Direct long-term observation of kinesin processivity at low load

Two Tetrahymena kinesin-9 family members exhibit slow plus-end-directed motility in vitro

The kinesin-9 family comprises two subfamilies specific to ciliated eukaryotic cells, and has recently attracted considerable attention because of its importance in ciliary bending and formation. However, only scattered data are available on the motor properties of kinesin-9 family members; these properties have not been compared under identical experimental conditions using kinesin-9 motors from the same species. Here, we report the comprehensive motor properties of two kinesin-9 molecules of Tetrahymena thermophila, TtK9A (Kif9/Klp1 ortholog) and TtK9B1 (Kif6 ortholog), using microtubule-based in vitro assays, including single-motor and multi-motor assays and microtubule-stimulated ATPase assays. Both subfamilies exhibit microtubule plus-end-directed, extremely slow motor activity, both in single and multiple molecules. TtK9A shows lower processivity than TtK9B1. Our findings indicate that the considerable slow movement of kinesin-9 that corresponds to low ATP hydrolysis rates is a common feature of the ciliary kinesin-9 family.

Myosin-induced F-actin fragmentation facilitates contraction of actin networks

Mechanical forces play a crucial role in diverse physiological processes, such as cell migration, cytokinesis, and morphogenesis. The actin cytoskeleton generates a large fraction of the mechanical forces via molecular interactions between actin filaments (F-actins) and myosin motors. Recent studies have shown that the common tendency of actomyosin networks to contract into a smaller structure deeply involves F-actin buckling induced by motor activities, fragmentation of F-actins, and the force-dependent unbinding of cross-linkers that inter-connect F-actins. The fragmentation of F-actins was shown to originate from either buckling or tensile force from previous single-molecule experiments. While the role of buckling in network contraction has been studied extensively, to date, the role of tension-induced F-actin fragmentation in network contraction has not been investigated. In this study, we employed in vitro experiments and an agent-based computational model to illuminate when and how the tension-induced F-actin fragmentation facilitates network contraction. Our experiments demonstrated that F-actins can be fragmented due to tensile forces, immediately followed by catastrophic rupture and contraction of networks. Using the agent-based model, we showed that F-actin fragmentation by tension results in distinct rupture dynamics different from that observed in networks only with cross-linker unbinding. Moreover, we found that tension-induced F-actin fragmentation is particularly important for the contraction of networks with high connectivity. Results from our study shed light on an important regulator of the contraction of actomyosin networks which has been neglected. In addition, our results provide insights into the rupture mechanisms of polymeric network structures and bio-inspired materials.

A circle of life: platelet and megakaryocyte cytoskeleton dynamics in health and disease

Platelets are blood cells derived from megakaryocytes that play a central role in regulating haemostasis and vascular integrity. The microtubule cytoskeleton of megakaryocytes undergoes a critical dynamic reorganization during cycles of endomitosis and platelet biogenesis. Quiescent platelets have a discoid shape maintained by a marginal band composed of microtubule bundles, which undergoes remarkable remodelling during platelet activation, driving shape change and platelet function. Disrupting or enhancing this process can cause platelet dysfunction such as bleeding disorders or thrombosis. However, little is known about the molecular mechanisms underlying the reorganization of the cytoskeleton in the platelet lineage. Recent studies indicate that the emergence of a unique platelet tubulin code and specific pathogenic tubulin mutations cause platelet defects and bleeding disorders. Frequently, these mutations exhibit dominant negative effects, offering valuable insights into both platelet disease mechanisms and the functioning of tubulins. This review will highlight our current understanding of the role of the microtubule cytoskeleton in the life and death of platelets, along with its relevance to platelet disorders.

Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics

Nanorobots powered by designed DNA molecular motors on DNA origami platforms are vigorously pursued but still short of fully autonomous and sustainable operation, as the reported systems rely on manually operated or autonomous but bridge-burning molecular motors. Expanding DNA nanorobotics requires origami-based autonomous non-bridge-burning motors, but such advanced artificial molecular motors are rare, and their integration with DNA origami remains a challenge. Here, we report an autonomous non-bridge-burning DNA motor tailor-designed for a triangle DNA origami substrate. This is a translational bipedal molecular motor but demonstrates effective translocation on both straight and curved segments of a self-closed circular track on the origami, including sharp ~90° turns by a single hand-over-hand step. The motor is highly directional and attains a record-high speed among the autonomous artificial molecular motors reported to date. The resultant DNA motor-origami system, with its complex translational-rotational motion and big nanorobotic capacity, potentially offers a self-contained "seed" nanorobotic platform to automate or scale up many applications.

Motor generated torque drives coupled yawing and orbital rotations of kinesin coated gold nanorods

Kinesin motor domains generate impulses of force and movement that have both translational and rotational (torque) components. Here, we ask how the torque component influences function in cargo-attached teams of weakly processive kinesins. Using an assay in which kinesin-coated gold nanorods (kinesin-GNRs) translocate on suspended microtubules, we show that for both single-headed KIF1A and dimeric ZEN-4, the intensities of polarized light scattered by the kinesin-GNRs in two orthogonal directions periodically oscillate as the GNRs crawl towards microtubule plus ends, indicating that translocating kinesin-GNRs unidirectionally rotate about their short (yaw) axes whilst following an overall left-handed helical orbit around the microtubule axis. For orientations of the GNR that generate a signal, the period of this short axis rotation corresponds to two periods of the overall helical trajectory. Torque force thus drives both rolling and yawing of near-spherical cargoes carrying rigidly-attached weakly processive kinesins, with possible relevance to intracellular transport.

