Single molecule measurements and molecular motors

Mechano-Nanoarchitectonics: Design and Function

Mechanical stimuli have rather ambiguous and less-specific features among various physical stimuli, but most materials exhibit a certain level of responses upon mechanical inputs. Unexplored sciences remain in mechanical responding systems as one of the frontiers of materials science. Nanoarchitectonics approaches for mechanically responding materials are discussed as mechano-nanoarchitectonics in this review article. Recent approaches on molecular and materials systems with mechanical response capabilities are first exemplified with two viewpoints: i) mechanical control of supramolecular assemblies and materials and ii) mechanical control and evaluation of atom/molecular level structures. In the following sections, special attentions on interfacial environments for mechano-nanoarchitectonics are emphasized. The section entitled iii) Mechanical Control of Molecular System at Dynamic Interface describes coupling of macroscopic mechanical forces and molecular-level phenomena. Delicate mechanical forces can be applied to functional molecules embedded at the air-water interface where operation of molecular machines and tuning of molecular receptors upon macroscopic mechanical actions are discussed. Finally, the important role of the interfacial media are further extended to the control of living cells as described in the section entitled iv) Mechanical Control of Biosystems. Pioneering approaches on cell fate regulations at liquid-liquid interfaces are discussed in addition to well-known mechanobiology.

Non-monotonic fluidization generated by fluctuating edge tensions in confluent tissues

In development and homeostasis, multi-cellular systems exhibit spatial and temporal heterogeneity in their biochemical and mechanical properties. Nevertheless, it remains unclear how spatiotemporally heterogeneous forces affect the dynamical and mechanical properties of confluent tissue. To address this question, we study the dynamical behavior of the two-dimensional cellular vertex model for epithelial monolayers in the presence of fluctuating cell-cell interfacial tensions, which is a biologically relevant source of mechanical spatiotemporal heterogeneity. In particular, we investigate the effects of the amplitude and persistence time of fluctuating tension on the tissue dynamics. We unexpectedly find that the long-time diffusion constant describing cell rearrangements depends non-monotonically on the persistence time, while it increases monotonically as the amplitude increases. Our analysis indicates that at low and intermediate persistence times tension fluctuations drive motion of vertices and promote cell rearrangements, while at the highest persistence times the tension in the network evolves so slowly that rearrangements become rare.

Magnetic Biohybrid Vesicles Transported by an Internal Propulsion Mechanism

Some biological microorganisms can crawl or swim due to coordinated motions of their cytoskeleton or the flagella located inside their bodies, which push the cells forward through intracellular forces. To date, there is no demonstration of synthetic systems propelling at low Reynolds number via the precise actuation of the material confined within an enclosing lipid membrane. Here, we report lipid vesicles and other more complex self-assembled biohybrid structures able to propel due to the advection flows generated by the actuated rotation of the superparamagnetic particles they contain. The proposed swimming and release strategies, based on cooperative hydrodynamic mechanisms and near-infrared laser pulse-triggered destabilization of the phospholipid membranes, open new possibilities for the on-command transport of minute quantities of drugs, fluid or nano-objects. The lipid membranes protect the confined substances from the outside environment during transportation, thus enabling them to work in physiological conditions.

Structure of actomyosin rigour complex at 5.2 Å resolution and insights into the ATPase cycle mechanism

Muscle contraction is driven by cyclic association and dissociation of myosin head of the thick filament with thin actin filament coupled with ATP binding and hydrolysis by myosin. However, because of the absence of actomyosin rigour structure at high resolution, it still remains unclear how the strong binding of myosin to actin filament triggers the release of hydrolysis products and how ATP binding causes their dissociation. Here we report the structure of mammalian skeletal muscle actomyosin rigour complex at 5.2 Å resolution by electron cryomicroscopy. Comparison with the structures of myosin in various states shows a distinctly large conformational change, providing insights into the ATPase-coupled reaction cycle of actomyosin. Based on our observations, we hypothesize that asymmetric binding along the actin filament could function as a Brownian ratchet by favouring directionally biased thermal motions of myosin and actin.

