ATP synthase

Scientists have created a working nanoscale electomotor. The science team designed a turbine engineered from DNA that is powered by hydrodynamic flow inside a nanopore, a nanometer-sized hole in a membrane of solid-state silicon nitride. The tiny motor could help spark research into future applications such as building molecular factories or even medical probes of molecules inside the bloodstream. Scientists have created the world's first working nanoscale electromotor, according to research published in the journal Nature Nanotechnology. The science team designed a turbine engineered from DNA that is powered by hydrodynamic flow inside a nanopore, a nanometer-sized hole in a membrane of solid-state silicon nitride. The tiny motor could help spark research into future applications such as building molecular factories for useful chemicals or medical probes of molecules inside the bloodstream to detect diseases such as cancer. "Common macroscopic machines become inefficient at the nanoscale," said study co-author professor Aleksei Aksimentiev, a professor of physics at the University of Illinois at Urbana-Champagne. "We have to develop new principles and physical mechanisms to realize electromotors at the very, very small scales." The experimental work on the tiny motor was conducted by Cees Dekker of the Delft University of Technology and Hendrik Dietz of the Technical University of Munich. Dietz is a world expert in DNA origami. His lab manipulated DNA molecules to make the tiny motor's turbine, which consisted of 30 double-stranded DNA helices engineered into an axle and three blades of about 72 base pair length. Decker's lab work demonstrated that the turbine can indeed rotate by applying an electric field. Aksimentiev's lab carried out all-atom molecular dynamics simulations on a system of five million atoms to characterize the physical phenomena of how the motor works. The system was the smallest representation that could yield meaningful results about the experiment; however, "it was one of the largest ever simulated from the DNA origami perspective," Aksimentiev said. Mission Impossible to Mission Possible The Texas Advanced Computing Center (TACC) awarded Aksimentiev a Leadership Resource Allocation to aid his study of mesoscale biological systems on the National Science Foundation (NSF)-funded Frontera, the top academic supercomputer in the U.S. "Frontera was instrumental in this DNA nanoturbine work," Aksimentiev said. "We obtained microsecond simulation trajectories in two to three weeks instead of waiting for a year or more on smaller computing systems. The big simulations were done on Frontera using about a quarter of the machine -- over 2,000 nodes," Aksimentiev said. "However, it's not just the hardware, but also the interaction with TACC staff. It's extremely important to make the best use of the resources once we have the opportunity." Aksimentiev was also awarded supercomputer allocations for this work by the NSF-funded Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) on Expanse of the San Diego Supercomputer Center and Anvil of Purdue University. "We had up to 100 different nanomotor systems to simulate. We had to run them for different conditions and in a speedy manner, which the ACCESS supercomputers assisted with perfectly," Aksimentiev said. "Many thanks to the NSF for their support -- we would not be able to do the science that we do without these systems." DNA as a Building Block The success with the working DNA nanoturbine builds on a previous study that also used Frontera and ACCESS supercomputers. The study showed that a single DNA helix is the tiniest electromotor that one can build -- it can rotate up to a billion revolutions per minute. DNA has emerged as a building material at the nanoscale, according to Aksimentiev. "The way DNA base pair is a very powerful programming tool. We can program geometrical, three-dimensional objects from DNA using the Cadnano software just by programming the sequence of letters that make up the rungs of the double helix," he explained. Another reason for using DNA as the building block is that it carries a negative charge, an essential characteristic to make the electromotor. "We wanted to reproduce one of the most spectacular biological machines -- ATP synthase, which is driven by electric field. We chose to do our motor with DNA," Aksimentiev said. "This new work is the first nanoscale motor where we can control the rotational speed and direction," he added. It's done by adjusting the electric field across the solid state nanopore membrane and the salt concentrations of the fluid that surrounds the rotor. "In the future, we might be able to synthetize a molecule using the new nanoscale electromotor, or we can use it to as an element of a bigger molecular factory, where things are moved around. Or we could imagine it as a vehicle for soft propulsion, where synthetic systems can go into a blood stream and probe molecules or cells one at a time," Aksimentiev said. If you think this sounds like something out of a 1960's sci-fi movie, you are right. In the movie Fantastic Voyage, a team of Americans in a nuclear submarine is shrunk and injected into a scientist's body to fix a blood clot and need to work quickly before the miniaturization wears off. As far-fetched as this might sound, Aksimentiev says that the concept and the elements of the machines we are developing today could enable something like this to happen. "We were able to accomplish this because of supercomputers," Aksimentiev said. "Supercomputers are becoming more and more indispensable as the complexity of the systems that we build increases. They're the computational microscopes, which at ultimate resolutions can see the motion of individual atoms and how that is coupled to a bigger system." Funding came from ERC Advanced Grant no. 883684 and the NanoFront and BaSyC programmes; ERC Consolidator Grant to H.D. (GA no. 724261), the Deutsche Forschungsgemeinschaft via the Gottfried-Wilhelm-Leibniz Programme (to H.D.) and the SFB863 Project ID 111166240 TPA9; National Science Foundation grant DMR-1827346; the Max Planck School Matter to Life and the MaxSynBio Consortium. Supercomputer time was provided through TACC Leadership Resource Allocation MCB20012 on Frontera and through ACCESS allocation MCA05S028.

