhibition in cyanobacterial F1-ATPase

The ATPase activity of chloroplast and bacterial F(1)-ATPase is strongly inhibited by both the endogenous inhibitor ε and tightly bound ADP. Although the physiological significance of these inhibitory mechanisms is not very well known for the membrane-bound F(0)F(1), these are very likely to be important in avoiding the futile ATP hydrolysis reaction and ensuring efficient ATP synthesis in vivo. In a previous study using the α(3)β(3)γ complex of F(1) obtained from the thermophilic cyanobacteria, Thermosynechococcus elongatus BP-1, we succeeded in determining the discrete stop position, ∼80° forward from the pause position for ATP binding, caused by ε-induced inhibition (ε-inhibition) during γ rotation (Konno, H., Murakami-Fuse, T., Fujii, F., Koyama, F., Ueoka-Nakanishi, H., Pack, C. G., Kinjo, M., and Hisabori, T. (2006) EMBO J. 25, 4596-4604). Because γ in ADP-inhibited F(1) also pauses at the same position, ADP-induced inhibition (ADP-inhibition) was assumed to be linked to ε-inhibition. However, ADP-inhibition and ε-inhibition should be independent phenomena from each other because the ATPase core complex, α(3)β(3)γ, also lapses into the ADP-inhibition state. By way of thorough biophysical and biochemical analyses, we determined that the ε subunit inhibition mechanism does not directly correlate with ADP-inhibition. We suggest here that the cyanobacterial ATP synthase ε subunit carries out an important regulatory role in acting as an independent "braking system" for the physiologically unfavorable ATP hydrolysis reaction.

Mechanism of the conformational change of the F1-ATPase β subunit revealed by free energy simulations

F(1)-ATPase is an ATP-driven rotary motor enzyme. The β subunit changes its conformation from an open to a closed form upon ATP binding. The motion in the β subunit is regarded as a major driving force for rotation of the central stalk. In this Article, we explore the conformational change of the β subunit using all-atom free energy simulations with explicit solvent and propose a detailed mechanism for the conformational change. The β subunit conformational change is accomplished roughly in two characteristic steps: changing of the hydrogen-bond network around ATP and the dynamic movement of the C-terminal domain via sliding of the B-helix. The details of the former step agree well with experimental data. In the latter step, sliding of the B-helix enhances the hydrophobic stabilization due to the exclusion of water molecules from the interface and improved packing in the hydrophobic core. This step contributes to a decrease in free energy, leading to the generation of torque in the F(1)-ATPase upon ATP binding.

How the N-terminal extremity of Saccharomyces cerevisiae IF1 interacts with ATP synthase: a kinetic approach

The N-terminal part of the inhibitory peptide IF1 interacts with the central γ subunit of mitochondrial isolated extrinsic part of ATP synthase in the inhibited complex (J.R. Gledhill, M.G. Montgomery, G.W. Leslie, J.E. Walker, 2007). To explore its role in the different steps of IF1 binding, kinetics of inhibition of the isolated and membrane-bound enzymes were investigated using Saccharomyces cerevisiae IF1 derivatives modified in N-terminal extremity. First, we studied peptides truncated in Nter up to the amino acid immediately preceding Phe17, a well-conserved residue thought to play a key role. These deletions did not affect or even improve the access of IF1 to its target. They decreased the stability of the inhibited complex but much less than previously proposed. We also mutated IF1-Phe17 and found this amino acid not mandatory for the inhibitory effect. The most striking finding came from experiments in which PsaE, a 8 kDa globular-like protein, was attached in Nter of IF1. Unexpectedly, such a modification did not appreciably affect the rate of IF1 binding. Taken together, these data show that IF1-Nter plays no role in the recognition step but contributes to stabilize the inhibited complex. Moreover, the data obtained using chimeric PsaE-IF1 suggest that before binding IF1 presents to the enzyme with its middle part facing a catalytic interface and its Nter extremity folded in the opposite direction.

Simultaneous observation of chemomechanical coupling of a molecular motor

F(1)-ATPase is the smallest rotary molecular motor ever found. Unidirectional rotation of the γ-shaft is driven by precisely coordinated sequential ATP hydrolysis reactions in three catalytic sites arranged 120° apart in the cylinder. Single-molecule observation allows us to directly watch the rotation of the shaft using micron-sized plastic beads. Additionally, an advanced version of "total internal reflection fluorescence microscope (TIRFM)" enables us to detect binding and release of energy currency through fluorescently labeled ATP. In this chapter, we describe how to set up the system for simultaneous observation of these two critical events. This specialized optical setup is applicable to a variety of research, not only molecular motors but also other single-molecule topics.

