Kinesin walks hand-over-hand

Tension-induced suppression of allosteric conformational changes coordinates kinesin-1 stepping

Kinesin-1 walks along microtubules by alternating ATP hydrolysis and movement of its two motor domains ("head"). The detached head preferentially binds to the forward tubulin-binding site after ATP binds to the microtubule-bound head, but the mechanism preventing premature microtubule binding while the partner head awaits ATP remains unknown. Here, we examined the role of the neck linker, the segment connecting two heads, in this mechanism. Structural analyses of the nucleotide-free head revealed a bulge just ahead of the neck linker's base, creating an asymmetric constraint on its mobility. While the neck linker can stretch freely backward, it must navigate around this bulge to extend forward. We hypothesized that increased neck linker tension suppresses premature binding of the tethered head, which was supported by molecular dynamics simulations and single-molecule fluorescence assays. These findings demonstrate a tension-dependent allosteric mechanism that coordinates the movement of two heads, where neck linker tension modulates the allosteric conformational changes rather than directly affecting the nucleotide state.

Factors Determining Kinesin Motors in a Predominant One-Head-Bound or Two-Heads-Bound State During Its Stepping Cycle

At physiological or saturating ATP concentrations, some families of kinesin motors, such as kinesin-1 and kinesin-2, exhibit a predominant two-heads-bound (2HB) state during their stepping cycle on microtubules, while others, such as kinesin-3, exhibit a predominant one-head-bound (1HB) state. An interesting but unclear issue is what factors determine a kinesin motor in the predominant 1HB and 2HB states. Here, on the basis of the general chemomechanical pathway of the kinesin motors, a theory is given on fractions of 1HB and 2HB states. With the theory, the factors affecting a kinesin motor in the predominant 1HB and 2HB states are determined. The results about the effects of ATP concentration, ADP concentration and external load on the fractions of 1HB and 2HB states are presented. Furthermore, the theory is applied to kinesin-1, kinesin-2, kinesin-3, kinesin-5 and kinesin-13 motors, with the theoretical results agreeing well with published experimental data.

Kinetic regulation of kinesin's two motor domains coordinates its stepping along microtubules

The two identical motor domains (heads) of dimeric kinesin-1 move in a hand-over-hand process along a microtubule, coordinating their ATPase cycles such that each ATP hydrolysis is tightly coupled to a step and enabling the motor to take many steps without dissociating. The neck linker, a structural element that connects the two heads, has been shown to be essential for head-head coordination; however, which kinetic step(s) in the chemomechanical cycle is 'gated' by the neck linker remains unresolved. Here, we employed pre-steady-state kinetics and single-molecule assays to investigate how the neck-linker conformation affects kinesin's motility cycle. We show that the backward-pointing configuration of the neck linker in the front kinesin head confers higher affinity for microtubule, but does not change ATP binding and dissociation rates. In contrast, the forward-pointing configuration of the neck linker in the rear kinesin head decreases the ATP dissociation rate but has little effect on microtubule dissociation. In combination, these conformation-specific effects of the neck linker favor ATP hydrolysis and dissociation of the rear head prior to microtubule detachment of the front head, thereby providing a kinetic explanation for the coordinated walking mechanism of dimeric kinesin.

Dual-mode, regenerated DNA motor for simultaneous detection of viral gene fragments and diagnosis of infectious disease

This study presents a dual-mode and regenerated DNA motor powered by exonuclease III (Exo III) for the simultaneous detection of viral gene fragments. The detection methodology is categorized into two distinct operational modes. The first mode emphasizes the simultaneous detection of two viral gene fragments from a specific virus. The presence of both genes triggers the operation of the DNA motor, generating a singular signal output. This mode operates on an "AND" logical mechanism, which enhances the precision of positive case identification. The second mode facilitates the simultaneous detection of three viral gene fragments from three different viruses within a single assay. The presence of these genes activates their respective motors, yielding distinct signal outputs. This mode supports the multiplex detection of three target genes, thereby aiding in the identification of previously uncharacterized viruses infecting patients and alleviating the logistical and financial burdens associated with multiple testing procedures. The detection limit in the "AND" logical mode is at the aM level, while in the multiplex mode, it reaches the fM level, facilitating the sensitive detection of viral gene fragments. The DNA motor can be regenerated by separating and reconstituting the utilized orbits, enabling its reuse for up to seven cycles in the "AND" logical mode and five cycles in the multiplex mode. Accurate diagnoses were achieved for patients exhibiting upper respiratory symptoms. Therefore, the proposed motor offers a novel and regenerative approach for viral gene fragments detection, demonstrating significant promise for application in the clinical diagnosis of viral infectious diseases.

Elucidating the interactions between Kinesin-5/BimC and the microtubule: insights from TIRF microscopy and molecular dynamics simulations

Kinesin-5 s are bipolar motor proteins that contribute to cell division by crosslinking and sliding apart antiparallel microtubules inside the mitotic spindle. However, the mechanism underlying the interactions between kinesin-5 and the microtubule remains poorly understood. In this study, we investigated the binding of BimC, a kinesin-5 motor from Aspergillus nidulans, to the microtubule using a combination of total internal reflection fluorescence (TIRF) microscopy and molecular dynamics (MD) simulations. TIRF microscopy experiments revealed that increasing the concentration of KCl in the motility buffer from 0 mM to 150 mM completely abolishes the ability of BimC to bind to the microtubule. Consistent with this experimental finding, MD simulations demonstrated a significant reduction in the strength of electrostatic interactions between BimC and microtubules at 150 mM KCl compared to 0 mM KCl. Furthermore, we identified several salt bridges at the BimC-microtubule interface, with positively charged residues on BimC interacting with negatively charged residues on the tubulin heterodimer. These results provide mechanistic insights into the role of electrostatic interactions in kinesin-5-microtubule binding, advancing our understanding of the molecular underpinnings of kinesin-5 motility.