F-Type ATP synthase, a catalytic complex of proteins, synthesizes adenosine triphosphate (ATP), the energy currency of living cells. A lot of ambiguity exists over the rotational mechanism of this spinning enzyme. Now, researchers from Japan have demonstrated how each chemical event of ATP metabolism is linked to the 'stepwise' rotational movement of the F1 component of ATPase. Especially, they clarified the angle of shaft rotation before ATP-cleavage, a long-standing enigma, to be 200°. F-Type ATP synthase, a catalytic complex of proteins, synthesizes adenosine triphosphate (ATP), the energy currency of living cells. A lot of ambiguity exists over the rotational mechanism of this spinning enzyme. Now, researchers from Japan have demonstrated how each chemical event of ATP metabolism is linked to the 'stepwise' rotational movement of the F1 component of ATPase. Especially, they clarified the angle of shaft rotation before ATP-cleavage, a long-standing enigma, to be 200°. Adenosine triphosphate (ATP) is the energy currency of cells. It powers various cellular processes that require energy, including enzymatic reactions. ATP is synthesized with the help of an enzyme complex called F-type ATP synthase. This enzyme complex has a bidirectional functionality, working to synthesize ATP as well as hydrolyzing it, depending on environmental and cellular cues. ATP synthase consists of two rotating motors―F1 and F0. The F1 subcomplex is mainly composed of α, β, and γ subunits. During the hydrolysis of ATP, the F1-ATPase show rotational motion. Therefore, F1-ATPase is also known as the world's smallest rotary biological molecule motor. However, the underlying mechanism of how ATP hydrolysis makes the molecule rotate remains unclear. To address this knowledge gap, a team of researchers from Japan, led by Associate Professor Tomoko Masaike from Tokyo University of Science, set out to investigate the events behind the rotational mechanism of F1-ATPase in the thermophilic bacterium, Bacillus PS3. Elaborating on the objectives of their study, Dr. Masaike explains, "We wanted to clarify the mechanism by which F1-ATPase rotates the central shaft during ATP hydrolysis. We focused on clarifying the angle of rotation of the central shaft between the binding of the substrate ATP to the enzyme and the cleavage of its high-energy phosphate bond." The study, which was undertaken in collaboration with Professor Takayuki Nishizaka from Gakushuin University and Yuh Hasimoto from Hamamatsu Photonics K.K., was made available online on 21 December 2022 and 7 February 2023 in print in Biophysical Journal. Previous investigations of the F1 subunits of Bacillus PS3 have established that ATP cleavage involves chemomechanical coupling, i.e., each rotational stepping motion is linked to a chemical reaction step. The angle of rotation between ATP binding and its cleavage at the same catalytic site has been previously estimated to be 200°. However, experimental evidence to substantiate this has so far been lacking. To address this, the researchers studied the rotation by creating a hybrid F1 using one mutant β and two wild type βs. Since the rate of both ATP cleavage and ATP binding was extremely slow in the mutant, the researchers could observe the pauses or dwells between rotational steps easily. Upon performing a single-molecule rotation assay with varying concentrations of ATP, they could observe three sets of short and long dwells associated alternately with 80° and 40° intervals per revolution. To investigate the events associated with the dwells, the authors performed dwell-time analyses. The long pause before the 40° sub-step was independent of ATP concentration and was confirmed as the 'catalytic dwell'―a pause in the rotation of the shaft due to ATP cleavage. Alternately, the short pause before the 80° step was clearly dependent on ATP concentration and thus identified as the 'ATP-waiting dwell' (pause to enable β subunit to bind ATP). "Upon investigating the rotation of the shaft, we could provide visible evidence through optical microscopy that the shaft angles at ATP-binding and cleaving events in Bacillus PS3 were 0° and 200°, respectively" says Hasimoto. With this study, the authors have resolved a long-term debate over the ATP-cleavage shaft angle and established the chemomechanical correlation of ATPase function. Talking about the future impacts of their novel study, Associate Prof. Masaike elaborates, "Since F1-ATPase is the world's smallest biological rotational motor protein, it can be used as a reference to understand the mechanism of energy transduction in living organisms. This knowledge can be revolutionary in developing efficient nanomachines. Moreover, ATP synthase from Mycobacterium tuberculosis has recently been identified as a potential target for drug discovery. Therefore, to stop its rotation using inhibitors, understanding the mechanism of rotation is quite important."

