Mitsuhiro Iwaki

Brownian search-and-catch mechanism for myosin-VI steps

The cargo transporter myosin-VI processively walks along actin filaments using its two heads. Here we use single-molecule nanometry to show that the strong binding by myosin heads to actin is greatly accelerated (approximately 30-fold) when backward strain is applied to weakly bound heads during the actin search. We propose that the myosin head searches for the forward actin target by Brownian motion and catches the actin in a strain-dependent manner.

Single molecule measurements and molecular motors

Single molecule imaging and manipulation are powerful tools in describing the operations of molecular machines like molecular motors. The single molecule measurements allow a dynamic behaviour of individual biomolecules to be measured. In this paper, we describe how we have developed single molecule measurements to understand the mechanism of molecular motors. The step movement of molecular motors associated with a single cycle of ATP hydrolysis has been identified. The single molecule measurements that have sensitivity to monitor thermal fluctuation have revealed that thermal Brownian motion is involved in the step movement of molecular motors. Several mechanisms have been suggested in different motors to bias random thermal motion to directional movement.

Entropic potential field formed for a linear-motor protein near a filament: Statistical-mechanical analyses using simple models.

We report a new progress in elucidating the mechanism of the unidirectional movement of a linear-motor protein (e.g., myosin) along a filament (e.g., F-actin). The basic concept emphasized here is that a potential field is entropically formed for the protein on the filament immersed in solvent due to the effect of the translational displacement of solvent molecules. The entropic potential field is strongly dependent on geometric features of the protein and the filament, their overall shapes as well as details of the polyatomic structures. The features and the corresponding field are judiciously adjusted by the binding of adenosine triphosphate (ATP) to the protein, hydrolysis of ATP into adenosine diphosphate (ADP)+Pi, and release of Pi and ADP. As the first step, we propose the following physical picture: The potential field formed along the filament for the protein without the binding of ATP or ADP+Pi to it is largely different from that for the protein with the binding, and the directed movement is realized by repeated switches from one of the fields to the other. To illustrate the picture, we analyze the spatial distribution of the entropic potential between a large solute and a large body using the three-dimensional integral equation theory. The solute is modeled as a large hard sphere. Two model filaments are considered as the body: model 1 is a set of one-dimensionally connected large hard spheres and model 2 is a double helical structure formed by two sets of connected large hard spheres. The solute and the filament are immersed in small hard spheres forming the solvent. The major findings are as follows. The solute is strongly confined within a narrow space in contact with the filament. Within the space there are locations with sharply deep local potential minima along the filament, and the distance between two adjacent locations is equal to the diameter of the large spheres constituting the filament. The potential minima form a ringlike domain in model 1 while they form a pointlike one in model 2. We then examine the effects of geometric features of the solute on the amplitudes and asymmetry of the entropic potential field acting on the solute along the filament. A large aspherical solute with a cleft near the solute-filament interface, which mimics the myosin motor domain, is considered in the examination. Thus, the two fields in our physical picture described above are qualitatively reproduced. The factors to be taken into account in further studies are also discussed.

Local Heat Activation of Single Myosins Based on Optical Trapping of Gold Nanoparticles

Myosin is a mechano-enzyme that hydrolyzes ATP in order to move unidirectionally along actin filaments. Here we show by single molecule imaging that myosin V motion can be activated by local heat. We constructed a dark-field microscopy that included optical tweezers to monitor 80 nm gold nanoparticles (GNP) bound to single myosin V molecules with nanometer and submillisecond accuracy. We observed 34 nm processive steps along actin filaments like those seen when using 200 nm polystyrene beads (PB) but dwell times (ATPase activity) that were 4.5 times faster. Further, by using DNA nanotechnology (DNA origami) and myosin V as a nanometric thermometer, the temperature gradient surrounding optically trapped GNP could be estimated with nanometer accuracy. We propose our single molecule measurement system should advance quantitative analysis of the thermal control of biological and artificial systems like nanoscale thermal ratchet motors.