Oblique line scan illumination enables expansive, accurate and sensitive single-protein measurements in solution and in living cells

An ideal tool for the study of cellular biology would enable the measure of molecular activity nondestructively within living cells. Single-molecule localization microscopy (SMLM) techniques, such as single-molecule tracking (SMT), enable in situ measurements in cells but have historically been limited by a necessary tradeoff between spatiotemporal resolution and throughput. Here we address these limitations using oblique line scan (OLS), a robust single-objective light-sheet-based illumination and detection modality that achieves nanoscale spatial resolution and sub-millisecond temporal resolution across a large field of view. We show that OLS can be used to capture protein motion up to 14 μm2 s-1 in living cells. We further extend the utility of OLS with in-solution SMT for single-molecule measurement of ligand-protein interactions and disruption of protein-protein interactions using purified proteins. We illustrate the versatility of OLS by showcasing two-color SMT, STORM and single-molecule fluorescence recovery after photobleaching. OLS paves the way for robust, high-throughput, single-molecule investigations of protein function required for basic research, drug screening and systems biology studies.

Impact of physiological ionic strength and crowding on kinesin-1 motility

The motility of biological molecular motors has typically been analyzed by in vitro reconstitution systems using motors isolated and purified from organs or expressed in cultured cells. The behavior of biomolecular motors within cells has frequently been reported to be inconsistent with that observed in reconstituted systems in vitro. Although this discrepancy has been attributed to differences in ionic strength and intracellular crowding, understanding how such parameters affect the motility of motors remains challenging. In this report, we investigated the impact of intracellular crowding in vitro on the mechanical properties of kinesin under a high ionic strength that is comparable to the cytoplasm. Initially, we characterized viscosity in a cell by using a kinesin motor lacking the cargo-binding domain. We then used polyethylene glycol to create a viscous environment in vitro comparable to the intracellular environment. Our results showed that kinesin frequently dissociated from microtubules under high ionic strength conditions. However, under conditions of both high ionic strength and crowding with polymers, the processive movement of kinesin persisted and increased in frequency. This setting reproduces the significant variations in the mechanical properties of motors measured in the intracellular environment and suggests a mechanism whereby kinesin maintains motility under the high ionic strengths found in cells.Key words: kinesin motility, molecular crowding, ionic strength, intracellular transport, processivity of molecular motors.

How energy determines spatial localisation and copy number of molecules in neurons

In neurons, the quantities of mRNAs and proteins are traditionally assumed to be determined by functional, electrical or genetic factors. Yet, there may also be global, currently unknown computational rules that are valid across different molecular species inside a cell. Surprisingly, our results show that the energy for molecular turnover is a significant cellular expense, en par with spiking cost, and which requires energy-saving strategies. We show that the drive to save energy determines transcript quantities and their location while acting differently on each molecular species depending on the length, longevity and other features of the respective molecule. We combined our own data and experimental reports from five other large-scale mRNA and proteomics screens, comprising more than ten thousand molecular species to reveal the underlying computational principles of molecular localisation. We found that energy minimisation principles explain experimentally-reported exponential rank distributions of mRNA and protein copy numbers. Our results further reveal robust energy benefits when certain mRNA classes are moved into dendrites, for example mRNAs of proteins with long amino acid chains or mRNAs with large non-coding regions and long half-lives proving surprising insights at the level of molecular populations.

Mechanism and regulation of kinesin motors

Kinesins are a diverse superfamily of microtubule-based motors that perform fundamental roles in intracellular transport, cytoskeletal dynamics and cell division. These motors share a characteristic motor domain that powers unidirectional motility and force generation along microtubules, and they possess unique tail domains that recruit accessory proteins and facilitate oligomerization, regulation and cargo recognition. The location, direction and timing of kinesin-driven processes are tightly regulated by various cofactors, adaptors, microtubule tracks and microtubule-associated proteins. This Review focuses on recent structural and functional studies that reveal how members of the kinesin superfamily use the energy of ATP hydrolysis to transport cargoes, depolymerize microtubules and regulate microtubule dynamics. I also survey how accessory proteins and post-translational modifications regulate the autoinhibition, cargo binding and motility of some of the best-studied kinesins. Despite much progress, the mechanism and regulation of kinesins are still emerging, and unresolved questions can now be tackled using newly developed approaches in biophysics and structural biology.

The Power of Three: Dynactin associates with three dyneins under load for greater force production

Cytoplasmic dynein is an essential microtubule motor protein that powers organelle transport and mitotic spindle assembly. Its activity depends on dynein-dynactin-cargo adaptor complexes, such as dynein-dynactin-BicD2 (DDB), which typically function with two dynein motors. We show that mechanical tension recruits a third dynein motor via an auxiliary BicD adaptor binding the light intermediate chain of the third dynein, stabilizing multi-dynein assemblies and enhancing force generation. Lis1 prevents dynein from transitioning into a force-limiting phi-like conformation, allowing single-dynein DDB to sustain forces up to ~4.5 pN, whereas force generation often ends at ~2.5 pN without Lis1. Complexes with two or three dyneins generate ~7 pN and ~9 pN, respectively, consistent with a staggered motor arrangement that enhances collective output. Under load, DDB primarily takes ~8 nm steps, challenging existing dynein coordination models. These findings reveal adaptive mechanisms that enable robust intracellular transport under varying mechanical demands.

A Two-Heads-Bound State Drives KIF1A Superprocessivity

KIF1A, a neuron-specific Kinesin-3 motor, is indispensable for long-distance axonal transport and nuclear migration, processes vital for neuronal function. Using MINFLUX tracking, we reveal that KIF1A predominantly adopts a two-heads-bound state, even under ATP-limiting conditions, challenging prior models proposing a one-head-bound rate-limiting step. This two-heads-bound conformation, stabilized by interactions between the positively charged K-loop and negatively charged tubulin tails, enhances microtubule affinity and minimizes detachment. The shorter neck linker facilitates inter-head tension, keeping the heads out of phase and enabling highly coordinated stepping. In contrast, Kinesin-1 (KIF5B) transitions to a one-head-bound state under similar conditions, limiting its processivity. Perturbing KIF1A's mechanochemical cycle by prolonging its one-head-bound state significantly reduces processivity, underscoring the critical role of the two-heads-bound state in motility. These findings establish a mechanistic framework for understanding KIF1A's adaptations for neuronal transport and dysfunction in neurological diseases.