Redox regulation of rotation of the cyanobacterial F1-ATPase containing thiol regulation switch

F(1)-ATP synthase (F(1)-ATPase) is equipped with a special mechanism that prevents the wasteful reverse reaction, ATP hydrolysis, when there is insufficient proton motive force to drive ATP synthesis. Chloroplast F(1)-ATPase is subject to redox regulation, whereby ATP hydrolysis activity is regulated by formation and reduction of the disulfide bond located on the γ subunit. To understand the molecular mechanism of this redox regulation, we constructed a chimeric F(1) complex (α(3)β(3)γ(redox)) using cyanobacterial F(1), which mimics the regulatory properties of the chloroplast F(1)-ATPase, allowing the study of its regulation at the single molecule level. The redox state of the γ subunit did not affect the ATP binding rate to the catalytic site(s) and the torque for rotation. However, the long pauses caused by ADP inhibition were frequently observed in the oxidized state. In addition, the duration of continuous rotation was relatively shorter in the oxidized α(3)β(3)γ(redox) complex. These findings lead us to conclude that redox regulation of CF(1)-ATPase is achieved by controlling the probability of ADP inhibition via the γ subunit inserted region, a sequence feature observed in both cyanobacterial and chloroplast ATPase γ subunits, which is important for ADP inhibition (Sunamura, E., Konno, H., Imashimizu-Kobayashi, M., Sugano, Y., and Hisabori, T. (2010) Plant Cell Physiol. 51, 855-865).

Inhibition of thermophilic F1-ATPase by the ε subunit takes different path from the ADP-Mg inhibition

The F₁-ATPase, the soluble part of FoF₁-ATP synthase, is a rotary molecular motor consisting of α₃β₃γδε. The γ and ε subunits rotate relative to the α₃β₃δ sub-complex on ATP hydrolysis by the β subunit. The ε subunit is known as an endogenous inhibitor of the ATPase activity of the F₁-ATPase and is believed to function as a regulator of the ATP synthase. This inhibition by the ε subunit (ε inhibition) of F₁-ATPase from thermophilic Bacillus PS3 was analyzed by single molecule measurements. By using a mutant ε subunit deficient in ATP binding, reversible transitions between active and inactive states were observed. Analysis of pause and rotation durations showed that the ε inhibition takes a different path from the ADP-Mg inhibition. Furthermore, the addition of the mutant ε subunit to the α₃β₃γ sub-complex was found to facilitate recovery of the ATPase activity from the ADP-Mg inhibition. Thus, it was concluded that these two inhibitions are essentially exclusive of each other.

Structural fluctuation and concerted motions in F(1)-ATPase: A molecular dynamics study

F(1)-ATPase is an adenosine tri-phosphate (ATP)-driven rotary motor enzyme. We investigated the structural fluctuations and concerted motions of subunits in F(1)-ATPase using molecular dynamics (MD) simulations. An MD simulation for the alpha(3)beta(3)gamma complex was carried out for 30 ns. Although large fluctuations of the N-terminal domain observed in simulations of the isolated beta(E) subunit were suppressed in the complex simulation, the magnitude of fluctuations in the C-terminal domain was clearly different among the three beta subunits (beta(E), beta(TP), and beta(DP)). Despite fairly similar conformations of the beta(TP) and beta(DP) subunits, the beta(DP) subunit exhibits smaller fluctuations in the C-terminal domain than the beta(TP) subunit due to their dissimilar interface configurations. Compared with the beta(TP) subunit, the beta(DP) subunit stably interacts with both the adjacent alpha(DP) and alpha(E) subunits. This sandwiched configuration in the beta(DP) subunit leads to strongly correlated motions between the beta(DP) and adjacent alpha subunits. The beta(DP) subunit exhibits an extensive network of highly correlated motions with bound ATP and the gamma subunit, as well as with the adjacent alpha subunits, suggesting that the structural changes occurring in the catalytically active beta(DP) subunit can effectively induce movements of the gamma subunit.