A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads

Mechanosensitive biological nanomachines such as motor proteins and ion channels regulate diverse cellular behaviour. Combined optical trapping with single-molecule fluorescence imaging provides a powerful methodology to clearly characterize the mechanoresponse, structural dynamics and stability of such nanomachines. However, this system requires complicated experimental geometry, preparation and optics, and is limited by low data-acquisition efficiency. Here we develop a programmable DNA origami nanospring that overcomes these issues. We apply our nanospring to human myosin VI, a mechanosensory motor protein, and demonstrate nanometre-precision single-molecule fluorescence imaging of the individual motor domains (heads) under force. We observe force-induced transitions of myosin VI heads from non-adjacent to adjacent binding, which correspond to adapted roles for low-load and high-load transport, respectively. Our technique extends single-molecule studies under force and clarifies the effect of force on biological processes.

Thermal fluctuations biased for directional motion in molecular motors

Recently developed single molecule measurements have demonstrated that the mechanisms for numerous protein functions involve thermal fluctuation, or Brownian motion. Protein interactions bias the random thermal noise in a manner such that the protein can perform its given functions. This phenomenon has been observed in molecular motor unidirectional movement where Brownian motion is used to preferentially bind the motor heads in one direction causing directional motility. This is analogous to that used by proteins in which spontaneous structural fluctuations are used to switch function. Seeing that two very different systems implement similar mechanisms suggests there exists a general scheme applied by diverse proteins that exploits thermal fluctuations in order to achieve their respective functions.

Transcriptional bursting is intrinsically caused by interplay between RNA polymerases on DNA

Cell-to-cell variability plays a critical role in cellular responses and decision-making in a population, and transcriptional bursting has been broadly studied by experimental and theoretical approaches as the potential source of cell-to-cell variability. Although molecular mechanisms of transcriptional bursting have been proposed, there is little consensus. An unsolved key question is whether transcriptional bursting is intertwined with many transcriptional regulatory factors or is an intrinsic characteristic of RNA polymerase on DNA. Here we design an in vitro single-molecule measurement system to analyse the kinetics of transcriptional bursting. The results indicate that transcriptional bursting is caused by interplay between RNA polymerases on DNA. The kinetics of in vitro transcriptional bursting is quantitatively consistent with the gene-nonspecific kinetics previously observed in noisy gene expression in vivo. Our kinetic analysis based on a cellular automaton model confirms that arrest and rescue by trailing RNA polymerase intrinsically causes transcriptional bursting.

Number Density Distribution of Small Particles around a Large Particle: Structural Analysis of a Colloidal Suspension

Some colloidal suspensions contain two types of particles-small and large particles-to improve the lubricating ability, light absorptivity, and so forth. Structural and chemical analyses of such colloidal suspensions are often performed to understand their properties. In a structural analysis study, the observation of the number density distribution of small particles around a large particle (gLS) is difficult because these particles are randomly moving within the colloidal suspension by Brownian motion. We obtain gLS using the data from a line optical tweezer (LOT) that can measure the potential of mean force between two large colloidal particles (ΦLL). We propose a theory that transforms ΦLL into gLS. The transform theory is explained in detail and tested. We demonstrate for the first time that LOT can be used for the structural analysis of a colloidal suspension. LOT combined with the transform theory will facilitate structural analyses of the colloidal suspensions, which is important for both understanding colloidal properties and developing colloidal products.

Detection of Thermal Processes of Protein Function

Single molecule detection techniques have been developed to improve the understanding of the mechanisms underlying molecular motors. The mechanical processes governing movement of myosin and kinesin are stochastic, indicating that the movement of these motors is driven thermally. Random thermal movement is biased utilizing the energy of the ATP hydrolysis. These studies have shown that molecular motors may harness thermal energy rather than functioning without being disturbed by thermal effects as it is the case for man-made machines. Thus the single molecule detection has made many great contributions to understanding the mechanism underlying these molecular machines.

Single-Molecule Analysis of Actomyosin in the Presence of Osmolyte

Actomyosin is a protein complex composed of myosin and actin, which is well known for being the minimal contractile unit of muscle. The chemical free energy of ATP is converted into mechanical work by the complex, and the single-molecule mechanical properties of myosin are well characterized in vitro. However, the aqueous solution environment in in vitro assay is far from that in cells, where biomolecules are crowded, which influences osmotic pressure, and processes such as folding, and association and diffusion of proteins. Here, to bridge the gap between in vitro and in-cell environment, we observed mechanical motion of actomyosin-V in the presence of the osmolyte sucrose, as a model system. Single-molecule observation of myosin-V motor domains (heads) on actin filament at varying sucrose concentration revealed modulated mechanical elementary processes suggesting increased affinity of heads with actin and more robust force generation possibly accompanied by a sliding motion of myosin head along actin.