Power Strokes in Molecular Motors: Predictive, Irrelevant, or Somewhere in Between?

For several decades, molecular motor directionality has been rationalized in terms of the free energy of molecular conformations visited before and after the motor takes a step, a so-called power stroke mechanism with analogues in macroscopic engines. Despite theoretical and experimental demonstrations of its flaws, the power stroke language is quite ingrained, and some communities still value power stroke intuition. By building a catalysis-driven motor into simulated numerical experiments, we here systematically report on how directionality responds when the motor is modified accordingly to power stroke intuition. We confirm that the power stroke mechanism generally does not predict motor directionality. Nevertheless, the simulations illustrate that the relative stability of molecular conformations should be included as a potential design element to adjust the motor directional bias. Though power strokes are formally unimportant for determining directionality, we show that practical attempts to alter a power stroke have side effects that can in fact alter the bias. The change in the bias can align with what power stroke intuition would have suggested, offering a potential explanation for why the flawed power stroke mechanism can retain apparent utility when engineering specific systems.

Tracking Single Kinesin in Live Cells Using MINFLUX

MINFLUX is a super-resolution fluorescence microscopy technique that enables single-molecule tracking in live cells at a single-nanometer spatial and sub-millisecond temporal resolution. This chapter describes a method for tracking fluorescently labeled human kinesin-1 in live cells using MINFLUX and analyzing kinesin stepping dynamics.

Multicolor Tracking of Molecular Motors at Nanometer Resolution

Molecular motors move processively along cytoskeletal filaments by stepping of their motor domains (MDs). Observation of how the MDs step relative to each other reveals the mechanism of motor processivity and various gating mechanisms used by motors to coordinate the catalytic cycles of their MDs. This chapter will discuss developments in simultaneous observation of the stepping motions of the two MDs of processive motors using two-color single-particle tracking microscopy.Techniques presented: FIONA, multicolor tracking/image registration.

Computational Modeling Reveals a Catch-and-Guide Interaction Between Kinesin-1 and Tubulin C-Terminal Tails

The delivery of intracellular cargoes by kinesins is modulated at scales ranging from the geometry of the microtubule networks down to interactions with individual tubulins and their code. The complexity of the tubulin code and the difficulty in directly observing motor-tubulin interactions have hindered progress in pinpointing the precise mechanisms by which kinesin's function is modulated. As one such example, past experiments show that cleaving tubulin C-terminal tails (CTTs) lowers kinesin-1's processivity and velocity on microtubules, but how these CTTs intertwine with kinesin's processive cycle remains unclear. In this work, we formulate and interrogate several plausible mechanisms by which CTTs contribute to and modulate kinesin motion. Computational modeling bridges the gap between effective transport observations (processivity, velocities) and microscopic mechanisms. Ultimately, we find that a guiding mechanism can best explain the observed differences in processivity and velocity. Altogether, our work adds a new understanding of how the CTTs and their modulation via the tubulin code may steer intracellular traffic in both health and disease.

The known unknowns of the Hsp90 chaperone

Molecular chaperones are vital proteins that maintain protein homeostasis by assisting in protein folding, activation, degradation, and stress protection. Among them, heat-shock protein 90 (Hsp90) stands out as an essential proteostasis hub in eukaryotes, chaperoning hundreds of 'clients' (substrates). After decades of research, several 'known unknowns' about the molecular function of Hsp90 remain unanswered, hampering rational drug design for the treatment of cancers, neurodegenerative, and other diseases. We highlight three fundamental open questions, reviewing the current state of the field for each, and discuss new opportunities, including single-molecule technologies, to answer the known unknowns of the Hsp90 chaperone.

The FHA domain is essential for autoinhibition of KIF1A/UNC-104 proteins

KIF1A/UNC-104 proteins, which are members of the kinesin superfamily of motor proteins, play a pivotal role in the axonal transport of synaptic vesicles and their precursors. Drosophila melanogaster UNC-104 (DmUNC-104) is a relatively recently discovered Drosophila kinesin. Although some point mutations that disrupt synapse formation have been identified, the biochemical properties of the DmUNC-104 protein have not been investigated. Here, we prepared recombinant full-length DmUNC-104 protein and determined its biochemical features. We analyzed the effect of a previously identified missense mutation in the forkhead-associated (FHA) domain, called bristly (bris). The bris mutation strongly promoted the dimerization of DmUNC-104 protein, whereas wild-type DmUNC-104 was a mixture of monomers and dimers. We further tested the G618R mutation near the FHA domain, which was previously shown to disrupt the autoinhibition of Caenorhabditis elegans UNC-104. The biochemical properties of the G618R mutant recapitulated those of the bris mutant. Finally, we found that disease-associated mutations also promote the dimerization of DmUNC-104. Collectively, our results suggest that the FHA domain is essential for autoinhibition of KIF1A/UNC-104 proteins, and that abnormal dimerization of KIF1A might be linked to human diseases.