Trapping single molecules in liposomes: surface interactions and freeze-thaw effects

We report on an improved method to encapsulate proteins and other macromolecules inside surface-tethered liposomes to reduce or eliminate environmental interference for single-molecule investigations. These lipid vesicles are large enough for the molecule to experience free diffusion but sufficiently small so that the molecule appears effectively immobile under the fluorescence microscope. Single-molecule fluorescence experiments were used to characterize this anchoring method relative to direct immobilization via biotin-streptavidin linkers. Multidimensional histograms of intensity, polarization, and lifetime revealed that molecules trapped in liposomes display a narrow distribution around a single peak, while the molecules directly immobilized on surface show highly dispersed values for all parameters. By hydrating the lipid film at low volumes, high encapsulation efficiencies can be achieved with ~10 times less biological material than previous protocols. We measured vesicle size distributions and found no significant advantage for using freeze-thaw cycles during vesicle preparation. On the contrary, the temperature jump can induce irreversible damage of fluorophores and it reduces significantly the functionality of proteins, as demonstrated on single-molecule binding experiments on STAT3. Our improved and biologically gentle molecule encapsulation protocol has a great potential for widespread applications in single-molecule fluorescence spectroscopy.

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.

Chemo-mechanical coupling in F(1)-ATPase revealed by catalytic site occupancy during catalysis

F(1)-ATPase is a rotary molecular motor in which the central gamma subunit rotates inside a cylinder made of alpha(3)beta(3) subunits. To clarify how ATP hydrolysis in three catalytic sites cooperate to drive rotation, we measured the site occupancy, the number of catalytic sites occupied by a nucleotide, while assessing the hydrolysis activity under identical conditions. The results show hitherto unsettled timings of ADP and phosphate releases: starting with ATP binding to a catalytic site at an ATP-waiting gamma angle defined as 0 degrees , phosphate is released at approximately 200 degrees , and ADP is released during quick rotation between 240 degrees and 320 degrees that is initiated by binding of a third ATP. The site occupancy remains two except for a brief moment after the ATP binding, but the third vacant site can bind a medium nucleotide weakly.

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.

Proton transport coupled ATP synthesis by the purified yeast H+ -ATP synthase in proteoliposomes

The H(+)/ATP synthase from yeast mitochondria, MF₀F₁, was purified and reconstituted into liposomes prepared from phosphatidylcholine and phosphatidic acid. Analysis by mass spectrometry revealed the presence of all subunits of the yeast enzyme with the exception of the K-subunit. The MF₀F₁ liposomes were energized by acid-base transitions (DeltapH) and a K(+)/valinomycin diffusion potential (Deltaphi). ATP synthesis was completely abolished by the addition of uncouplers as well as by the inhibitor oligomycin. The rate of ATP synthesis was optimized as a function of various parameters and reached a maximum value (turnover number) of 120s⁻¹ at a transmembrane pH difference of 3.2 units (at pH(in)=4.8 and pH(out)=8.0) and a Deltaphi of 133mV (Nernst potential). Functional studies showed that the monomeric MF₀F₁, was fully active in ATP synthesis. The turnover increased in a sigmoidal way with increasing internal and decreasing external proton concentration. The dependence of the turnover on the phosphate concentration and the dependence of K(M) on pH(out) indicated that the substrate for ATP synthesis is the monoanionic phosphate species H₂PO⁻₄.

FoF1-ATPase, rotary motor and biosensor

F(o)F(1)-ATPase is an amazing molecular rotary motor at the nanoscale. Single molecule technologies have contributed much to the understanding of the motor. For example, fluorescence imaging and spectroscopy revealed the physical rotation of isolated F(1) and F(o), or F(o)F(1) holoenzyme. Magnetic tweezers were employed to manipulate the ATP synthesis/hydrolysis in F(1), and proton translation in F(o). Here, we briefly review our recent works including a systematic kinetics study of the holoenzyme, the mechanochemical coupling mechanism, reconstituting the delta-free F(o)F(1)-ATPase, direct observation of F(o) rotation at single molecule level and activity regulation through external links on the stator.

