The path to visualization of walking myosin V by high-speed atomic force microscopy

Memory induced-mechanism of noise attenuator of myosin V molecular motors

Depending on the chemical energy from ATP hydrolysis, myosin V can drive the multistep and continuous coupled cycling process to transport cellular cargo to targeted regions. However, it is still obscure how the molecular memory induced by the multistep coupled transported process could regulate the dynamic behavior of the motor state of myosin V. Here, we propose a novel non-Markovian polymorphic mechanochemical model to investigate the effect of the molecular memory on the mechanic of noise attenuation of myosin V system. We first define an effective transition rate for a multistep coupled reaction process which is the function of memory and system states to transform equivalently the non-Markovian process into the classical Markov process. By noise decomposition technology, it is observed that both the intrinsic and extrinsic noises of the ADP-myosin V bound state (AM ⋅ ADP) exhibit a monotonically decreasing trend with lengthening the molecular memory. Molecular memory as a regulation factor can amplify the contribution of intrinsic noise to the overall noise while reducing the influence of extrinsic noise on the AM ⋅ ADP. Moreover, the modulation of molecular memory could induce stochastic focusing. These results indicate that the role of molecular memory in the myosin V state transition can not only offer a handle to maintain the robustness of the motion system but also serve as a paradigm for studying more complex molecular motors.

Atomic Force Microscopy: An Introduction

Imaging of nano-sized particles and sample features is crucial in a variety of research fields, for instance, in biological sciences, where it is paramount to investigate structures at the single particle level. Often, two-dimensional images are not sufficient, and further information such as topography and mechanical properties are required. Furthermore, to increase the biological relevance, it is desired to perform the imaging in close to physiological environments. Atomic force microscopy (AFM) meets these demands in an all-in-one instrument. It provides high-resolution images including surface height information leading to three-dimensional information on sample morphology. AFM can be operated both in air and in buffer solutions. Moreover, it has the capacity to determine protein and membrane material properties via the force spectroscopy mode. Here we discuss the principles of AFM operation and provide examples of how biomolecules can be studied. New developments in AFM are discussed, and by including approaches such as bimodal AFM and high-speed AFM (HS-AFM), we show how AFM can be used to study a variety of static and dynamic single biomolecules and biomolecular assemblies.

Physical pictures of rotation mechanisms of F1- and V1-ATPases: Leading roles of translational, configurational entropy of water

We aim to develop a theory based on a concept other than the chemo-mechanical coupling (transduction of chemical free energy of ATP to mechanical work) for an ATP-driven protein complex. Experimental results conflicting with the chemo-mechanical coupling have recently emerged. We claim that the system comprises not only the protein complex but also the aqueous solution in which the protein complex is immersed and the system performs essentially no mechanical work. We perform statistical-mechanical analyses on V₁-ATPase (the A₃B₃DF complex) for which crystal structures in more different states are experimentally known than for F₁-ATPase (the α₃β₃γ complex). Molecular and atomistic models are employed for water and the structure of V₁-ATPase, respectively. The entropy originating from the translational displacement of water molecules in the system is treated as a pivotal factor. We find that the packing structure of the catalytic dwell state of V₁-ATPase is constructed by the interplay of ATP bindings to two of the A subunits and incorporation of the DF subunit. The packing structure represents the nonuniformity with respect to the closeness of packing of the atoms in constituent proteins and protein interfaces. The physical picture of rotation mechanism of F₁-ATPase recently constructed by Kinoshita is examined, and common points and differences between F₁- and V₁-ATPases are revealed. An ATP hydrolysis cycle comprises binding of ATP to the protein complex, hydrolysis of ATP into ADP and Pi in it, and dissociation of ADP and Pi from it. During each cycle, the chemical compounds bound to the three A or β subunits and the packing structure of the A₃B₃ or α₃β₃ complex are sequentially changed, which induces the unidirectional rotation of the central shaft for retaining the packing structure of the A₃B₃DF or α₃β₃γ complex stabilized for almost maximizing the water entropy. The torque driving the rotation is generated by water with no input of chemical free energy. The presence of ATP is indispensable as a trigger of the torque generation. The ATP hydrolysis or synthesis reaction is tightly coupled to the rotation of the central shaft in the normal or inverse direction through the water-entropy effect.