Single molecule dynamics in a virtual cell combining a 3-dimensional matrix model with random walks

Recent advances in light microscopy have enabled single molecules to be imaged and tracked within living cells and this approach is impacting our understanding of cell biology. Computer modeling and simulation are important adjuncts to the experimental cycle since they aid interpretation of experimental results and help refine, test and generate hypotheses. Object-oriented computer modeling is particularly well-suited for simulating random, thermal, movements of individual molecules as they interact with other molecules and subcellular structures, but current models are often limited to idealized systems consisting of unit volumes or planar surfaces. Here, a simulation tool is described that combines a 3-dimensional, voxelated, representation of the cell consisting of subcellular structures (e.g. nucleus, endoplasmic reticulum, cytoskeleton, vesicles, and filopodia) combined with numerical floating-point precision simulation of thousands of individual molecules moving and interacting within the 3-dimensional space. Simulations produce realistic time-series video sequences comprising single fluorophore intensities and realistic background noise which can be directly compared to experimental fluorescence video microscopy data sets.

Kinesin-14 HSET and KlpA are non-processive microtubule motors with load-dependent power strokes

Accurate chromosome segregation during cell division relies on coordinated actions of microtubule (MT)-based motor proteins in the mitotic spindle. Kinesin-14 motors play vital roles in spindle assembly and maintenance by crosslinking antiparallel MTs at the spindle midzone and anchoring spindle MTs' minus ends at the poles. In this study, we investigate the force generation and motility of the Kinesin-14 motors HSET and KlpA. Our findings reveal that both motors are non-processive, producing single load-dependent power strokes per MT encounter, with estimated load-free power strokes of ~30 and ~35 nm, respectively. Each homodimeric motor generates forces of ~0.5 pN, but when assembled in teams, they cooperate to generate forces of 1 pN or more. Notably, the cooperative activity among multiple motors leads to increased MT-sliding velocities. These results quantitatively elucidate the structure-function relationship of Kinesin-14 motors and underscore the significance of cooperative behavior in their cellular functions.

Subunit Communication within Dimeric SF1 DNA Helicases

Monomers of the Superfamily (SF) 1 helicases, E. coli Rep and UvrD, can translocate directionally along single stranded (ss) DNA, but must be activated to function as helicases. In the absence of accessory factors, helicase activity requires Rep and UvrD homo-dimerization. The ssDNA binding sites of SF1 helicases contain a conserved aromatic amino acid (Trp250 in Rep and Trp256 in UvrD) that stacks with the DNA bases. Here we show that mutation of this Trp to Ala eliminates helicase activity in both Rep and UvrD. Rep(W250A) and UvrD(W256A) can still dimerize, bind DNA, and monomers still retain ATP-dependent ssDNA translocase activity, although with ∼10-fold lower rates and lower processivities than wild type monomers. Although neither wtRep monomers nor Rep(W250A) monomers possess helicase activity by themselves, using both ensemble and single molecule methods, we show that helicase activity is achieved upon formation of a Rep(W250A)/wtRep hetero-dimer. An ATPase deficient Rep monomer is unable to activate a wtRep monomer indicating that ATPase activity is needed in both subunits of the Rep hetero-dimer. We find the same results with E. coli UvrD and its equivalent mutant (UvrD(W256A)). Importantly, Rep(W250A) is unable to activate a wtUvrD monomer and UvrD(W256A) is unable to activate a wtRep monomer indicating that specific dimer interactions are required for helicase activity. We also demonstrate subunit communication within the dimer by virtue of Trp fluorescence signals that only are present within the Rep dimer, but not the monomers. These results bear on proposed subunit switching mechanisms for dimeric helicase activity.

Uncovering kinesin dynamics in neurites with MINFLUX

Neurons grow neurites of several tens of micrometers in length, necessitating active transport from the cell body by motor proteins. By tracking fluorophores as minimally invasive labels, MINFLUX is able to quantify the motion of those proteins with nanometer/millisecond resolution. Here we study the substeps of a truncated kinesin-1 mutant in primary rat hippocampal neurons, which have so far been mainly observed on polymerized microtubules deposited onto glass coverslips. A gentle fixation protocol largely maintains the structure and surface modifications of the microtubules in the cell. By analyzing the time between the substeps, we identify the ATP-binding state of kinesin-1 and observe the associated rotation of the kinesin-1 head in neurites. We also observed kinesin-1 switching microtubules mid-walk, highlighting the potential of MINFLUX to study the details of active cellular transport.

ATP Concentration-Dependent Fractions of One-Head-Bound and Two-Head-Bound States of the Kinesin Motor during Its Chemomechanical Coupling Cycle

Kinesin is a typical motor protein that can use the chemical energy of ATP hydrolysis to step processively on microtubules, alternating between one-head-bound and two-head-bound states. Some published experimental results showed that the duration of the one-head-bound state increases greatly with a decrease in ATP concentration, whereas the duration of the two-head-bound state is independent of ATP concentration, indicating that ATP binding occurs in the one-head-bound state. On the contrary, other experimental results showed that the duration of the two-head-bound state increases greatly with a decrease in ATP concentration, whereas the duration of the one-head-bound state increases slightly with a decrease in ATP concentration, indicating that ATP binding occurs mainly in the two-head-bound state. Here, we explain consistently and quantitatively these contradictory experimental results, resolving the controversy that is critical to the chemomechanical coupling mechanism of the kinesin motor.

Design of artificial molecular motor inheriting directionality and scalability

Realizing artificial molecular motors with autonomous functionality and high performance is a major challenge in biophysics. Such motors not only provide new perspectives in biotechnology but also offer a novel approach for the bottom-up elucidation of biological molecular motors. Directionality and scalability are critical factors for practical applications. However, the simultaneous realization of both remains challenging. In this study, we propose a novel design for a rotary motor that can be fabricated using a currently available technology, DNA origami, and validate its functionality through simulations with practical parameters. We demonstrate that the motor rotates unidirectionally and processively in the direction defined by structural asymmetry, which induces kinetic asymmetry in motor motion. The motor also exhibits scalability, such that increasing the number of connections between the motor and stator allows for a larger speed, run length, and stall force.