Energetic effects of magnesium in the recognition of adenosine nucleotides by the F(1)-ATPase beta subunit

Nucleotide-induced conformational changes of the catalytic beta subunits play a crucial role in the rotary mechanism of F(1)-ATPase. To gain insights into the energetic bases that govern the recognition of nucleotides by the isolated beta subunit from thermophilic Bacillus PS3 (Tbeta), the binding of this monomer to Mg(II)-free and Mg(II)-bound adenosine nucleotides was characterized using high-precision isothermal titration calorimetry. The interactions of Mg(II) with free ATP or ADP were also measured calorimetrically. A model that considers simultaneously the interactions of Tbeta with Mg.ATP or with ATP and in which ATP is able to bind two Mg(II) atoms sequentially was used to determine the formation parameters of the Tbeta-Mg.ATP complex from calorimetric data. This analysis yielded significantly different DeltaH(b) and DeltaS(b) values in relation to those obtained using a single-binding site model, while DeltaG(b) was almost unchanged. Published calorimetric data for the titration of Tbeta with Mg.ADP [Perez-Hernandez, G., et al. (2002) Arch. Biochem. Biophys. 408, 177-183] were reanalyzed with the ternary model to determine the corresponding true binding parameters. Interactions of Tbeta with Mg.ATP, ATP, Mg.ADP, or ADP were enthalpically driven. Larger differences in thermodynamic properties were observed between Tbeta-Mg.ATP and Tbeta-ATP complexes than between Tbeta-Mg.ADP and Tbeta-ADP complexes or between Tbeta-Mg.ATP and Tbeta-Mg.ADP complexes. These binding data, in conjunction with those for the association of Mg(II) with free nucleotides, allowed for a determination of the energetic effects of the metal ion on the recognition of adenosine nucleotides by Tbeta [i.e., Tbeta.AT(D)P + Mg(II) right harpoon over left harpoon Tbeta.AT(D)P-Mg]. Because of a more favorable binding enthalpy, Mg(II) is recognized more avidly by the Tbeta.ATP complex, indicating better stereochemical complementarity than in the Tbeta.ADP complex. Furthermore, a structural-energetic analysis suggests that Tbeta adopts a more closed conformation when it is bound to Mg.ATP than to ATP or Mg.ADP, in agreement with recently published NMR data [Yagi, H., et al. (2009) J. Biol. Chem. 284, 2374-2382]. Using published binding data, a similar analysis of Mg(II) energetic effects was performed for the free energy change of F(1) catalytic sites, in the framework of bi- or tri-site binding models.

Stiffness of γ subunit of F(1)-ATPase

F(1)-ATPase is a molecular motor in which the γ subunit rotates inside the α(3)β(3) ring upon adenosine triphosphate (ATP) hydrolysis. Recent works on single-molecule manipulation of F(1)-ATPase have shown that kinetic parameters such as the on-rate of ATP and the off-rate of adenosine diphosphate (ADP) strongly depend on the rotary angle of the γ subunit (Hirono-Hara et al. 2005; Iko et al. 2009). These findings provide important insight into how individual reaction steps release energy to power F(1) and also have implications regarding ATP synthesis and how reaction steps are reversed upon reverse rotation. An important issue regarding the angular dependence of kinetic parameters is that the angular position of a magnetic bead rotation probe could be larger than the actual position of the γ subunit due to the torsional elasticity of the system. In the present study, we assessed the stiffness of two different portions of F(1) from thermophilic Bacillus PS3: the internal part of the γ subunit embedded in the α(3)β(3) ring, and the complex of the external part of the γ subunit and the α(3)β(3) ring (and streptavidin and magnetic bead), by comparing rotational fluctuations before and after crosslinkage between the rotor and stator. The torsional stiffnesses of the internal and remaining parts were determined to be around 223 and 73 pNnm/radian, respectively. Based on these values, it was estimated that the actual angular position of the internal part of the γ subunit is one-fourth of the magnetic bead position upon stalling using an external magnetic field. The estimated elasticity also partially explains the accommodation of the intrinsic step size mismatch between F(o) and F(1)-ATPase.

Physiological impact of intrinsic ADP inhibition of cyanobacterial FoF1 conferred by the inherent sequence inserted into the gammasubunit

The F(o)F(1)-ATPase, which synthesizes ATP with a rotary motion, is highly regulated in vivo in order to function efficiently, although there remains a limited understanding of the physiological significance of this regulation. Compared with its bacterial and mitochondrial counterparts, the gamma subunit of cyanobacterial F(1), which makes up the central shaft of the motor enzyme, contains an additional inserted region. Although deletion of this region results in the acceleration of the rate of ATP hydrolysis, the functional significance of the region has not yet been determined. By analysis of rotation, we successfully determined that this region confers the ability to shift frequently into an ADP inhibition state; this is a highly conserved regulatory mechanism which prevents ATP synthase from carrying out the reverse reaction. We believe that the physiological significance of this increased likelihood of shifting into the ADP inhibition state allows the intracellular ATP levels to be maintained, which is especially critical for photosynthetic organisms.