Myosin V-mediated transport of Snc1 and Vps10 toward the trans-Golgi network

Retrieval of cargo proteins from the endosome towards the trans-Golgi network (TGN) is a crucial intracellular process for cellular homeostasis. Its dysfunction is associated with pathogenesis of Alzheimer and Parkinson's diseases. Myosin family proteins are cellular motors walking along actin filaments by utilizing the chemical energy from ATP hydrolysis, known to involve in pleiotropic cellular trafficking pathways. However, the question of whether myosins play a role in the trafficking of Snc1 and Vps10 has not been addressed yet. The present study assesses the potential roles of all five yeast myosins in the recycling of two membrane cargo, Snc1 and Vps10. It appears that all myosins except Myo2 are not required for the Snc1 traffic, while it was found that Myo1 and 2 play important roles for Vps10 retrieval from the endosome and the vacuole. Multiple myo2 mutants harboring a point mutation in the actin binding or the cargo binding tail domain were characterized to demonstrate abnormal Vps10-GFP and GFP-Snc1 distribution phenotypes, suggesting a severe defect in their sorting and trafficking at the endosome. Furthermore, Vps10-GFP patches in all tested myo2 mutants were found to be near stationary with quantitative live cell imaging. Finally, we found that actin cables in the myo2 mutant cells were considerably disrupted, which may aggravate the trafficking of Vps10 from the endosome. Together, our results provide novel insights into the function of Myo-family proteins in the recycling traffic of Vps10 and Snc1 destined for the TGN.

Myosin Structures

Directed movements on actin filaments within the cell are powered by molecular motors of the myosin superfamily. On actin filaments, myosin motors convert the energy from ATP into force and movement. Myosin motors power such diverse cellular functions as cytokinesis, membrane trafficking, organelle movements, and cellular migration. Myosin generates force and movement via a number of structural changes associated with hydrolysis of ATP, binding to actin, and release of the ATP hydrolysis products while bound to actin. Herein we provide an overview of those structural changes and how they relate to the actin-myosin ATPase cycle. These structural changes are the basis of chemo-mechanical transduction by myosin motors.

Single-Molecule Biophysical Techniques to Study Actomyosin Force Transduction

Inside the cellular environment, molecular motors can work in concert to conduct a variety of important physiological functions and processes that are vital for the survival of a cell. However, in order to decipher the mechanism of how these molecular motors work, single-molecule microscopy techniques have been popular methods to understand the molecular basis of the emerging ensemble behavior of these motor proteins.In this chapter, we discuss various single-molecule biophysical imaging techniques that have been used to expose the mechanics and kinetics of myosins. The chapter should be taken as a general overview and introductory guide to the many existing techniques; however, since other chapters will discuss some of these techniques more thoroughly, the readership should refer to those chapters for further details and discussions. In particular, we will focus on scattering-based single-molecule microscopy methods, some of which have become more popular in the recent years and around which the work in our laboratories has been centered.

High-Speed Atomic Force Microscopy to Study Myosin Motility

High-speed atomic force microscopy (HS-AFM) is a unique tool that enables imaging of protein molecules during their functional activity at sub-100 ms temporal and submolecular spatial resolution. HS-AFM is suited for the study of highly dynamic proteins, including myosin motors. HS-AFM images of myosin V walking on actin filaments provide irrefutable evidence for the swinging lever arm motion propelling the molecule forward. Moreover, molecular behaviors that have not been noticed before are also displayed on the AFM movies. This chapter describes the principle, underlying techniques and performance of HS-AFM, filmed images of myosin V, and mechanistic insights into myosin motility provided from the filmed images.

Force Generation by Myosin Motors: A Structural Perspective

Generating force and movement is essential for the functions of cells and organisms. A variety of molecular motors that can move on tracks within cells have evolved to serve this role. How these motors interact with their tracks and how that, in turn, leads to the generation of force and movement is key to understanding the cellular roles that these motor-track systems serve. This review is focused on the best understood of these systems, which is the molecular motor myosin that moves on tracks of filamentous (F-) actin. The review highlights both the progress and the limits of our current understanding of how force generation can be controlled by F-actin-myosin interactions. What has emerged are insights they may serve as a framework for understanding the design principles of a number of types of molecular motors and their interactions with their tracks.

Characteristics of Myosin V Processivity

Myosin V is a processive doubled-headed biomolecular motor involved in many intracellular organelle and vesicle transport. The unidirectional movement is coupled with the adenosine triphosphate (ATP) hydrolysis and product release cycle. With the progress of experimental techniques and the enhancement of measuring directness, detailed knowledge of the motility of myosin V has been obtained. Following the ATPase cycle, the 4-state mechanochemical model of the myosin V's processive movement is used. The transitions between various states take place in a stochastic manner. We can use the master equation to analyze and calculate quantitatively. Meanwhile, the effect of the reverse reaction is taken fully into account. We fit the mean velocity, the mean dwell time, the mean run length, and the ratio of forward/backward steps as a functionof ATP, ADP, and Pi concertration. The theoretical curves are generally in line with the experimental data. This work provides a new insight for the characteristic of myosin V.