Torque generating properties of Tetrahymena ciliary three-headed outer-arm dynein

Eukaryotic cilia/flagella are cellular bio-machines that drive the movement of microorganisms. Molecular motor axonemal dyneins in the axoneme, which consist of an 9 + 2 arrangement of microtubules, play an essential role in ciliary beating. Some axonemal dyneins have been shown to generate torque coupled with the longitudinal motility of microtubules across an array of dyneins fixed to the coverglass surface, resulting in a corkscrew-like translocation of microtubules. In this study, we performed three-dimensional tracking of a microbead coated with axonemal outer-arm dyneins on a freely suspended microtubule. We found that microbeads coated with multiple outer-arm dyneins exhibited continuous right-handed helical trajectories around the microtubule. This unidirectional helical motion differs from that of other types of cytoplasmic dyneins, which exhibit bidirectional helical motility. We also found that, in an in vitro microtubule gliding assay, gliding microtubules driven by outer-arm dyneins tend to turn to the left, causing a curved path, suggesting that the outer-arm dynein itself is able to rotate on its own axis. Two types of torque generated by the axonemal dyneins, corresponding to the forces used to rotate the microtubule unidirectionally with respect to the long and short axes, may regulate ciliary beating with complex waveforms.

Anchoring geometry is a significant factor in determining the direction of kinesin-14 motility on microtubules

Kinesin-14 microtubule-based motors have an N-terminal tail attaching the catalytic core to its load and usually move towards microtubule minus ends, whilst most other kinesins have a C-terminal tail and move towards plus ends. Loss of conserved sequences external to the motor domain causes kinesin-14 to switch to plus-end motility, showing that an N-terminal attachment is compatible with plus-end motility. However, there has been no systematic study on the role of attachment position in minus-end motility. We therefore examined the motility of monomeric kinesin-14s differing only in their attachment point. We find that a C-terminal attachment point causes kinesin-14s to become plus-end-directed, with microtubule corkscrewing rotation direction and pitch in motility assays similar to that of kinesin-1, suggesting that both C-kinesin kinesins-14 and N-kinesin kinesin-1 share a highly conserved catalytic core function with an intrinsic plus-end bias. Thus, an N-terminal attachment is one of the requirements for minus-end motility in kinesin-14.

Cargo surface fluidity can reduce inter-motor mechanical interference, promote load-sharing and enhance processivity in teams of molecular motors

In cells, multiple molecular motors work together as teams to carry cargoes such as vesicles and organelles over long distances to their destinations by stepping along a network of cytoskeletal filaments. How motors that typically mechanically interfere with each other, work together as teams is unclear. Here we explored the possibility that purely physical mechanisms, such as cargo surface fluidity, may potentially enhance teamwork, both at the single motor and cargo level. To explore these mechanisms, we developed a three dimensional simulation of cargo transport along microtubules by teams of kinesin-1 motors. We accounted for cargo membrane fluidity by explicitly simulating the Brownian dynamics of motors on the cargo surface and considered both the load and ATP dependence of single motor functioning. Our simulations show that surface fluidity could lead to the reduction of negative mechanical interference between kinesins and enhanced load sharing thereby increasing the average duration of single motors on the filament. This, along with a cooperative increase in on-rates as more motors bind leads to enhanced collective processivity. At the cargo level, surface fluidity makes more motors available for binding, which can act synergistically with the above effects to further increase transport distances though this effect is significant only at low ATP or high motor density. Additionally, the fluid surface allows for the clustering of motors at a well defined location on the surface relative to the microtubule and the fluid-coupled motors can exert more collective force per motor against loads. Our work on understanding how teamwork arises in cargo-coupled motors allows us to connect single motor properties to overall transport, sheds new light on cellular processes, reconciles existing observations, encourages new experimental validation efforts and can also suggest new ways of improving the transport of artificial cargo powered by motor teams.

Characterization of the motility of monomeric kinesin-5/Cin8

Cin8, the Saccharomyces cerevisiae kinesin-5, has an essential role in mitosis. In in vitro motility assays, tetrameric and dimeric Cin8 constructs showed bidirectional motility in response to ionic strength or Cin8 motor density. However, whether property-switching directionality is present in a monomeric form of Cin8 is unknown. Here we engineered monomeric Cin8 constructs with and without the Cin8-specific ∼99 residues in the loop 8 domain and examined the directionality of these constructs using an in vitro polarity-marked microtubule gliding assay within the range of the motor density or ionic strength. We found that both monomeric constructs showed only plus end-directed activity over the ranges measured, which suggested that minus end-directed motility driven by Cin8 is necessary for at least dimeric forms. Using an in vitro microtubule corkscrewing assay, we also found that monomeric Cin8 corkscrewed microtubules around their longitudinal axes with a constant left-handed pitch. Overall, our results imply that plus-end-directed and left-handed motor activity comprise the intrinsic properties of the Cin8 motor domain as with other monomeric N-kinesins.

Drag-induced directionality switching of kinesin-5 Cin8 revealed by cluster-motility analysis

Directed active motion of motor proteins is a vital process in virtually all eukaryotic cells. Nearly a decade ago, the discovery of directionality switching of mitotic kinesin-5 motors challenged the long-standing paradigm that individual kinesin motors are characterized by an intrinsic directionality. The underlying mechanism, however, remains unexplained. Here, we studied clustering-induced directionality switching of the bidirectional kinesin-5 Cin8. Based on the characterization of single-molecule and cluster motility, we developed a model that predicts that directionality switching of Cin8 is caused by an asymmetric response of its active motion to opposing forces, referred to as drag. The model shows excellent quantitative agreement with experimental data obtained under high and low ionic strength conditions. Our analysis identifies a robust and general mechanism that explains why bidirectional motor proteins reverse direction in response to seemingly unrelated experimental factors including changes in motor density and molecular crowding, and in multimotor motility assays.