Modulation of Skeletal Muscle Contraction by Myosin Phosphorylation

The striated muscle sarcomere is a highly organized and complex enzymatic and structural organelle. Evolutionary pressures have played a vital role in determining the structure-function relationship of each protein within the sarcomere. A key part of this multimeric assembly is the light chain-binding domain (LCBD) of the myosin II motor molecule. This elongated "beam" functions as a biological lever, amplifying small interdomain movements within the myosin head into piconewton forces and nanometer displacements against the thin filament during the cross-bridge cycle. The LCBD contains two subunits known as the essential and regulatory myosin light chains (ELC and RLC, respectively). Isoformic differences in these respective species provide molecular diversity and, in addition, sites for phosphorylation of serine residues, a highly conserved feature of striated muscle systems. Work on permeabilized skeletal fibers and thick filament systems shows that the skeletal myosin light chain kinase catalyzed phosphorylation of the RLC alters the "interacting head motif" of myosin motor heads on the thick filament surface, with myriad consequences for muscle biology. At rest, structure-function changes may upregulate actomyosin ATPase activity of phosphorylated cross-bridges. During activation, these same changes may increase the Ca2+ sensitivity of force development to enhance force, work, and power output, outcomes known as "potentiation." Thus, although other mechanisms may contribute, RLC phosphorylation may represent a form of thick filament activation that provides a "molecular memory" of contraction. The clinical significance of these RLC phosphorylation mediated alterations to contractile performance of various striated muscle systems are just beginning to be understood. © 2017 American Physiological Society. Compr Physiol 7:171-212, 2017.

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 (g_LS) is difficult because these particles are randomly moving within the colloidal suspension by Brownian motion. We obtain g_LS using the data from a line optical tweezer (LOT) that can measure the potential of mean force between two large colloidal particles (Φ_LL). We propose a theory that transforms Φ_LL into g_LS. 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.

Local heating of molecular motors using single carbon nanotubes

Temperature globally affects all chemical processes and biomolecules in living cells. Elevating the temperature of an entire cell accelerates so many biomolecular reactions simultaneously that it is difficult to distinguish the various mechanisms involved. The ability to localize temperature changes to the nanometer range within a cell could provide a powerful new tool for regulating biomolecular activity at the level of individual molecules. The search for a nanoheater for biological research has prompted experiments with carbon nanotubes (CNTs), which have the highest conductivity of any known material. The adsorption of skeletal muscle myosin molecules along the length of single multi-walled CNTs (~10 μm) has allowed researchers to observe the ATP-driven sliding of fluorescently labeled actin filaments. In one study, red-laser irradiation focused on one end of a myosin-coated CNT was used to heat myosin motors locally without directly heating the surrounding water; this laser irradiation instantly accelerated the actin-filament sliding speeds from ~6 to ~12 μm/s in a reversible manner, indicating a local, real-time heating of myosin motors by approximately Δ12 K. Calculation of heat transfer using the finite element method, based on the estimated temperature along a single CNT with a diameter of 170 nm, indicated a high thermal conductivity of ~1540 Wm^-1K^-1 in solution, consistent with values measured in vacuum in earlier studies. Temperature distribution indicated by half-decrease distances was ~3660 nm along the length of the CNT and ~250 nm perpendicular to the length. These results suggest that single-CNT-based heating at the nanometer- or micrometer-range could be used to regulate various biomolecules in many areas of biological, physical, and chemical research.