A Systematic Review of Continuum Modeling of Skeletal Muscles: Current Trends, Limitations, and Recommendations

Finite elasticity theory has been commonly used to model skeletal muscle. A very large range of heterogeneous constitutive laws has been proposed. In this review, the most widely used continuum models of skeletal muscles were synthetized and discussed. Trends and limitations of these laws were highlighted to propose new recommendations for future researches. A systematic review process was performed using two reliable search engines as PubMed and ScienceDirect. 40 representative studies (13 passive muscle materials and 27 active muscle materials) were included into this review. Note that exclusion criteria include tendon models, analytical models, 1D geometrical models, supplement papers, and indexed conference papers. Trends of current skeletal muscle modeling relate to 3D accurate muscle representation, parameter identification in passive muscle modeling, and the integration of coupled biophysical phenomena. Parameter identification for active materials, assumed fiber distribution, data assumption, and model validation are current drawbacks. New recommendations deal with the incorporation of multimodal data derived from medical imaging, the integration of more biophysical phenomena, and model reproducibility. Accounting for data uncertainty in skeletal muscle modeling will be also a challenging issue. This review provides, for the first time, a holistic view of current continuum models of skeletal muscles to identify potential gaps of current models according to the physiology of skeletal muscle. This opens new avenues for improving skeletal muscle modeling in the framework of in silico medicine.

Unconventional Imaging Methods to Capture Transient Structures during Actomyosin Interaction

Half a century has passed since the cross-bridge structure was recognized as the molecular machine that generates muscle tension. Despite various approaches by a number of scientists, information on the structural changes in the myosin heads, particularly its transient configurations, remains scant even now, in part because of their small size and rapid stochastic movements during the power stroke. Though progress in cryo-electron microscopy is eagerly awaited as the ultimate means to elucidate structural details, the introduction of some unconventional methods that provide high-contrast raw images of the target protein assemblies is quite useful, if available, to break the current impasse. Quick-freeze deep–etch–replica electron microscopy coupled with dedicated image analysis procedures, and high-speed atomic-force microscopy are two such candidates. We have applied the former to visualize actin-associated myosin heads under in vitro motility assay conditions, and found that they take novel configurations similar to the SH1–SH2-crosslinked myosin that we characterized recently. By incorporating biochemical and biophysical results, we have revised the cross-bridge mechanism to involve the new conformer as an important main player. The latter “microscopy” is unique and advantageous enabling continuous observation of various protein assemblies as they function. Direct observation of myosin-V’s movement along actin filaments revealed several unexpected behaviors such as foot-stomping of the leading head and unwinding of the coiled-coil tail. The potential contribution of these methods with intermediate spatial resolution is discussed.

Atomic Force Microscopy: An Introduction

Imaging of nano-sized particles and sample features is crucial in a variety of research fields. For instance in biological sciences, where it is paramount to investigate structures at the single particle level. Often two-dimensional images are not sufficient and further information such as topography and mechanical properties are required. Furthermore, to increase the biological relevance, it is desired to perform the imaging in close to physiological environments. Atomic force microscopy (AFM) meets these demands in an all-in-one instrument. It provides high-resolution images including surface height information leading to three-dimensional information on sample morphology. AFM can be operated both in air and in buffer solutions. Moreover, it has the capacity to determine protein and membrane material properties via the force spectroscopy mode. Here we discuss the principles of AFM operation and provide examples of how biomolecules can be studied. By including new approaches such as high-speed AFM (HS-AFM) we show how AFM can be used to study a variety of static and dynamic single biomolecules and biomolecular assemblies.

Direct AFM Visualization of the Nanoscale Dynamics of Biomolecular Complexes

High-speed AFM (HS-AFM) is an advanced technique with numerous applications in biology, particularly in molecular biophysics. Developed as a time-lapse AFM technique for direct imaging fully hydrated biological molecules, HS-AFM is currently capable of visualizing the dynamics of biological molecules and their complexes at a video-data acquisition rate. Spatial resolution at the nanometer level is another important characteristic of HS-AFM. This review focuses on examples of primarily protein-DNA complexes to illustrate the high temporal and spatial resolution capabilities of HS-AFM that have resulted in novel models and/or the functional mechanisms of these biological systems.