Simple dark-field microscopy with nanometer spatial precision and microsecond temporal resolution

Molecular motors such as kinesin, myosin, and F(1)-ATPase are responsible for many important cellular processes. These motor proteins exhibit nanometer-scale, stepwise movements on micro- to millisecond timescales. So far, methods developed to measure these small and fast movements with high spatial and temporal resolution require relatively complicated experimental systems. Here, we describe a simple dark-field imaging system that employs objective-type evanescent illumination to selectively illuminate a thin layer on the coverslip and thus yield images with high signal/noise ratios. Only by substituting the dichroic mirror in conventional objective-type total internal reflection fluorescence microscope with a perforated mirror, were nanometer spatial precision and microsecond temporal resolution simultaneously achieved. This system was applied to the study of the rotary mechanism of F(1)-ATPase. The fluctuation of a gold nanoparticle attached to the gamma-subunit during catalytic dwell and the stepping motion during torque generation were successfully visualized with 9.1-mus temporal resolution. Because of the simple optics, this system will be applicable to various biophysical studies requiring high spatial and temporal resolution in vitro and also in vivo.

Nonequilibrium energetics of a single F1-ATPase molecule

Molecular motors drive mechanical motions utilizing the free energy liberated from chemical reactions such as ATP hydrolysis. Although it is essential to know the efficiency of this free energy transduction, it has been a challenge due to the system's microscopic scale. Here, we evaluate the single-molecule energetics of a rotary molecular motor, F1-ATPase, by applying a recently derived nonequilibrium equality together with an electrorotation method. We show that the sum of the heat flow through the probe's rotational degree of freedom and the work against an external load is almost equal to the free energy change per a single ATP hydrolysis under various conditions. This implies that F1-ATPase works at an efficiency of nearly 100% in a thermally fluctuating environment.

Mechanical control of ATP synthase function: activation energy difference between tight and loose binding sites

Despite exhaustive chemical and crystal structure studies, the mechanistic details of how F(o)F(1)-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent high-resolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO(3)(-) ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the gamma-subunit rotation, may effectively block the back reaction in beta(TP) and, thus, promote ATP.

Out-of-equilibrium conformational cycling of GroEL under saturating ATP concentrations

The molecular chaperone GroEL exists in at least two allosteric states, T and R, that interconvert in an ATP-controlled manner. Thermodynamic analysis suggests that the T-state population becomes negligible with increasing ATP concentrations, in conflict with the requirement for conformational cycling, which is essential for the operation of molecular machines. To solve this conundrum, we performed fluorescence correlation spectroscopy on the single-ring version of GroEL, using a fluorescent switch recently built into its structure, which turns "on," i.e., increases its fluorescence dramatically, when ATP is added. A series of correlation functions was measured as a function of ATP concentration and analyzed using singular-value decomposition. The analysis assigned the signal to two states whose dynamics clearly differ. Surprisingly, even at ATP saturation, approximately 50% of the molecules still populate the T state at any instance of time, indicating constant out-of-equilibrium cycling between T and R. Only upon addition of the cochaperonin GroES does the T-state population vanish. Our results suggest a model in which the T/R ratio is controlled by the rate of ADP release after hydrolysis, which can be determined accordingly.

Molecular bio-motors in living cells

The final goal of our group is to establish the missing link between chemical reaction and mechanical event in molecular motors. To achieve this, we have developed advanced versions of conventional optical microscopes and applied them into single-molecule techniques. In this chapter we present two studies: one is about the kinesin-microtubule system and the other F(1)-ATPase. These techniques are applicable to other molecular machines, hopefully in more sophisticated ways, and we hope to investigate this in future studies.