A kinetic dissection of the fast and superprocessive kinesin-3 KIF1A reveals a predominant one-head-bound state during its chemomechanical cycle

The kinesin-3 family contains the fastest and most processive motors of the three neuronal transport kinesin families, yet the sequence of states and rates of kinetic transitions that comprise the chemomechanical cycle and give rise to their unique properties are poorly understood. We used stopped-flow fluorescence spectroscopy and single-molecule motility assays to delineate the chemomechanical cycle of the kinesin-3, KIF1A. Our bacterially expressed KIF1A construct, dimerized via a kinesin-1 coiled-coil, exhibits fast velocity and superprocessivity behavior similar to WT KIF1A. We established that the KIF1A forward step is triggered by hydrolysis of ATP and not by ATP binding, meaning that KIF1A follows the same chemomechanical cycle as established for kinesin-1 and -2. The ATP-triggered half-site release rate of KIF1A was similar to the stepping rate, indicating that during stepping, rear-head detachment is an order of magnitude faster than in kinesin-1 and kinesin-2. Thus, KIF1A spends the majority of its hydrolysis cycle in a one-head-bound state. Both the ADP off-rate and the ATP on-rate at physiological ATP concentration were fast, eliminating these steps as possible rate-limiting transitions. Based on the measured run length and the relatively slow off-rate in ADP, we conclude that attachment of the tethered head is the rate-limiting transition in the KIF1A stepping cycle. Thus, KIF1A's activity can be explained by a fast rear-head detachment rate, a rate-limiting step of tethered-head attachment that follows ATP hydrolysis, and a relatively strong electrostatic interaction with the microtubule in the weakly bound post-hydrolysis state.

A bio-pen for direct writing of single molecules on user-functionalized surfaces

Advancing ultrahigh resolution (below 10 nm) direct writing technologies could lead to impacts in areas as diverse as disease detection, genetic analysis and nanomanufacturing. Current methods based on electron-beams and photo- or dip-pen nanolithography are laborious and lack flexibility when aiming to create single molecule patterns for application specific integration. We hypothesize that a novel strategy could be developed to allow for writing of parallel and yet individually addressable patterns of single molecules on user-controlled surfaces. The strategy is based on using in vitro self-recognition of tubulin protein to assemble rigid protofilaments of microtubules, with one such microtubule to be subsequently used as a "bio-pen" capable of writing "inks" of single kinesin molecules in user-defined environments. Our results show that single kinesin inks could be written under the energy of adenosine triphosphate hydrolysis and observed by both atomic force and optical microscopy. Upon extending ink functionalities, the integration of soft and hard materials for nanostructure assembly and complex single molecule pattern formation is envisioned.

Circular orientation fluorescence emitter imaging (COFEI) of rotational motion of motor proteins

Single-molecule fluorescence polarization technique has been utilized to detect structural changes in biomolecules and intermolecular interactions. Here we developed a single-molecule fluorescence polarization measurement system, named circular orientation fluorescence emitter imaging (COFEI), in which a ring pattern of an acquired fluorescent image (COFEI image) represents an orientation of a polarization and a polarization factor. Rotation and pattern change of the COFEI image allow us to find changes in the polarization by eye and further values of the parameters of a polarization are determined by simple image analysis with high accuracy. We validated its potential applications of COFEI by three assays: 1) Detection of stepwise rotation of F₁-ATPase via single quantum nanorod attached to the rotary shaft γ; 2) Visualization of binding of fluorescent ATP analog to the catalytic subunit in F₁-ATPase; and 3) Association and dissociation of one head of dimeric kinesin-1 on the microtubule during its processive movement through single bifunctional fluorescent probes attached to the head. These results indicate that the COFEI provides us the advantages of the user-friendly measurement system and persuasive data presentations.

Unbinding of Kinesin from Microtubule in the Strongly Bound States Enhances under Assisting Forces

The ability to predict the cellular dynamics of intracellular transport has enormous potential to impact human health. A key transporter is kinesin-1, an ATP-driven molecular motor that shuttles cellular cargos along microtubules (MTs). The dynamics of kinesins depends critically on their unbinding rate from MT, which varies depending on the force direction applied on the motor, i.e. the force-unbinding rate relation is asymmetric. However, it remains unclear how changing the force direction from resisting (applied against the motion direction) to assisting (applied in the motion direction) alters the kinesin's unbinding and stepping. Here, we propose a theoretical model for the influence of the force direction on the stepping dynamics of a single kinesin. The model shows that the asymmetry of the force-unbinding rate relation is independent of ATP concentration. It also reveals that the synthesis of ATP from backward stepping under assisting forces is less likely than under resisting forces. It then finds that the unbinding of kinesin in the strongly MT-bound kinetic states enhances under assisting forces.

Quantitative Determination of the Probability of Multiple-Motor Transport in Bead-Based Assays

With their longest dimension typically being less than 100 nm, molecular motors are significantly below the optical-resolution limit. Despite substantial advances in fluorescence-based imaging methodologies, labeling with beads remains critical for optical-trapping-based investigations of molecular motors. A key experimental challenge in bead-based assays is that the number of motors on a bead is not well defined. Particularly for single-molecule investigations, the probability of single- versus multiple-motor events has not been experimentally investigated. Here, we used bead travel distance as an indicator of multiple-motor transport and determined the lower-bound probability of bead transport by two or more motors. We limited the ATP concentration to increase our detection sensitivity for multiple- versus single-kinesin transport. Surprisingly, for all but the lowest motor number examined, our measurements exceeded estimations of a previous model by ≥2-fold. To bridge this apparent gap between theory and experiment, we derived a closed-form expression for the probability of bead transport by multiple motors, and constrained the only free parameter in this model using our experimental measurements. Our data indicate that kinesin extends to ∼57 nm during bead transport, suggesting that kinesin exploits its conformational flexibility to interact with microtubules at highly curved interfaces such as those present for vesicle transport in cells. To our knowledge, our findings provide the first experimentally constrained guide for estimating the probability of multiple-motor transport in optical trapping studies. The experimental approach utilized here (limiting ATP concentration) may be generally applicable to studies in which molecular motors are labeled with cargos that are artificial or are purified from cellular extracts.