Nano-assembly of nanodiamonds by conjugation to actin filaments

Fluorescent nanodiamonds (NDs) are remarkable objects. They possess unique mechanical and optical properties combined with high surface areas and controllable surface reactivity. They are non-toxic and hence suited for use in biological environments. NDs are also readily available and commercially inexpensive. Here, the exceptional capability of controlling and tailoring their surface chemistry is demonstrated. Small, bright diamond nanocrystals (size ˜30 nm) are conjugated to protein filaments of actin (length ˜3-7 µm). The conjugation to actin filaments is extremely selective and highly target-specific. These unique features, together with the relative simplicity of the conjugation-targeting method, make functionalised nanodiamonds a powerful and versatile platform in biomedicine and quantum nanotechnologies. Applications ranging from using NDs as superior biological markers to, potentially, developing novel bottom-up approaches for the fabrication of hybrid quantum devices that would bridge across the bio/solid-state interface are presented and discussed.

Optical trapping of individual human immunodeficiency viruses in culture fluid reveals heterogeneity with single-molecule resolution

Optical tweezers use the momentum of photons to trap and manipulate microscopic objects, contact-free, in three dimensions. Although this technique has been widely used in biology and nanotechnology to study molecular motors, biopolymers and nanostructures, its application to study viruses has been very limited, largely due to their small size. Here, using optical tweezers that can simultaneously resolve two-photon fluorescence at the single-molecule level, we show that individual HIV-1 viruses can be optically trapped and manipulated, allowing multi-parameter analysis of single virions in culture fluid under native conditions. We show that individual HIV-1 differs in the numbers of envelope glycoproteins by more than one order of magnitude, which implies substantial heterogeneity of these virions in transmission and infection at the single-particle level. Analogous to flow cytometry for cells, this fluid-based technique may allow ultrasensitive detection, multi-parameter analysis and sorting of viruses and other nanoparticles in biological fluid with single-molecule resolution.

Thermal fluctuation statistics in a molecular motor described by a multidimensional master equation

We present a theoretical investigation of thermal fluctuation statistics in a molecular motor. Energy transfer in the motor is described using a multidimensional discrete master equation with nearest-neighbor hopping. In this theory, energy transfer leads to statistical correlations between thermal fluctuations in different degrees of freedom. For long times, the energy transfer is a multivariate diffusion process with constant drift and diffusion. The fluctuations and drift align in the strong-coupling limit enabling a one-dimensional description along the coupled coordinate. We derive formal expressions for the probability distribution and simulate single trajectories of the system in the near- and far-from-equilibrium limits both for strong and weak coupling. Our results show that the hopping statistics provide an opportunity to distinguish different operating regimes.

Micropattern-controlled local microtubule nucleation, transport, and mesoscale organization

Microtubule organization in living cells is determined by spatial control of microtubule nucleation, their dynamic properties, and transport by molecular motors. Here, we establish a new micropattern-guided method for controlling local microtubule nucleation by spatially confined immobilization of a microtubule polymerase and show that these nucleated microtubules can be transported and organized in space by motor proteins. This assay provides a new platform for deciphering the principles underlying mesoscale microtubule organization.

Switching of myosin-V motion between the lever-arm swing and brownian search-and-catch

Motor proteins are force-generating nanomachines that are highly adaptable to their ever-changing biological environments and have a high energy conversion efficiency. Here we constructed an imaging system that uses optical tweezers and a DNA handle to visualize elementary mechanical processes of a nanomachine under load. We apply our system to myosin-V, a well-known motor protein that takes 72 nm 'hand-over-hand' steps composed of a 'lever-arm swing' and a 'brownian search-and-catch'. We find that the lever-arm swing generates a large proportion of the force at low load (<0.5 pN), resulting in 3 k(B)T of work. At high load (1.9 pN), however, the contribution of the brownian search-and-catch increases to dominate, reaching 13 k(B)T of work. We believe the ability to switch between these two force-generation modes facilitates myosin-V function at high efficiency while operating in a dynamic intracellular environment.

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.