Biologists demonstrate how the auxiliary factor CGL160 contributes to the synthesis of crucial parts of the photosynthetic machinery. LMU biologists demonstrate how the auxiliary factor CGL160 contributes to the synthesis of crucial parts of the photosynthetic machinery. Photosynthesis is the means by which plants, algae, and cyanobacteria extract their 'food' in the form of energy-rich biomolecules from sunlight, carbon dioxide, and water. It is a complex process, from which researchers are still coaxing many new details. A team led by LMU biologists Thilo Rühle, Bennet Reiter, and Prof. Dario Leister has now solved another piece of the puzzle of this essential process and elucidated the role of the auxiliary factor CGL160, as the scientists report in the journal The Plant Cell. Photosynthesis takes place in several partial reactions at the so-called thylakoid membranes in the chloroplasts, where various pigments absorb the electromagnetic radiation of sunlight. Specific protein complexes in conjunction with ATP synthases then convert this light energy into chemical energy in the form of ATP. This enables the plant, among other things, to synthesize carbohydrates as energy-rich 'fuel' for cellular respiration. As 'molecular machines,' ATP synthases are therefore a vital component of plant metabolism. How ATP synthases are assembled in the cell has not yet been fully clarified. Based on the model organism Arabidopsis thaliana, the researchers have now been able to demonstrate that the protein CGL160 plays a key role in the process by recruiting the coupling factor CF1 of the ATP synthase. "The protein CGL160 sits with its base in the thylakoid membrane, while its N-terminal domain protrudes like a rod and fishes the soluble CF1 portion of the ATP synthases out of the fluid inside the chloroplasts. This portion of the protein binds the CF1 'headpiece' and facilitates linkage with the portion of the ATP synthase embedded in the thylakoid membrane, making its formation considerably more efficient," explains Thilo Rühle. Evolutionary roots and adaptations Even under unfavorable growth conditions, the presence of auxiliary factors such as CGL160 prove to be advantageous: The LMU biologists discovered that an absence of CGL160, with its CF1-binding function, under conditions of light deficiency negatively impacts the development of chloroplasts. "We observed that the chloroplast structure of corresponding mutants suffers more during short days with just eight hours of daylight. We advance the hypothesis therefore that the interaction between the N-terminal domain of CGL160 and CF1 is also an evolutionary adaptation that enables plants to cope better in various light conditions," says Rühle. The researchers also found clues as to the evolutionary origin of CGL160. In experiments with Arabidopsis thaliana, they succeeded in functionally replacing the membrane domain of CGL160 with the Atp1 protein from cyanobacteria of the genus Synechocystis. "Around 80 percent of the function can be restored in this way. This suggests that CGL160 in land plants may have come from a predecessor protein of cyanobacteria," says Rühle. Indeed, plant cells acquired their chloroplasts through incorporation and functional integration of cyanobacteria. Potential route to regulation of photosynthesis This set in train the emergence of a complex synthesis plan for photosynthetic machinery. To better understand this plan, the LMU biologists now want to identify all auxiliary factors -- in addition to CGL160 and a handful of other currently known factors -- that are important for the assembly and function of ATP synthases in plant thylakoid membranes. "We assume that there are much fewer factors involved here than in the photosystems themselves -- accordingly, ATP synthase is an easier potential route for the regulation of photosynthesis," says Rühle. "In the future, people could use this knowledge for various applications, such as modifying plants so that they can optimally cover their ATP requirements even when exposed to stressors like heat or extreme light conditions."