Torque generation by axonemal outer-arm dynein

Outer-arm dynein is the main engine providing the motive force in cilia. Using three-dimensional tracking microscopy, we found that contrary to previous reports Tetrahymena ciliary three-headed outer-arm dynein (αβγ) as well as proteolytically generated two-headed (βγ) and one-headed (α) subparticles showed clockwise rotation of each sliding microtubule around its longitudinal axis in microtubule corkscrewing assays. By measuring the rotational pitch as a function of ATP concentration, we also found that the microtubule corkscrewing pitch is independent of ATP concentration, except at low ATP concentrations where the pitch generated by both three-headed αβγ and one-headed α exhibited significantly longer pitch. In contrast, the pitch driven by two-headed βγ did not display this sensitivity. In the assays on lawns containing mixtures of α and βγ at various ratios, the corkscrewing pitch increased dramatically in a nonlinear fashion as the ratio of α in the mixture increased. Even small proportions of α-subparticle could significantly increase the corkscrewing pitch of the mixture. Our data show that torque generation does not require the three-headed outer-arm dynein (αβγ) but is an intrinsic property of the subparticles of axonemal dyneins and also suggest that each subparticle may have distinct mechanical properties.

A self-powered kinesin-microtubule system for smart cargo delivery

A smart self-powered cargo delivery system that is composed of creatine phosphate kinase (CPK) microspheres, kinesins and microtubules is demonstrated. The CPK microsphere not only acts as an ATP generation and buffering system, but also as a carrier for cargo transport, thus realizing the easy loading and self-powered delivery of cargos at the same time.

Computational modeling of kinesin stepping

Kinesin is a walking motor protein that shuttles cellular cargoes along microtubules (MTs). This protein is considered as an information processor capable of sensing cellular inputs and transforming them into mechanical steps. Here, we propose a computational model to describe the mechanochemical kinetics underlying forward and backward stepping behavior of kinesin motor as a digital circuit designed based on an adenosine triphosphate (ATP)-driven finite state machine. Kinetic analysis suggests that the backward stepping of kinesin is mainly driven by ATP hydrolysis, whereas ATP synthesis rises the duration of this stepping. It is shown that kinesin pausing due to waiting for ATP binding at limiting ATP concentration ([ATP]) and low backward loads could be longer than that caused by low rate of ATP synthesis under high backward loads. These findings indicate that the pausing duration of kinesin in MT-bound (M·K) kinetic state is affected by [ATP], which in turn affects its velocity at fixed loads. We show that the proposed computational model accurately simulates the forward and backward stepping behavior of kinesin motor under different [ATP] and loads.

A stochastic automaton model for simulating kinesin processivity

MOTIVATION

Cellular interactions of kinesin-1, an adenosine triphosphate (ATP)-driven motor protein capable of undergoing multiple steps on a microtubule (MT), affect its mechanical processivity, the number of steps taken per encounter with MT. Even though the processivity of kinesin has been widely studied, a detailed study of the factors that affect the stepping of the motor along MT is still lacking.

RESULTS

We model the cellular interactions of kinesin as a probabilistic timed automaton and use the model to simulate the mechanical processivity of the motor. Theoretical analysis suggests: (i) backward stepping tends to be powered by ATP hydrolysis, rather than ATP synthesis, (ii) backward stepping powered by ATP synthesis is more likely to happen with limiting ATP concentration ([ATP]) at high loads and (iii) with increasing load the frequency of backward stepping powered by ATP hydrolysis at high [ATP] is greater than that powered by ATP synthesis at limiting [ATP]. Together, the higher frequency of backward stepping powered by ATP hydrolysis than by ATP synthesis is found to be a reason for the more dramatic falling of kinesin processivity with rising load at high [ATP] compared with that at low [ATP]. Simulation results further show that the processivity of kinesin can be determined by the number of ATP hydrolysis and synthesis kinetic cycles taken by the motor before becoming inactive. It is also found that the duration of a backward stepping cycle at high loads is more likely to be less than that of a forward stepping cycle.

CONTACT

h.r.khataee@griffithuni.edu.au or a.liew@griffith.edu.au.

Kinesin-8 is a low-force motor protein with a weakly bound slip state

During the cell cycle, kinesin-8s control the length of microtubules by interacting with their plus ends. To reach these ends, the motors have to be able to take many steps without dissociating. However, the underlying mechanism for this high processivity and how stepping is affected by force are unclear. Here, we tracked the motion of yeast (Kip3) and human (Kif18A) kinesin-8s with high precision under varying loads using optical tweezers. Surprisingly, both kinesin-8 motors were much weaker compared with other kinesins. Furthermore, we discovered a force-induced stick-slip motion: the motor frequently slipped, recovered from this state, and then resumed normal stepping motility without detaching from the microtubule. The low forces are consistent with kinesin-8s being regulators of microtubule dynamics rather than cargo transporters. The weakly bound slip state, reminiscent of a molecular safety leash, may be an adaptation for high processivity.

A mathematical model describing the mechanical kinetics of kinesin stepping

MOTIVATION

Kinesin is a smart motor protein that steps processively forward and backward along microtubules (MTs). The mechanical kinetics of kinesin affecting its stepping behavior is not fully understood. Here, we propose a mathematical model to study the mechanical kinetics of forward and backward stepping of kinesin motor based on the four-state discrete stochastic model of the motor.

