Pause and rotation of F(1)-ATPase during catalysis.

F(1)-ATPase is a rotary motor enzyme in which a single ATP molecule drives a 120 degrees rotation of the central gamma subunit relative to the surrounding alpha(3)beta(3) ring. Here, we show that the rotation of F(1)-ATPase spontaneously lapses into long (approximately 30 s) pauses during steady-state catalysis. The effects of ADP-Mg and mutation on the pauses, as well as kinetic comparison with bulk-phase catalysis, strongly indicate that the paused enzyme corresponds to the inactive state of F(1)-ATPase previously known as the ADP-Mg inhibited form in which F(1)-ATPase fails to release ADP-Mg from catalytic sites. The pausing position of the gamma subunit deviates from the ATP-waiting position and is most likely the recently found intermediate 90 degrees position.

[Hypersensitivity pneumonitis caused by a factory humidifier. A case report].

A 64-year-old man was hospitalized for productive cough and dyspnea. Both chest radiographs and CT scans showed areas of ground-glass opacity in the middle and lower lung fields on both sides. The BAL and TBLB findings were compatible with hypersensitivity pneumonitis. The serum was negative for antibodies against Trichosporon species, and the result of a lymphocyte stimulating test for administered drugs including a Chinese medicine was also negative. A humidifier was suspected as the cause because it had been used for more than 10 years in the factory where the patient had been working. An inhalation test using the humidifier fluid successfully provoked dyspnea, fever and fine crackle, and laboratory tests demonstrated hypoxemia, reduction in vital capacity and the elevation of CRP. Agar gel diffusion using the patient's serum showed a precipitating line against Cephalosporium acremonium, but this line did not fuse with any precipitating line formed between the humidifier fluid and the serum, indicating that no Cephalosporium was Present in the humidifier fluid. Since a high level of beta-D glucan was detected in the humidifier fluid, an unidentified fungus was suspected to be the antigen.

Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase.

Helical filaments driven by linear molecular motors are anticipated to rotate around their axis, but rotation consistent with the helical pitch has not been observed. 14S dynein and non-claret disjunctional protein (ncd) rotated a microtubule more efficiently than expected for its helical pitch, and myosin rotated an actin filament only poorly. For DNA-based motors such as RNA polymerase, transcription-induced supercoiling of DNA supports the general picture of tracking along the DNA helix. Here we report direct and real-time optical microscopy measurements of rotation rate that are consistent with high-fidelity tracking. Single RNA polymerase molecules attached to a glass surface rotated DNA for >100 revolutions around the right-handed screw axis of the double helix with a rotary torque of >5 pN nm. This real-time observation of rotation opens the possibility of resolving individual transcription steps.

Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase.

The enzyme F1-ATPase has been shown to be a rotary motor in which the central gamma-subunit rotates inside the cylinder made of alpha3beta3 subunits. At low ATP concentrations, the motor rotates in discrete 120 degrees steps, consistent with sequential ATP hydrolysis on the three beta-subunits. The mechanism of stepping is unknown. Here we show by high-speed imaging that the 120 degrees step consists of roughly 90 degrees and 30 degrees substeps, each taking only a fraction of a millisecond. ATP binding drives the 90 degrees substep, and the 30 degrees substep is probably driven by release of a hydrolysis product. The two substeps are separated by two reactions of about 1 ms, which together occupy most of the ATP hydrolysis cycle. This scheme probably applies to rotation at full speed ( approximately 130 revolutions per second at saturating ATP) down to occasional stepping at nanomolar ATP concentrations, and supports the binding-change model for ATP synthesis by reverse rotation of F1-ATPase.

Purine but not pyrimidine nucleotides support rotation of F(1)-ATPase.

The binding change model for the F(1)-ATPase predicts that its rotation is intimately correlated with the changes in the affinities of the three catalytic sites for nucleotides. If so, subtle differences in the nucleotide structure may have pronounced effects on rotation. Here we show by single-molecule imaging that purine nucleotides ATP, GTP, and ITP support rotation but pyrimidine nucleotides UTP and CTP do not, suggesting that the extra ring in purine is indispensable for proper operation of this molecular motor. Although the three purine nucleotides were bound to the enzyme at different rates, all showed similar rotational characteristics: counterclockwise rotation, 120 degrees steps each driven by hydrolysis of one nucleotide molecule, occasional back steps, rotary torque of approximately 40 piconewtons (pN).nm, and mechanical work done in a step of approximately 80 pN.nm. These latter characteristics are likely to be determined by the rotational mechanism built in the protein structure, which purine nucleotides can energize. With ATP and GTP, rotation was observed even when the free energy of hydrolysis was -80 pN.nm/molecule, indicating approximately 100% efficiency. Reconstituted F(o)F(1)-ATPase actively translocated protons by hydrolyzing ATP, GTP, and ITP, but CTP and UTP were not even hydrolyzed. Isolated F(1) very slowly hydrolyzed UTP (but not CTP), suggesting possible uncoupling from rotation.