Gene transfer, expression, and sarcomeric incorporation of a headless myosin molecule in cardiac myocytes: evidence for a reserve in myofilament motor function

The purpose of this study was to implement a living myocyte in vitro model system to test whether a motor domain-deleted headless myosin construct could be incorporated into the sarcomere and affect contractility. To this end we used gene transfer to express a "headless" myosin heavy chain (headless-MHC) in complement with the native full-length myosin motors in the cardiac sarcomere. An NH2-terminal Flag epitope was used for unique detection of the motor domain-deleted headless-MHC. Total MHC content (i.e., headless-MHC+endogenous MHC) remained constant, while expression of the headless-MHC in transduced myocytes increased from 24 to 72 h after gene transfer until values leveled off at 96 h after gene transfer, at which time the headless-MHC comprised ∼20% of total MHC. Moreover, immunofluorescence labeling and confocal imaging confirmed expression and demonstrated incorporation of the headless-MHC in the A band of the cardiac sarcomere. Functional measurements in intact myocytes showed that headless-MHC modestly reduced amplitude of dynamic twitch contractions compared with controls (P<0.05). In chemically permeabilized myocytes, maximum steady-state isometric force and the tension-pCa relationship were unaltered by the headless-MHC. These data suggest that headless-MHC can express to 20% of total myosin and incorporate into the sarcomere yet have modest to no effects on dynamic and steady-state contractile function. This would indicate a degree of functional tolerance in the sarcomere for nonfunctional myosin molecules.

A primary hydrogen-deuterium isotope effect observed at the single-molecule level

The covalent chemistry of reactants tethered within a single protein pore can be monitored by observing the time-dependence of ionic current flow through the pore, which responds to bond making and breaking in individual reactant molecules. Here we use this 'nanoreactor' approach to examine the reaction of a quinone with a thiol to form a substituted hydroquinone by reductive 1,4-Michael addition. Remarkably, a primary hydrogen-deuterium isotope effect is readily detected at the single-molecule level during prototropic rearrangement of an initial adduct. The observation of individual reaction intermediates allows the measurement of an isotope effect whether or not the step involved is rate limiting, which would not be the case in an ensemble measurement.

Mechanical characterization of one-headed myosin-V using optical tweezers

Class V myosin (myosin-V) is a cargo transporter that moves along an actin filament with large (approximately 36-nm) successive steps. It consists of two heads that each includes a motor domain and a long (23 nm) neck domain. One of the more popular models describing these steps, the hand-over-hand model, assumes the two-headed structure is imperative. However, we previously succeeded in observing successive large steps by one-headed myosin-V upon optimizing the angle of the acto-myosin interaction. In addition, it was reported that wild type myosin-VI and myosin-IX, both one-headed myosins, can also generate successive large steps. Here, we describe the mechanical properties (stepsize and stepping kinetics) of successive large steps by one-headed and two-headed myosin-Vs. This study shows that the stepsize and stepping kinetics of one-headed myosin-V are very similar to those of the two-headed one. However, there was a difference with regards to stability against load and the number of multisteps. One-headed myosin-V also showed unidirectional movement that like two-headed myosin-V required 3.5 k(B)T from ATP hydrolysis. This value is also similar to that of smooth muscle myosin-II, a non-processive motor, suggesting the myosin family uses a common mechanism for stepping regardless of the steps being processive or non-processive. In this present paper, we conclude that one-headed myosin-V can produce successive large steps without following the hand-over-hand mechanism.

Myosin VI: an innovative motor that challenged the swinging lever arm hypothesis

The swinging crossbridge hypothesis states that energy from ATP hydrolysis is transduced to mechanical movement of the myosin head while bound to actin. The light chain-binding region of myosin is thought to act as a lever arm that amplifies movements near the catalytic site. This model has been challenged by findings that myosin VI takes larger steps along actin filaments than early interpretations of its structure seem to allow. We now know that myosin VI does indeed operate by an unusual approximately 180 degrees lever arm swing and achieves its large step size using special structural features in its tail domain.