RESULTS

Results show that the probabilities of forward and backward stepping can be modeled using the mean probabilities of forward and backward kinetic transitions, respectively. We show that the backward stepping of kinesin motor starts when the probability of adenosine diphosphate (ADP) binding to the motor is much higher than that of adenosine triphosphate (ATP) binding. Furthermore, our results indicate that the backward stepping is related to both ATP hydrolysis and synthesis with rate limiting factor being ATP synthesis. Low rate of ATP synthesis under high backward loads above 10 pN is also suggested as a reason for the detachment of kinesin motor from MT in the kinetic state MTċKinesinċADPċPi.

AVAILABILITY AND IMPLEMENTATION

The code for this work is written in Visual C# and is available by request from the authors.

Revealing nature's synthetic potential through the study of ribosomal natural product biosynthesis

Ribosomally synthesized posttranslationally modified peptides (RiPPs) are a rapidly growing class of natural products with diverse structures and activities. In recent years, a great deal of progress has been made in elucidating the biosynthesis of various RiPP family members. As with the study of nonribosomal peptide and polyketide biosynthetic enzymes, these investigations have led to the discovery of entirely new biological chemistry. With each unique enzyme investigated, a more complex picture of Nature's synthetic potential is revealed. This Review focuses on recent reports (since 2008) that have changed the way that we think about ribosomal natural product biosynthesis and the enzymology of complex bond-forming reactions.

Tuning multiple motor travel via single motor velocity

Microtubule-based molecular motors often work in small groups to transport cargos in cells. A key question in understanding transport (and its regulation in vivo) is to identify the sensitivity of multiple-motor-based motion to various single molecule properties. Whereas both single-motor travel distance and microtubule binding rate have been demonstrated to contribute to cargo travel, the role of single-motor velocity is yet to be explored. Here, we recast a previous theoretical study, and make explicit a potential contribution of velocity to cargo travel. We test this possibility experimentally, and demonstrate a strong negative correlation between single-motor velocity and cargo travel for transport driven by two motors. Our study thus discovers a previously unappreciated role of single-motor velocity in regulating multiple-motor transport.

Reconstructing the free-energy landscape associated to molecular motors processivity

We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and considers the presence of a competitive inhibition reaction by ADP. We first reconstruct a continuous free-energy landscape of the cycle catalyst process that allows us to calculate the number of steps given by a single molecular motor. Then, we calculate an analytical expression associated to the translational velocity and the stopping time of the molecular motor in terms of time and ATP concentration. An energetic interpretation of motor processivity is discussed in quantitative form by using experimental data. We also predict a time duration of collective processes that agrees with experimental reports.

Nanoscale localization sampling based on nanoantenna arrays for super-resolution imaging of fluorescent monomers on sliding microtubules

Sub-diffraction-limited imaging of fluorescent monomers on sliding microtubules in vitro by nanoscale localization sampling (NLS) is reported. NLS is based on periodic nanohole antenna arrays that create locally amplified electromagnetic hot spots through surface plasmon localization. The localized near-field hot spot temporally samples microtubular movement for enhanced spatial resolution. A fourfold improvement in spatial resolution compared to conventional wide-field microscopy is demonstrated. The resolution enhancement is achieved by imaging rhodamine-labeled microtubules that are sampled by the hot spots to provide sub-diffraction-limited images at 76 nm resolution in the direction of movement and 135 nm orthogonally. The intensity distribution produced by the NLS is measured to be broader than that of conventional imaging, which is consistent with the improvement of imaging resolution. Correlation studies between neighboring nanoantennas are also performed. This confirms the possibility of measuring microtubular transport dynamics. NLS can be useful for moving objects that have a high labeling density or for performing fluctuation spectroscopy in small volumes, and may allow "super-resolution on demand" by customizing nanoantenna structures for specific resolution needs.

Neck-linker docking coordinates the kinetics of kinesin's heads

Conventional kinesin is a two-headed homodimeric motor protein, which is able to walk along microtubules processively by hydrolyzing ATP. Its neck linkers, which connect the two motor domains and can undergo a docking/undocking transition, are widely believed to play the key role in the coordination of the chemical cycles of the two motor domains and, consequently, in force production and directional stepping. Although many experiments, often complemented with partial kinetic modeling of specific pathways, support this idea, the ultimate test of the viability of this hypothesis requires the construction of a complete kinetic model. Considering the two neck linkers as entropic springs that are allowed to dock to their head domains, and incorporating only the few most relevant kinetic and structural properties of the individual heads, we develop here the first, to our knowledge, detailed, thermodynamically consistent model of kinesin that can 1), explain the cooperation of the heads (including their gating mechanisms) during walking, and 2), reproduce much of the available experimental data (speed, dwell-time distribution, randomness, processivity, hydrolysis rate, etc.) under a wide range of conditions (nucleotide concentrations, loading force, neck-linker length and composition, etc.). Besides revealing the mechanism by which kinesin operates, our model also makes it possible to look into the experimentally inaccessible details of the mechanochemical cycle and predict how certain changes in the protein affect its motion.

Nucleotide-dependent behavior of single molecules of cytoplasmic dynein on microtubules in vitro

We visualized the nucleotide-dependent behavior of single molecules of mammalian native cytoplasmic dynein using fragments of dynactin p150 with or without its N-terminal microtubule binding domain. The results indicate that the binding affinity of dynein for microtubules is high in AMP-PNP, middle in ADP or no nucleotide, and low in ADP.Pi conditions. It is also demonstrated that the microtubule binding domain of dynactin p150 maintains the association of dynein with microtubules without altering the motile property of dynein in the weak binding state. In addition, we observed bidirectional movement of dynein in the presence of ATP as well as in ADP/Vi condition, suggesting that the bidirectional movement is driven by diffusion rather than active transport.