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 mechanism of rotating proton pumping ATPases

Two proton pumps, the F-ATPase (ATP synthase, FoF1) and the V-ATPase (endomembrane proton pump), have different physiological functions, but are similar in subunit structure and mechanism. They are composed of a membrane extrinsic (F1 or V1) and a membrane intrinsic (Fo or Vo) sector, and couple catalysis of ATP synthesis or hydrolysis to proton transport by a rotational mechanism. The mechanism of rotation has been extensively studied by kinetic, thermodynamic and physiological approaches. Techniques for observing subunit rotation have been developed. Observations of micron-length actin filaments, or polystyrene or gold beads attached to rotor subunits have been highly informative of the rotational behavior of ATP hydrolysis-driven rotation. Single molecule FRET experiments between fluorescent probes attached to rotor and stator subunits have been used effectively in monitoring proton motive force-driven rotation in the ATP synthesis reaction. By using small gold beads with diameters of 40-60 nm, the E. coli F1 sector was found to rotate at surprisingly high speeds (>400 rps). This experimental system was used to assess the kinetics and thermodynamics of mutant enzymes. The results revealed that the enzymatic reaction steps and the timing of the domain interactions among the beta subunits, or between the beta and gamma subunits, are coordinated in a manner that lowers the activation energy for all steps and avoids deep energy wells through the rotationally-coupled steady-state reaction. In this review, we focus on the mechanism of steady-state F1-ATPase rotation, which maximizes the coupling efficiency between catalysis and rotation.

Activation and stiffness of the inhibited states of F1-ATPase probed by single-molecule manipulation

F(1)-ATPase (F(1)), a soluble portion of F(o)F(1)-ATP synthase (F(o)F(1)), is an ATP-driven motor in which gammaepsilon subunits rotate in the alpha(3)beta(3) cylinder. Activity of F(1) and F(o)F(1) from Bacillus PS3 is attenuated by the epsilon subunit in an inhibitory extended form. In this study we observed ATP-dependent transition of epsilon in single F(1) molecules from extended form to hairpin form by fluorescence resonance energy transfer. The results justify the previous bulk experiments and ensure that fraction of F(1) with hairpin epsilon directly determines the fraction of active F(1) at any ATP concentration. Next, mechanical activation and stiffness of epsilon-inhibited F(1) were examined by the forced rotation of magnetic beads attached to gamma. Compared with ADP inhibition, which is another manner of inhibition, rotation by a larger angle was required for the activation from epsilon inhibition when the beads were forced to rotate to ATP hydrolysis direction, and more torque was required to reach the same rotation angle when beads were forced to rotate to ATP synthesis direction. The results imply that if F(o)F(1) is resting in the epsilon-inhibited state, F(o) motor must transmit to gamma a torque larger than expected from thermodynamic equilibrium to initiate ATP synthesis.

Stimulation of F(1)-ATPase activity by sodium dodecyl sulfate

F(1)-ATPase is a rotary molecular motor in which the gamma subunit rotates inside the cylinder made of alpha(3)beta(3) subunits. We have studied the effects of sodium dodecyl sulfate (SDS) on the rotational and ATP hydrolysis activities of F(1)-ATPase. Bulk hydrolysis activity at various SDS concentrations was examined at 2mM ATP. Maximal stimulation was obtained at 0.003% (w/v) SDS, the initial (least inhibited) activity being about 1.4 times and the steady-state activity 3-4 times the values in the absence of SDS. Rotation rates observed with a 40-nm gold bead or a 0.29-mum bead duplex as well as the torque were unaffected by the presence of 0.003% SDS. The fraction of beads that rotated, in contrast, tended to increase in the presence of SDS. SDS seems to bring inactive F(1) molecules into an active form but it does not alter or enhance the function of already active F(1) molecules significantly.

Single-biomolecule kinetics: the art of studying a single enzyme

The potential of single-enzyme studies to unravel the complex energy landscape of these polymeric catalysts is the next critical step in enzymology. From its inception in Rotman's emulsion experiments in the 1960s, the field of single-molecule enzymology has now advanced into the time-resolved age. Technological advances have enabled individual enzymatic turnover reactions to be observed with a millisecond time resolution. A number of initial studies have revealed the underlying static and dynamic disorder in the catalytic rates originating from conformational fluctuations. Although these experiments are still in their infancy, they may be able to relate the topography of the energy landscape to the biological function and regulation of enzymes. This review summarizes some of the experimental techniques and data-analysis methods that have been used to study individual enzyme molecules in search of a deeper understanding of their kinetics.