MINSTED tracking of single biomolecules

Here we show that MINSTED localization, a method whereby the position of a fluorophore is identified with precisely controlled beams of a STED microscope, tracks fluorophores and hence labeled biomolecules with nanometer/millisecond spatiotemporal precision. By updating the position for each detected photon, MINSTED recognizes fluorophore steps of 16 nm within <250 μs using about 13 photons. The power of MINSTED tracking is demonstrated by resolving the stepping of the motor protein kinesin-1 walking on microtubules and switching protofilaments.

Self-Feedback DNAzyme Motor for Cascade-Amplified Imaging of mRNA in Live Cells and In Vivo

DNA motors have attracted extensive interest in biosensing and bioimaging. However, the amplification capacity of the existing DNA motor systems is limited since the products from the walking process are unable to feedback into the original DNA motor systems. As a result, the sensitivities of such systems are limited in the contexts of biosensing and bioimaging. In this study, we report a novel self-feedback DNAzyme motor for the sensitive imaging of tumor-related mRNA in live cells and in vivo with cascade signal amplification capacity. Gold nanoparticles (AuNPs) are modified with hairpin-locked DNAzyme walker and track strands formed by hybridizing Cy5-labeled DNA trigger-incorporated substrate strands with assistant strands. Hybridization of the target mRNA with the hairpin strands activates DNAzyme and promotes the autonomous walking of DNAzyme on AuNPs through DNAzyme-catalyzed substrate cleavage, resulting in the release of many Cy5-labeled substrate segments containing DNA triggers and the generation of an amplified fluorescence signal. Moreover, each released DNA trigger can also bind with the hairpin strand to activate and operate the original motor system, which induces further signal amplification via a feedback mechanism. This motor exhibits a 102-fold improvement in detection sensitivity over conventional DNAzyme motors and high selectivity for target mRNA. It has been successfully applied to distinguish cancer cells from normal cells and diagnose tumors in vivo based on mRNA imaging. The proposed DNAzyme motor provides a promising paradigm for the amplified detection and sensitive imaging of low-abundance biomolecules in vivo.

Effect of small molecular crowders on dynamics of kinesin molecular motors

Kinesin is a motor protein that can convert chemical energy of ATP hydrolysis into mechanical energy of moving processively on microtubules. Apart from the load and ATP concentration affecting the dynamics of the motor such as velocity, run length, dissociation rate, etc., the increase of solution viscosity by supplementing crowding agents of low molecular weight into the buffer can also affect the dynamics. Here, based on our proposed model for the chemomechanical coupling of the kinesin motor, a systematically theoretical study of the motor dynamics under the variation of the viscosity and load is presented. Both the load on the motor's stalk and that on one of the two heads are considered. The theoretical results provide a consistent explanation of the available contradictory experimental results, with some showing that increasing viscosity decreases sensitively the velocity whereas others showing that increasing viscosity has little effect on the velocity. The theoretical results reproduce quantitatively the puzzling experimental data showing that under different directions of the load on the stalk, increasing viscosity has very different effects on the change of run length or dissociation rate. The theoretical results predict that in both the pure and crowded buffers the dependence of the run length on the load acting one of the two heads has very different feature from that on the load acting on the stalk.

Light-activated microtubule-based two-dimensional active nematic

We assess the ability of two light responsive kinesin motor clusters to drive dynamics of microtubule-based active nematics: opto-K401, a processive motor, and opto-K365, a non-processive motor. Measurements reveal an order of magnitude improvement in the contrast of nematic flow speeds between maximally- and minimally-illuminated states for opto-K365 motors when compared to opto-K401 construct. For opto-K365 nematics, we characterize both the steady-state flow and defect density as a function of applied light. We also examine the transient behavior as the system switches between steady-states upon changes in light intensities. Although nematic flows reach a steady state within tens of seconds, the defect density exhibits transient behavior for up to 10 minutes, showing a separation between small-scale active flows and system-scale structural states. Our work establishes an experimental platform that can exploit spatiotemporally-heterogeneous patterns of activity to generate targeted dynamical states.

New insights into the mechanochemical coupling mechanism of kinesin-microtubule complexes from their high-resolution structures

Kinesin motor proteins couple mechanical movements in their motor domain to the binding and hydrolysis of ATP in their nucleotide-binding pocket. Forces produced through this 'mechanochemical' coupling are typically used to mobilize kinesin-mediated transport of cargos along microtubules or microtubule cytoskeleton remodeling. This review discusses the recent high-resolution structures (<4 Å) of kinesins bound to microtubules or tubulin complexes that have resolved outstanding questions about the basis of mechanochemical coupling, and how family-specific modifications of the motor domain can enable its use for motility and/or microtubule depolymerization.

Molecular mechanism of interaction between kinesin motors affecting their residence times on microtubule lattice and end

Kinesin superfamily can be classified into 14 subfamilies. Some families of kinesin motors such as kinesin-1 are responsible for long-distance intracellular transports and thus the motors are required to reside on the microtubule (MT) lattice for a longer time than at the end. Some families such as kinesin-8 Kip3 and kinesin-5 Eg5 are responsible for the regulation of MT length by depolymerizing or polymerizing the MT from the plus end and thus the motors are required to reside at the MT end for a long time. Under the crowded condition of the motors, it was found experimentally that the residence times of the kinesin-8 Kip3 and kinesin-5 Eg5 at the MT end are reduced greatly compared to the single-motor case. However, the underlying mechanism of different families of kinesin motors having different MT-end residence times is unknown. The molecular mechanism by which the interaction between the two motors greatly reduces the residence time of the motor at the MT end is elusive. In addition, during the processive stepping on the MT lattice, when two kinesin motors meet it is unknown how the interaction between them affects their dissociation rates. To address the above unclear issues, here we make a consistent and theoretical study of the residence times of the kinesin-1, kinesin-8 Kip3 and kinesin-5 Eg5 motors on the MT lattice and at the end under both the single-motor condition and multiple-motors or crowded condition.