Novel ways to determine kinesin-1's run length and randomness using fluorescence microscopy

The molecular motor protein Kinesin-1 drives intracellular transport of vesicles, by binding to microtubules and making hundreds of consecutive 8-nm steps along them. Three important parameters define the motility of such a linear motor: velocity, run length (the average distance traveled), and the randomness (a measure of the stochasticity of stepping). We used total internal reflection fluorescence microscopy to measure these parameters under conditions without external load acting on the motor. First, we tracked the motility of single motor proteins at different adenosine triphosphate (ATP) concentrations and determined both velocity and (for the first time, to our knowledge, by using single-molecule fluorescence assays) randomness. We show that the rate of Kinesin-1 at zero load is limited by two or more exponentially distributed processes at high ATP concentrations, but that an additional, ATP-dependent process becomes the sole rate-limiting process at low ATP concentrations. Next, we measured the density profile of moving Kinesin-1 along a microtubule. This allowed us to determine the average run length in a new way, without the need to resolve single-molecules and to correct for photobleaching. At saturating ATP concentration, we measured a run length of 1070 +/- 30 nm. This value did not significantly change for different ATP concentrations.

Obstacles on the microtubule reduce the processivity of Kinesin-1 in a minimal in vitro system and in cell extract

Inside cells, a multitude of molecular motors and other microtubule-associated proteins are expected to compete for binding to a limited number of binding sites available on microtubules. Little is known about how competition for binding sites affects the processivity of molecular motors and, therefore, cargo transport, organelle positioning, and microtubule organization, processes that all depend on the activity of more or less processive motors. Very few studies have been performed in the past to address this question directly. Most studies reported only minor effects of crowding on the velocity of motors. However, a controversy appears to exist regarding the effect of crowding on motor processivity. Here, we use single-molecule imaging of mGFP-labeled minimal dimeric kinesin-1 constructs in vitro to study the effects of competition on kinesin's processivity. For competitors, we use kinesin rigor mutants as static roadblocks, minimal wild-type kinesins as motile obstacles, and a cell extract as a complex mixture of microtubule-associated proteins. We find that mGFP-labeled kinesin-1 detaches prematurely from microtubules when it encounters obstacles, leading to a strong reduction of its processivity, a behavior that is largely independent of the type of obstacle used here. Kinesin has a low probability to wait briefly when encountering roadblocks. Our data suggest, furthermore, that kinesin can occasionally pass obstacles on the protofilament track.

Diffusive movement of processive kinesin-1 on microtubules

The processive motor kinesin-1 moves unidirectionally toward the plus end of microtubules. This process can be visualized by total internal reflection fluorescence microscopy of kinesin bound to a carboxylated quantum dot (Qdot), which acts both as cargo and label. Surprisingly, when kinesin is bound to an anti-HIS Qdot, it shows diffusive movement on microtubules, which decreased in favor of processive runs with increasing salt concentration. This observation implies that kinesin movement on microtubules is governed by its conformation, as it is well established that kinesin undergoes a salt-dependent transition from a folded (inactive) to an extended (active) molecule. A truncated kinesin lacking the last 75 amino acids (kinesin-Delta C) showed both processive and diffusive movement on microtubules. The extent of each behavior depends on the relative amounts of ADP and ATP, with purely diffusive movement occurring in ADP alone. Taken together, these data imply that folded kinesin.ADP can exist in a state that diffuses along the microtubule lattice without expending energy. This mechanism may facilitate the ability of kinesin to pick up cargo, and/or allow the kinesin/cargo complex to stay bound after encountering obstacles.

The processivity of kinesin-2 motors suggests diminished front-head gating

Kinesin-2 motors, which are involved in intraflagellar transport and cargo transport along cytoplasmic microtubules, differ from motors in the canonical kinesin-1 family by having a heterodimeric rather than homodimeric structure and possessing a three amino acid insertion in their neck linker domain. To determine how these structural features alter the chemomechanical coupling in kinesin-2, we used single-molecule bead experiments to measure the processivity and velocity of mouse kinesin-2 heterodimer (KIF3A/B) and the engineered homodimers KIF3A/A and KIF3B/B and compared their behavior to Drosophila kinesin-1 heavy chain (KHC). Single-motor run lengths of kinesin-2 were 4-fold shorter than those of kinesin-1. Extending the kinesin-1 neck linker by three amino acids led to a similar reduction in processivity. Furthermore, kinesin-2 processivity varied inversely with ATP concentration. Stochastic simulations of the kinesin-1 and kinesin-2 hydrolysis cycles suggest that "front-head gating," in which rearward tension prevents ATP binding to the front head when both heads are bound to the microtubule, is diminished in kinesin-2. Because the mechanical tension that underlies front-head gating must be transmitted through the neck linker domains, we propose that the diminished coordination in kinesin-2 is a result of its longer and, hence, more compliant neck linker element.

Complexity of mitochondrial dynamics in neurons and its control by ADP produced during synaptic activity

This review focuses on different aspects of dynamics of mitochondria in neuronal cytoplasm which play an important role in the life and fate of neurons. It starts with description of the energy supply in the brain; considers the typical patterns of mitochondrial movements; relates them to the neuronal activity and in particular at the synapses; extends to the analysis of the origin of local ATP changes in the cytoplasm; considers main features of motor-assisted movements of mitochondria and their role in determining a transport velocity; describes the measurements of ATP gradients in neuronal processes and relates them to spatial variations in the mobility of mitochondria that occur in the vicinity of synapses due to the local ADP increases; considers the influence of hypoxia and intracellular signalling pathways on mitochondria movements. Finally, the recent views on the mechanisms and possible functional role of mitochondrial network as a whole in neurons are discussed and unresolved issues and future perspectives in this field of research are delineated.