Characterization of single actomyosin rigor bonds: load dependence of lifetime and mechanical properties.

Load dependence of the lifetime of the rigor bonds formed between a single myosin molecule (either heavy meromyosin, HMM, or myosin subfragment-1, S1) and actin filament was examined in the absence of nucleotide by pulling the barbed end of the actin filament with optical tweezers. For S1, the relationship between the lifetime (tau) and the externally imposed load (F) at absolute temperature T could be expressed as tau(F) = tau(0).exp(-F.d/k(B)T) with tau(0) of 67 s and an apparent interaction distance d of 2.4 nm (k(B) is the Boltzmann constant). The relationship for HMM was expressed by the sum of two exponentials, with two sets of tau(0) and d being, respectively, 62 s and 2.7 nm, and 950 s and 1.4 nm. The fast component of HMM coincides with tau(F) for S1, suggesting that the fast component corresponds to single-headed binding and the slow component to double-headed binding. These large interaction distances, which may be a common characteristic of motor proteins, are attributed to the geometry for applying an external load. The pulling experiment has also allowed direct estimation of the number of myosin molecules interacting with an actin filament. Actin filaments tethered to a single HMM molecule underwent extensive rotational Brownian motion, indicating a low torsional stiffness for HMM. From these results, we discuss the characteristics of interaction between actin and myosin, with the focus on the manner of binding of myosin.

A rotary molecular motor that can work at near 100% efficiency.

A single molecule of F1-ATPase is by itself a rotary motor in which a central gamma-subunit rotates against a surrounding cylinder made of alpha3beta3-subunits. Driven by the three betas that sequentially hydrolyse ATP, the motor rotates in discrete 120 degree steps, as demonstrated in video images of the movement of an actin filament bound, as a marker, to the central gamma-subunit. Over a broad range of load (hydrodynamic friction against the rotating actin filament) and speed, the F1 motor produces a constant torque of ca. 40 pN nm. The work done in a 120 degree step, or the work per ATP molecule, is thus ca. 80 pN nm. In cells, the free energy of ATP hydrolysis is ca. 90 pN nm per ATP molecule, suggesting that the F1 motor can work at near 100% efficiency. We confirmed in vitro that F1 indeed does ca. 80 pN nm of work under the condition where the free energy per ATP is 90 pN nm. The high efficiency may be related to the fully reversible nature of the F1 motor: the ATP synthase, of which F1 is a part, is considered to synthesize ATP from ADP and phosphate by reverse rotation of the F1 motor. Possible mechanisms of F1 rotation are discussed.

Stepping rotation of F1-ATPase visualized through angle-resolved single-fluorophore imaging.

Orientation dependence of single-fluorophore intensity was exploited in order to videotape conformational changes in a protein machine in real time. The fluorophore Cy3 attached to the central subunit of F(1)-ATPase revealed that the subunit rotates in the molecule in discrete 120 degrees steps and that each step is driven by the hydrolysis of one ATP molecule. These results, unlike those from the previous study under a frictional load, show that the 120 degrees stepping is a genuine property of this molecular motor. The data also show that the rate of ATP binding is insensitive to the load exerted on the rotor subunit.

The role of the DELSEED motif of the beta subunit in rotation of F1-ATPase.

F(1)-ATPase is a rotary motor protein, and ATP hydrolysis generates torque at the interface between the gamma subunit, a rotor shaft, and the alpha(3)beta(3) substructure, a stator ring. The region of conserved acidic "DELSEED" motif of the beta subunit has a contact with gamma subunit and has been assumed to be involved in torque generation. Using the thermophilic alpha(3)beta(3)gamma complex in which the corresponding sequence is DELSDED, we replaced each residue and all five acidic residues in this sequence with alanine. In addition, each of two conserved residues at the counterpart contact position of gamma subunit was also replaced. Surprisingly, all of these mutants rotated with as much torque as the wild-type. We conclude that side chains of the DELSEED motif of the beta subunit do not have a direct role in torque generation.

Observations of rotation within the F(o)F(1)-ATP synthase: deciding between rotation of the F(o)c subunit ring and artifact.