Kinesin-14 HSET and KlpA are non-processive microtubule motors with load-dependent power strokes

Accurate chromosome segregation during cell division relies on coordinated actions of microtubule (MT)-based motor proteins in the mitotic spindle. Kinesin-14 motors play vital roles in spindle assembly and maintenance by crosslinking antiparallel MTs at the spindle midzone and anchoring spindle MTs' minus ends at the poles. We investigate the force generation and motility of the Kinesin-14 motors HSET and KlpA, revealing that both motors function as non-processive motors under load, producing single power strokes per MT encounter. Each homodimeric motor generates forces of ∼0.5 pN, but when assembled in teams, they cooperate to generate forces of 1 pN or more. Importantly, cooperative activity among multiple motors leads to increased MT-sliding velocities. Our findings deepen our understanding of the structure-function relationship of Kinesin-14 motors and underscore the significance of cooperative behavior in their cellular functions.

Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids

Microtubule-based active fluids exhibit turbulent-like autonomous flows, which are driven by the molecular motor powered motion of filamentous constituents. Controlling active stresses in space and time is an essential prerequisite for controlling the intrinsically chaotic dynamics of extensile active fluids. We design single-headed kinesin molecular motors that exhibit optically enhanced clustering and thus enable precise and repeatable spatial and temporal control of extensile active stresses. Such motors enable rapid, reversible switching between flowing and quiescent states. In turn, spatio-temporal patterning of the active stress controls the evolution of the ubiquitous bend instability of extensile active fluids and determines its critical length dependence. Combining optically controlled clusters with conventional kinesin motors enables one-time switching from contractile to extensile active stresses. These results open a path towards real-time control of the autonomous flows generated by active fluids.

Direct observation of motor protein stepping in living cells using MINFLUX

Dynamic measurements of molecular machines can provide invaluable insights into their mechanism, but these measurements have been challenging in living cells. Here, we developed live-cell tracking of single fluorophores with nanometer spatial and millisecond temporal resolution in two and three dimensions using the recently introduced super-resolution technique MINFLUX. Using this approach, we resolved the precise stepping motion of the motor protein kinesin-1 as it walked on microtubules in living cells. Nanoscopic tracking of motors walking on the microtubules of fixed cells also enabled us to resolve the architecture of the microtubule cytoskeleton with protofilament resolution.

MINFLUX dissects the unimpeded walking of kinesin-1

We introduce an interferometric MINFLUX microscope that records protein movements with up to 1.7 nanometer per millisecond spatiotemporal precision. Such precision has previously required attaching disproportionately large beads to the protein, but MINFLUX requires the detection of only about 20 photons from an approximately 1-nanometer-sized fluorophore. Therefore, we were able to study the stepping of the motor protein kinesin-1 on microtubules at up to physiological adenosine-5'-triphosphate (ATP) concentrations. We uncovered rotations of the stalk and the heads of load-free kinesin during stepping and showed that ATP is taken up with a single head bound to the microtubule and that ATP hydrolysis occurs when both heads are bound. Our results show that MINFLUX quantifies (sub)millisecond conformational changes of proteins with minimal disturbance.

Regulatory mechanisms of the dynein-2 motility by post-translational modification revealed by MD simulation

Intraflagellar transport for ciliary assembly and maintenance is driven by dynein and kinesins specific to the cilia. It has been shown that anterograde and retrograde transports run on different regions of the doublet microtubule, i.e., separate train tracks. However, little is known about the regulatory mechanism of this selective process. Since the doublet microtubule is known to display specific post-translational modifications of tubulins, i.e., "tubulin code", for molecular motor regulations, we investigated the motility of ciliary specific dynein-2 under different post-translational modification by coarse-grained molecular dynamics. Our setup allows us to simulate the landing behaviors of dynein-2 on un-modified, detyrosinated, poly-glutamylated and poly-glycylated microtubules in silico. Our study revealed that poly-glutamylation can play an inhibitory effect on dynein-2 motility. Our result indicates that poly-glutamylation of the B-tubule of the doublet microtubule can be used as an efficient means to target retrograde intraflagellar transport onto the A-tubule.

Bicontinuous oxide heteroepitaxy with enhanced photoconductivity

Self-assembled systems have recently attracted extensive attention because they can display a wide range of phase morphologies in nanocomposites, providing a new arena to explore novel phenomena. Among these morphologies, a bicontinuous structure is highly desirable based on its high interface-to-volume ratio and 3D interconnectivity. A bicontinuous nickel oxide (NiO) and tin dioxide (SnO₂) heteroepitaxial nanocomposite is revealed here. By controlling their concentration, we fabricated tuneable self-assembled nanostructures from pillars to bicontinuous structures, as evidenced by TEM-energy-dispersive X-ray spectroscopy with a tortuous compositional distribution. The experimentally observed growth modes are consistent with predictions by first-principles calculations. Phase-field simulations are performed to understand 3D microstructure formation and extract key thermodynamic parameters for predicting microstructure morphologies in SnO₂:NiO nanocomposites of other concentrations. Furthermore, we demonstrate significantly enhanced photovoltaic properties in a bicontinuous SnO₂:NiO nanocomposite macroscopically and microscopically. This research shows a pathway to developing innovative solar cell and photodetector devices based on self-assembled oxides.

Energy landscapes of rotary DNA origami devices determined by fluorescence particle tracking

Biomolecular nanomechanical devices are of great interest as tools for the processing and manipulation of molecules, thereby mimicking the function of nature's enzymes. DNA nanotechnology provides the capability to build molecular analogs of mechanical machine elements such as joints and hinges via sequence-programmable self-assembly, which are otherwise known from traditional mechanical engineering. Relative to their size, these molecular machine elements typically do not reach the same relative precision and reproducibility that we know from their macroscopic counterparts; however, as they are scaled down to molecular sizes, physical effects typically not considered by mechanical engineers such as Brownian motion, intramolecular forces, and the molecular roughness of the devices begin to dominate their behavior. In order to investigate the effect of different design choices on the roughness of the mechanical energy landscapes of DNA nanodevices in greater detail, we here study an exemplary DNA origami-based structure, a modularly designed rotor-stator arrangement, which resembles a rotatable nanorobotic arm. Using fluorescence tracking microscopy, we follow the motion of individual rotors and record their corresponding energy landscapes. We then utilize the modular construction of the device to exchange its constituent parts individually and systematically test the effect of different design variants on the movement patterns. This allows us to identify the design parameters that most strongly affect the shape of the energy landscapes of the systems. Taking into account these insights, we are able to create devices with significantly flatter energy landscapes, which translates to mechanical nanodevices with improved performance and behaviors more closely resembling those of their macroscopic counterparts.