Directly watching biomolecules in action by high-speed atomic force microscopy

Proteins are dynamic in nature and work at the single molecule level. Therefore, directly watching protein molecules in dynamic action at high spatiotemporal resolution must be the most straightforward approach to understanding how they function. To make this observation possible, high-speed atomic force microscopy (HS-AFM) has been developed. Its current performance allows us to film biological molecules at 10-16 frames/s, without disturbing their function. In fact, dynamic structures and processes of various proteins have been successfully visualized, including bacteriorhodopsin responding to light, myosin V walking on actin filaments, and even intrinsically disordered proteins undergoing order/disorder transitions. The molecular movies have provided insights that could not have been reached in other ways. Moreover, the cantilever tip can be used to manipulate molecules during successive imaging. This capability allows us to observe changes in molecules resulting from dissection or perturbation. This mode of imaging has been successfully applied to myosin V, peroxiredoxin and doublet microtubules, leading to new discoveries. Since HS-AFM can be combined with other techniques, such as super-resolution optical microscopy and optical tweezers, the usefulness of HS-AFM will be further expanded in the near future.

A Cryosectioning Technique for the Observation of Intracellular Structures and Immunocytochemistry of Tissues in Atomic Force Microscopy (AFM)

The use of cryosectioning facilitates the morphological analysis and immunocytochemistry of cells in tissues in atomic force microscopy (AFM). The cantilever can access all parts of a tissue sample in cryosections after the embedding medium (sucrose) has been replaced with phosphate-buffered saline (PBS), and this approach has enabled the production of a type of high-resolution image. The images resembled those obtained from freeze-etching replica electron microscopy (EM) rather than from thin-section EM. The AFM images showed disks stacked and enveloped by the cell membrane in rod photoreceptor outer segments (ROS) at EM resolution. In addition, ciliary necklaces on the surface of connecting cilium, three-dimensional architecture of synaptic ribbons, and the surface of the post-synaptic membrane facing the active site were revealed, which were not apparent using thin-section EM. AFM could depict the molecular binding of anti-opsin antibodies conjugated to a secondary fluorescent antibody bound to the disk membrane. The specific localization of the anti-opsin binding sites was verified through correlation with immunofluorescence signals in AFM combined with confocal fluorescence microscope. To prove reproducibility in other tissues besides retina, cryosectioning-AFM was also applied to elucidate molecular organization of sarcomere in a rabbit psoas muscle.

Catalytic robustness and torque generation of the F1-ATPase

The F₁-ATPase is the catalytic portion of the F_oF₁ ATP synthase and acts as a rotary molecular motor when it hydrolyzes ATP. Two decades have passed since the single-molecule rotation assay of F₁-ATPase was established. Although several fundamental issues remain elusive, basic properties of F-type ATPases as motor proteins have been well characterized, and a large part of the reaction scheme has been revealed by the combination of extensive structural, biochemical, biophysical, and theoretical studies. This review is intended to provide a concise summary of the fundamental features of F₁-ATPases, by use of the well-described model F₁ from the thermophilic Bacillus PS3 (TF₁). In the last part of this review, we focus on the robustness of the rotary catalysis of F₁-ATPase to provide a perspective on the re-designing of novel molecular machines.

Live-cell single-molecule labeling and analysis of myosin motors with quantum dots

Quantum dots (QDs) are a powerful tool for quantitative biology, but two challenges are associated with using them to track intracellular molecules in live cells. A simple and convenient method is presented for labeling intracellular molecules by using HaloTag technology and electroporation and is used to successfully track myosins within live cells.

Quantum dots (QDs) are a powerful tool for quantitatively analyzing dynamic cellular processes by single-particle tracking. However, tracking of intracellular molecules with QDs is limited by their inability to penetrate the plasma membrane and bind to specific molecules of interest. Although several techniques for overcoming these problems have been proposed, they are either complicated or inconvenient. To address this issue, in this study, we developed a simple, convenient, and nontoxic method for labeling intracellular molecules in cells using HaloTag technology and electroporation. We labeled intracellular myosin motors with this approach and tracked their movement within cells. By simultaneously imaging myosin movement and F-actin architecture, we observed that F-actin serves not only as a rail but also as a barrier for myosin movement. We analyzed the effect of insulin on the movement of several myosin motors, which have been suggested to regulate intracellular trafficking of the insulin-responsive glucose transporter GLUT4, but found no significant enhancement in myosin motor motility as a result of insulin treatment. Our approach expands the repertoire of proteins for which intracellular dynamics can be analyzed at the single-molecule level.