F(o)F(1)-ATP synthase mediates coupling of proton flow in F(o) and ATP synthesis/hydrolysis in F(1) through rotation of central rotor subunits. A ring structure of F(o)c subunits is widely believed to be a part of the rotor. Using an attached actin filament as a probe, we have observed the rotation of the F(o)c subunit ring in detergent-solubilized F(o)F(1)-ATP synthase purified from Escherichia coli. Similar studies have been performed and reported recently [Sambongi et al. (1999) Science 286, 1722-1724]. However, in our hands this rotation has been observed only for the preparations which show poor sensitivity to dicyclohexylcarbodiimde, an F(o) inhibitor. We have found that detergents which adequately disperse the enzyme for the rotation assay also tend to transform F(o)F(1)-ATP synthase into an F(o) inhibitor-insensitive state in which F(1) can hydrolyze ATP regardless of the state of the F(o). Our results raise the important issue of whether rotation of the F(o)c ring in isolated F(o)F(1)-ATP synthase can be demonstrated unequivocally with the approach adopted here and also used by Sambongi et al.

[A Shigella sonnei outbreak in Nagasaki].

We have experienced an outbreak of dysentery in Nagasaki. Shigella sonnei were positively cultured from 467 patients out of suspected 821 cases, and 346 patients were admitted. 121 patients were treated with oral antimicrobials in the outpatient clinic. Five patients were diagnosed as secondary infection. We treated a total of 96 patients in Nagasaki Municipal Medical Center, and studied the clinical and bacterial features in these 96 patients. Chief complaints included fever, abdominal pain and diarrhea. Most diarrheal patients showed waterly diarrhea and only a few were bloody (3 of 47). Treatment of levofloxacine 300 mg a day for 5 days successfully eliminated S. sonnei from all culture positive patients. An environmental surveillance revealed that water in a well at the university to which many patients were using was the origin of the infection with positive cultures of S. sonnei. No difference between the clinical and environmental isolates was observed in results on biochemical, serological and enzymatic tests. All isolates were susceptible to levofloxacin and to ofloxacin, but three isolates showed resistance of fosfomycin with MIC above 64 micrograms/ml. In analysis of pulsed-field gel electrophoresis, both clinical and environmental isolates were considered to be closely related.

F1-ATPase: a highly efficient rotary ATP machine.

A single molecule of F1-ATPase is by itself a rotary motor in which a central subunit, gamma, rotates against a surrounding stator cylinder made of alpha 3 beta 3 hexamer. Driven by the three beta subunits that hydrolyse ATP sequentially, the motor runs with discrete 120 degrees steps at low ATP concentrations. Over broad ranges of load and speed, the motor produces a constant torque of 40 pN.nm. The mechanical work the motor does in the 120 degrees step, or the work per ATP hydrolysed, is also constant and amounts to 80-90 pN.nm, which is close to the free energy of ATP hydrolysis. Thus this motor can work at near 100% efficiency.

Rotation of F(1)-ATPase and the hinge residues of the beta subunit.

Rotation of a motor protein, F(1)-ATPase, was demonstrated using a unique single-molecule observation system. This paper reviews what has been clarified by this system and then focuses on the role of residues at the hinge region of the beta subunit. We have visualised rotation of a single molecule of F(1)-ATPase by attaching a fluorescent actin filament to the top of the beta subunit in the immobilised F(1)-ATPase, thus settling a major controversy regarding the rotary catalysis. The rotation of the beta subunit was exclusively in one direction, as could be predicted by the crystal structure of bovine heart F(1)-ATPase. Rotation at low ATP concentrations revealed that one revolution consists of three 120 degrees steps, each fuelled by the binding of an ATP to the beta subunit. The mean work done by a 120 degrees step was approximately 80 pN nm, a value close to the free energy liberated by hydrolysis of one ATP molecule, implying nearly 100% efficiency of energy conversion. The torque is probably generated by the beta subunit, which undergoes large opening-closing domain motion upon binding of AT(D)P. We identified three hinge residues, betaHis179, betaGly180 and betaGly181, whose peptide bond dihedral angles are drastically changed during domain motion. Simultaneous substitution of these residues with alanine resulted in nearly complete loss (99%) of ATPase activity. Single or double substitution of the two Gly residues did not abolish the ATPase activity. However, reflecting the shift of the equilibrium between the open and closed forms of the beta subunit, single substitution caused changes in the propensity to generate the kinetically trapped Mg-ADP inhibited form: Gly180Ala enhanced the propensity and Gly181Ala abolished the propensity. In spite of these changes, the mean rotational torque was not changed significantly for any of the mutants.

Imaging of thermal activation of actomyosin motors.