Direction and speed of microtubule movements driven by kinesin motors arranged on catchin thick filaments

Conventional kinesin (Kinesin-1) is a microtubule-based molecular motor that supports intracellular vesicle/organelle transport in various eukaryotic cells. To arrange kinesin motors similarly to myosin motors on thick filaments in muscles, the motor domain of rat conventional kinesin (amino acid residues 1-430) fused to the C-terminal 829 amino acid residues of catchin (KHC430Cat) was bacterially expressed and attached to catchin filaments that can attach to and arrange myosin molecules in a bipolar manner on their surface. Unlike the case of myosin where actin filaments move toward the center much faster than in the opposite direction along the catchin filaments, microtubules moved at the same speed in both directions. In addition, many microtubules moved across the filaments at the same speed with various angles between the axes of the microtubule and catchin filament. Kinesin/catchin chimera proteins with a shorter kinesin neck domain were also prepared. Those without the whole hinge 1 domain and the C-terminal part of the neck helix moved microtubules toward the center of the catchin filaments significantly, but only slightly, faster than in the opposite direction, although the movements in both directions were slower than those of the KHC430Cat construct. The results suggest that kinesin has substantial mechanical flexibility within the motor domain, possibly within the neck linker, enabling its interaction with microtubules having any orientation.

Modeling motility of the kinesin dimer from molecular properties of individual monomers

Conventional kinesin is a homodimeric motor protein that unidirectionally transports organelles along filamentous microtubule (MT) by hydrolyzing ATP molecules. There remain two central questions in biophysical studies of kinesin: (1) the molecular physical mechanism by which the kinesin dimer, made of two sequentially identical monomers, selects a unique direction (MT plus end) for long-range transport and (2) the detailed mechanisms by which local molecular properties of individual monomers affect the motility properties of the dimer motor as a whole. On the basis of a previously proposed molecular physical model for the unidirectionality of kinesin, this study investigates the synergic motor performance of the dimer from well-defined molecular properties of individual monomers. During cargo transportation and also in single-molecule mechanical measurements, a load is often applied to the coiled-coil dimerization domain linking the two motor domains ("heads"). In this study, the share of load directly born by each head is calculated, allowing for an unambiguous estimation of load effects on the ATP turnover and random diffusion of individual heads. The results show that the load modulations of ATP turnover and head diffusion are both essential in determining the performance of the dimer under loads. It is found that the consecutive run length of the dimer critically depends upon a few pathways, leading to the detachment of individual heads from MT. Modifying rates for these detachment pathways changes the run length but not the velocity of the dimer, consistent with mutant experiments. The run length may increase with or without the ATP concentration, depending upon a single rate for pure mechanical detachment. This finding provides an explanation to a previous controversy concerning ATP dependence of the run length, and related quantitative predictions of this study can be tested by a future experiment. This study also finds that the experimental observations for assisting loads can be quantitatively explained by load-biased head diffusion. We thus conclude that the dimer motility under resisting as well as assisting loads is governed by essentially the same mechanisms.

ADP regulates movements of mitochondria in neurons

Mitochondria often reside in subcellular regions with high metabolic demands. We examined the mechanisms that can govern the relocation of mitochondria to these sites in respiratory neurons. Mitochondria were visualized using tetramethylrhodamineethylester, and their movements were analyzed by applying single-particle tracking. Intracellular ATP ([ATP](i)) was assessed by imaging the luminescence of luciferase, the fluorescence of the ATP analog TNP-ATP, and by monitoring the activity of K(ATP) channels. Directed movements of mitochondria were accompanied by transient increases in TNP-ATP fluorescence. Application of glutamate and hypoxia reversibly decreased [ATP](i) levels and inhibited the directed transport. Injections of ATP did not rescue the motility of mitochondria after its inhibition by hypoxia. Introduction of ADP suppressed mitochondrial movements and occluded the effects of subsequent hypoxia. Mitochondria decreased their velocity in the proximity of synapses that correlated with local [ATP](i) depletions. Using a model of motor-assisted transport and Monte Carlo simulations, we showed that mitochondrial traffic is more sensitive to increases in [ADP](i) than to [ATP](i) depletions. We propose that consumption of synaptic ATP can produce local increases in [ADP](i) and facilitate the targeting of mitochondria to synapses.

Dynactin Enhances the Processivity of Kinesin-2

Kinesin-2 is a major microtubule-based motor in most cell types. Its in vitro motile properties have been analyzed extensively and been found to differ considerably from kinesin-1. Although recombinant kinesin-2 heterodimers exhibit processive movement, the processivity of the native kinesin-2 holoenzyme has never been evaluated. Kinesin-2 can interact with dynactin, a 'processivity factor' for cytoplasmic dynein, which may alter its motile properties. In this study, we analyze the in vitro motility of single native kinesin-2 molecules and determine the effects of dynactin on motor processivity. We find that individual native kinesin-2 molecules travel processively. Dynactin has no effect on velocity but significantly increases the run length of kinesin-2 movements. These results show that the interaction with dynactin has important functional consequences on the activity of the kinesin-2 motor.

Mechanochemical couplings of kinesin motors

Kinesins are molecular motors capable of moving processively along microtubule in a stepwise manner by hydrolyzing ATP. Numerous experimental results on various aspects of their dynamical behaviours are available in literature. Although a number of models of tightly coordinated mechanism have been proposed to explain some experimental results, up to now no good explanation has been given to all these experimental results by using a single model. We have recently proposed such a model of partially coordinated hand-over-hand moving mechanism. In this paper, we use this model to study in detail various aspects of the dynamical properties of single kinesin molecules. We show that kinesin dimers walk hand-over-hand along microtubules in a partially coordinated rather than a tightly coordinated manner. The degree of coordination depends on the ratio of the two heads' ATPase rates that are in turn determined by both internal elastic force and external load. We have tested this model using various available experimental results on different samples and obtained a good agreement between the theory and the experiments.