Extract Motive Energy from Single-Molecule Trajectories

Single-molecule trajectories from nonequilibrium unfolding experiments are widely used to recover a biomolecule's intrinsic free-energy profile. Trajectories of molecular motors from similar single-molecule experiments may be mapped to biased diffusion over an inclined free-energy profile. Such an effective potential is not a static equilibrium property anymore, and how it can benefit molecular motor study is unclear. Here, we introduce a method to deduce this effective potential from motor trajectories with realistic temporal-spatial resolution and find that the potential yields a motor's stall force─a quantity that not only characterizes a motor's force-generating capacity but also largely determines its energy efficiency. Interestingly, this potential allows the extraction of a motor's stall force from trajectories recorded at a single resisting force or even zero force, as verified with trajectories from two molecular motor models and also experimental trajectories from a real artificial motor. This finding drastically reduces the difficulty of stall force measurement, making it accessible even to force-incapable optical tracking experiments (commonly regarded as irrelevant to stall force determination). This study further provides a method for experimentally measuring a second-law-decreed least energy price for submicroscopic directionality─a previously elusive but thermodynamically important quantity pertinent to efficient energy conversion of molecular motors.

Magic-angle-spinning NMR structure of the kinesin-1 motor domain assembled with microtubules reveals the elusive neck linker orientation

Microtubules (MTs) and their associated proteins play essential roles in maintaining cell structure, organelle transport, cell motility, and cell division. Two motors, kinesin and cytoplasmic dynein link the MT network to transported cargos using ATP for force generation. Here, we report an all-atom NMR structure of nucleotide-free kinesin-1 motor domain (apo-KIF5B) in complex with paclitaxel-stabilized microtubules using magic-angle-spinning (MAS) NMR spectroscopy. The structure reveals the position and orientation of the functionally important neck linker and how ADP induces structural and dynamic changes that ensue in the neck linker. These results demonstrate that the neck linker is in the undocked conformation and oriented in the direction opposite to the KIF5B movement. Chemical shift perturbations and intensity changes indicate that a significant portion of ADP-KIF5B is in the neck linker docked state. This study also highlights the unique capability of MAS NMR to provide atomic-level information on dynamic regions of biological assemblies.

Using Catalysis to Drive Chemistry Away from Equilibrium: Relating Kinetic Asymmetry, Power Strokes, and the Curtin-Hammett Principle in Brownian Ratchets

Chemically fueled autonomous molecular machines are catalysis-driven systems governed by Brownian information ratchet mechanisms. One fundamental principle behind their operation is kinetic asymmetry, which quantifies the directionality of molecular motors. However, it is difficult for synthetic chemists to apply this concept to molecular design because kinetic asymmetry is usually introduced in abstract mathematical terms involving experimentally inaccessible parameters. Furthermore, two seemingly contradictory mechanisms have been proposed for chemically driven autonomous molecular machines: Brownian ratchet and power stroke mechanisms. This Perspective addresses both these issues, providing accessible and experimentally useful design principles for catalysis-driven molecular machinery. We relate kinetic asymmetry to the Curtin-Hammett principle using a synthetic rotary motor and a kinesin walker as illustrative examples. Our approach describes these molecular motors in terms of the Brownian ratchet mechanism but pinpoints both chemical gating and power strokes as tunable design elements that can affect kinetic asymmetry. We explain why this approach to kinetic asymmetry is consistent with previous ones and outline conditions where power strokes can be useful design elements. Finally, we discuss the role of information, a concept used with different meanings in the literature. We hope that this Perspective will be accessible to a broad range of chemists, clarifying the parameters that can be usefully controlled in the design and synthesis of molecular machines and related systems. It may also aid a more comprehensive and interdisciplinary understanding of biomolecular machinery.

Propofol attenuates kinesin-mediated axonal vesicle transport and fusion

Propofol is a widely used general anesthetic, yet the understanding of its cellular effects is fragmentary. General anesthetics are not as innocuous as once believed and have a wide range of molecular targets that include kinesin motors. Propofol, ketamine, and etomidate reduce the distances that Kinesin-1 KIF5 and Kinesin-2 KIF3 travel along microtubules in vitro. These transport kinesins are highly expressed in the CNS, and their dysfunction leads to a range of human pathologies including neurodevelopmental and neurodegenerative diseases. While in vitro data suggest that general anesthetics may disrupt kinesin transport in neurons, this hypothesis remains untested. Here we find that propofol treatment of hippocampal neurons decreased vesicle transport mediated by Kinesin-1 KIF5 and Kinesin-3 KIF1A ∼25-60%. Propofol treatment delayed delivery of the KIF5 cargo NgCAM to the distal axon. Because KIF1A participates in axonal transport of presynaptic vesicles, we tested whether prolonged propofol treatment affects synaptic vesicle fusion mediated by VAMP2. The data show that propofol-induced transport delay causes a significant decrease in vesicle fusion in distal axons. These results are the first to link a propofol-induced delay in neuronal trafficking to a decrease in axonal vesicle fusion, which may alter physiological function during and after anesthesia.