We have developed temperature-pulse microscopy in which the temperature of a microscopic sample is raised reversibly in a square-wave fashion with rise and fall times of several ms, and locally in a region of approximately 10 micrometers in diameter with a temperature gradient up to 2 degrees C/micrometers. Temperature distribution was imaged pixel by pixel by image processing of the fluorescence intensity of rhodamine phalloidin attached to (single) actin filaments. With short pulses, actomyosin motors could be activated above physiological temperatures (higher than 60 degrees C at the peak) before thermally induced protein damage began to occur. When a sliding actin filament was heated to 40-45 degrees C, the sliding velocity reached 30 micrometers/s at 25 mM KCl and 50 micrometers/s at 50 mM KCl, the highest velocities reported for skeletal myosin in usual in vitro assay systems. Both the sliding velocity and force increased by an order of magnitude when heated from 18 degrees C to 40-45 degrees C. Temperature-pulse microscopy is expected to be useful for studies of biomolecules and cells requiring temporal and/or spatial thermal modulation.

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.

Tying a molecular knot with optical tweezers.

Filamentous structures are abundant in cells. Relatively rigid filaments, such as microtubules and actin, serve as intracellular scaffolds that support movement and force, and their mechanical properties are crucial to their function in the cell. Some aspects of the behaviour of DNA, meanwhile, depend critically on its flexibility-for example, DNA-binding proteins can induce sharp bends in the helix. The mechanical characterization of such filaments has generally been conducted without controlling the filament shape, by the observation of thermal motions or of the response to external forces or flows. Controlled buckling of a microtubule has been reported, but the analysis of the buckled shape was complicated. Here we report the continuous control of the radius of curvature of a molecular strand by tying a knot in it, using optical tweezers to manipulate the strand's ends. We find that actin filaments break at the knot when the knot diameter falls below 0.4 microm. The pulling force at breakage is around 1 pN, two orders of magnitude smaller than the tensile stress of a straight filament. The flexural rigidity of the filament remained unchanged down to this diameter. We have also knotted a single DNA molecule, opening up the possibility of studying curvature-dependent interactions with associated proteins. We find that the knotted DNA is stronger than actin.

Protrusive growth from giant liposomes driven by actin polymerization.

Development of protrusions in the cell is indispensable in the process of cell motility. Membrane protrusion has long been suggested to occur as a result of actin polymerization immediately beneath the cell membrane at the leading edge, but elucidation of the mechanism is insufficient because of the complexity of the cell. To study the mechanism, we prepared giant liposomes containing monomeric actin (100 or 200 microM) and introduced KCl into individual liposomes by an electroporation technique. On the electroporation, the giant liposomes deformed. Most importantly, protrusive structure grew from the liposomes containing 200 microM actin at rates (ranging from 0.3 to 0.7 micrometer/s) similar to those obtained in the cell. The deformation occurred in a time range (30 approximately 100 s) similar to that of actin polymerization monitored in a cuvette (ca. 50 s). Concomitant with deformation, Brownian motion of micron-sized particles entrapped in the liposomes almost ceased. From these observations, we conclude that actin polymerization in the liposomes caused the protrusive formation.

Real time imaging of rotating molecular machines.

Observation of true rotation has been relatively rare in living systems, but there may be many molecular machines that rotate. Molecular rotations accompanying function can be imaged in real time under an optical microscope by attaching to the protein machine either a small tag such as a single fluorophore or a tag that is huge compared with the size of the protein. As an example of the former approach, axial rotation of an actin filament sliding over myosin has been measured quantitatively by attaching a fluorophore rigidly to the filament and imaging the orientation of the fluorophore continuously by polarization microscopy. As a huge tag in the latter approach, an actin filament turned out to be quite useful. Using this tag, the enzyme F1-ATPase has been shown to be a rotary stepper motor made of a single molecule. Further, the efficiency of this ATP-fueled motor has been shown to reach almost 100%. The two examples above demonstrate that one can now image conformational changes, which necessarily involve reorientation, in a single protein molecule during function. Single-molecule physiology is no longer a dream.

F1-ATPase is a highly efficient molecular motor that rotates with discrete 120 degree steps.

A single molecule of F1-ATPase, a portion of ATP synthase, is by itself a rotary motor in which a central gamma subunit rotates against a surrounding cylinder made of alpha3beta3 subunits. Driven by three catalytic betas, each fueled with ATP, gamma makes discrete 120 degree steps, occasionally stepping backward. The work done in each step is constant over a broad range of imposed load and is close to the free energy of hydrolysis of one ATP molecule.