Processivity of kinesin motility is enhanced on increasing temperature

Kinesin is a motor protein that processively moves step by step along a microtubule. To investigate the effects of temperature on run length, i.e., processivity of kinesin motility, we performed a single-molecular bead assay at temperature range of 20–40°C. An increase in the walking velocity of kinesin corresponded to the Arrhenius activation enthalpy of 48 kJ/mol, being consistent with the previous reports. Here, we found that the run length increased, that is, the kinesin processivity enhanced with increasing temperature. Then, we estimated the probability of detachment of kinesin from a microtubule per one 8-nm stepping event, and found that it diminishes from 0.014 to 0.006/step with increasing temperature from 20 to 40°C. And we noticed that prolonged incubation at 30, 35 and 40°C significantly slowed down the walking velocity, but further increased the run length and duration. Those results are interpreted according to the effect of temperature on the rate constants of some key kinetic steps in the ATPase cycle.

Microtubule-binding properties of dynactin p150 expedient for dynein motility

Dynactin is a hetero-oligomeric protein complex that has an important role in dynein-based intracellular transport. The expressed N-terminal fragments of dynactin p150 bound to microtubules in the ratio of one to one tubulin dimer, independent from the binding of dynein stalk head. Single molecule observation revealed that these fragments moved around on microtubules by Brownian motion. When the dynein-dynactin complex moves on microtubules, p150 can support dynein to maintain contact with microtubules and does not interfere with the motility of dynein, and thus, the dynein-dynactin complex can efficiently achieve long-distance carriage of the cargo.

Processive movement of single kinesins on crowded microtubules visualized using quantum dots

Kinesin-1 is a processive molecular motor transporting cargo along microtubules. Inside cells, several motors and microtubule-associated proteins compete for binding to microtubules. Therefore, the question arises how processive movement of kinesin-1 is affected by crowding on the microtubule. Here we use total internal reflection fluorescence microscopy to image in vitro the runs of single quantum dot-labelled kinesins on crowded microtubules under steady-state conditions and to measure the degree of crowding on a microtubule at steady-state. We find that the runs of kinesins are little affected by high kinesin densities on a microtubule. However, the presence of high densities of a mutant kinesin that is not able to step efficiently reduces the average speed of wild-type kinesin, while hardly changing its processivity. This indicates that kinesin waits in a strongly bound state on the microtubule when encountering an obstacle until the obstacle unbinds and frees the binding site for kinesin's next step. A simple kinetic model can explain quantitatively the behaviour of kinesin under both crowding conditions.

Millimeter Scale Alignment of Magnetic Nanoparticle Functionalized Microtubules in Magnetic Fields

The conjugation of 14 nm diameter CoFe2O4 nanoparticles to the surface of biotinylated microtubules enables their manipulation with externally applied magnetic fields of small, permanent NdFeB magnets. Microtubules are selectively patterned on kinesin motor-modified glass surfaces in coparallel arrays that mimic the orientation of the magnetic field lines over millimeter distances. The magnetic field is simultaneously used to increase surface loading of microtubules. We demonstrate that motility across the kinesin motor surface is retained following magnetic functionalization of the microtubules, while gliding speed is dependent on loading level of the neutravidin linker as well as magnetic nanoparticles.

A torque component in the kinesin-1 power stroke

Kinesin-1 is a twin-headed molecular motor that moves along microtubules in 8-nm steps, using a walking action in which the two heads interact alternately with the microtubule. Constructs with only one head can also produce impulses of force and motion, indicating that the walking action is an amplification strategy that leverages an underlying force-generating event. Recent work suggests that directional force is produced either by directionally biased selection of microtubule binding sites or by a conformational change subsequent to the binding event. We report here that surface-attached rat kinesin-1 monomers drive counterclockwise rotation of sliding microtubules around their axes, and that by manipulating the assay geometry, we could reduce or block the torsional motion with negligible effects on the axial motion. We can account for this behavior on the simple assumption that kinesin heads tend to bind to the closest available tubulin heterodimer in the lattice, but only in the case where an additional biasing process is present that shifts the start position for diffusion-to-capture toward the microtubule plus end by approximately 1 nm.

A high-speed atomic force microscope for studying biological macromolecules in action

The atomic force microscope (AFM), which was invented by Binnig et al. in 1986, can image at nanometer resolution individual biological macromolecules on a substrate in solution. This unique capability awoke an expectation of imaging processes occurring in biological macromolecules at work. However, this expectation was not met, because the imaging rate with available AFMs was too low to capture biological processes. This expectation has at last been realized by the high-speed AFM developed by our research group at Kanazawa University. In this article, after a brief review of the development of our apparatus, its recent advancement and imaging data obtained with motor proteins are presented.

Single-molecule fluorescence spectroscopy and microscopy of biomolecular motors

The methods of single-molecule fluorescence spectroscopy and microscopy have been recently utilized to explore the mechanism of action of several members of the kinesin and myosin biomolecular motor protein families. Whereas ensemble averaging is removed in single-molecule studies, heterogeneity in the behavior of individual motors can be directly observed, without synchronization. Observation of translocation by individual copies of motor proteins allows analysis of step size, rate, pausing, and other statistical properties of the process. Polarization microscopy as a function of nucleotide state has been particularly useful in revealing new and highly rotationally mobile forms of particular motors. These experiments complement X-ray and biochemical studies and provide a detailed view into the local dynamical behavior of motor proteins.