A method for single particle tracking through a multimode fiber

Multimode optical fiber (MMF) endoscopes have recently gained widespread attention as a novel tool for imaging deep within tissue using light microscopy. We here present a method for particle tracking through the MMF, which overcomes the lack of a fast enough wide-field fluorescence imaging modality for this type of endoscope, namely a discrete implementation of orbital particle tracking. We achieve biologically relevant tracking speeds (up to 1.2 μm/s) despite using a slow SLM for the wavefront shaping. We demonstrate a tracking accuracy of λ/50 for a 0.3 NA fiber and show tracking of a pinhole moving to mimic Brownian motion with diffusion rates of up to 0.3 μm²/s.

DNAzyme motor systems and logic gates facilitated by toehold exchange translators

DNAzyme motor systems using gold nanoparticles (AuNPs) as scaffolds are useful for biosensing and in situ amplification because these systems are free of protein enzymes, isothermal, homogeneous, and sensitive. However, detecting different targets using the available DNAzyme motor techniques requires redesigns of the DNAzyme motor. We report here a toehold-exchange translator and the translator-mediated DNAzyme motor systems, which enable sensitive responses to various nucleic acid targets using the same DNAzyme motor without requiring redesign. The translator is able to efficiently convert different nucleic acid targets into a specific output DNA that further activates the pre-silenced DNAzyme motor and consequently initiates the autonomous walking of the DNAzyme motor. Simply adjusting the target-binding region of the translator enables the same DNAzyme motor system to respond to various nucleic acid targets. The translator-mediated DNAzyme motor system is able to detect as low as 2.5 pM microRNA-10b and microRNA-21 under room temperature without the need of separation or washing. We further demonstrate the versatility of the translator and the DNAzyme motor by successful construction and operation of four logic gates, including OR, AND, NOR, and NAND logic gates. These logic gates use two microRNA targets as inputs and generate amplified fluorescence signals from the operation of the same DNAzyme motor. Incorporation of the toehold-exchange translator into the DNAzyme motor technology improves the biosensing applications of DNA motors to diverse nucleic acid targets.

Kinesin-3 motors are fine-tuned at the molecular level to endow distinct mechanical outputs

BACKGROUND

Kinesin-3 family motors drive diverse cellular processes and have significant clinical importance. The ATPase cycle is integral to the processive motility of kinesin motors to drive long-distance intracellular transport. Our previous work has demonstrated that kinesin-3 motors are fast and superprocessive with high microtubule affinity. However, chemomechanics of these motors remain poorly understood.

RESULTS

We purified kinesin-3 motors using the Sf9-baculovirus expression system and demonstrated that their motility properties are on par with the motors expressed in mammalian cells. Using biochemical analysis, we show for the first time that kinesin-3 motors exhibited high ATP turnover rates, which is 1.3- to threefold higher compared to the well-studied kinesin-1 motor. Remarkably, these ATPase rates correlate to their stepping rate, suggesting a tight coupling between chemical and mechanical cycles. Intriguingly, kinesin-3 velocities (KIF1A > KIF13A > KIF13B > KIF16B) show an inverse correlation with their microtubule-binding affinities (KIF1A < KIF13A < KIF13B < KIF16B). We demonstrate that this differential microtubule-binding affinity is largely contributed by the positively charged residues in loop8 of the kinesin-3 motor domain. Furthermore, microtubule gliding and cellular expression studies displayed significant microtubule bending that is influenced by the positively charged insert in the motor domain, K-loop, a hallmark of kinesin-3 family.

CONCLUSIONS

Together, we propose that a fine balance between the rate of ATP hydrolysis and microtubule affinity endows kinesin-3 motors with distinct mechanical outputs. The K-loop, a positively charged insert in the loop12 of the kinesin-3 motor domain promotes microtubule bending, an interesting phenomenon often observed in cells, which requires further investigation to understand its cellular and physiological significance.

Real-Time Feedback-Driven Single-Particle Tracking: A Survey and Perspective

Real-time feedback-driven single-particle tracking (RT-FD-SPT) is a class of techniques in the field of single-particle tracking that uses feedback control to keep a particle of interest in a detection volume. These methods provide high spatiotemporal resolution on particle dynamics and allow for concurrent spectroscopic measurements. This review article begins with a survey of existing techniques and of applications where RT-FD-SPT has played an important role. Each of the core components of RT-FD-SPT are systematically discussed in order to develop an understanding of the trade-offs that must be made in algorithm design and to create a clear picture of the important differences, advantages, and drawbacks of existing approaches. These components are feedback tracking and control, ranging from simple proportional-integral-derivative control to advanced nonlinear techniques, estimation to determine particle location from the measured data, including both online and offline algorithms, and techniques for calibrating and characterizing different RT-FD-SPT methods. Then a collection of metrics for RT-FD-SPT is introduced to help guide experimentalists in selecting a method for their particular application and to help reveal where there are gaps in the techniques that represent opportunities for further development. Finally, this review is concluded with a discussion on future perspectives in the field.

A DNA origami rotary ratchet motor

To impart directionality to the motions of a molecular mechanism, one must overcome the random thermal forces that are ubiquitous on such small scales and in liquid solution at ambient temperature. In equilibrium without energy supply, directional motion cannot be sustained without violating the laws of thermodynamics. Under conditions away from thermodynamic equilibrium, directional motion may be achieved within the framework of Brownian ratchets, which are diffusive mechanisms that have broken inversion symmetry^1-5. Ratcheting is thought to underpin the function of many natural biological motors, such as the F₁F₀-ATPase^6-8, and it has been demonstrated experimentally in synthetic microscale systems (for example, to our knowledge, first in ref. ³) and also in artificial molecular motors created by organic chemical synthesis^9-12. DNA nanotechnology¹³ has yielded a variety of nanoscale mechanisms, including pivots, hinges, crank sliders and rotary systems^14-17, which can adopt different configurations, for example, triggered by strand-displacement reactions^18,19 or by changing environmental parameters such as pH, ionic strength, temperature, external fields and by coupling their motions to those of natural motor proteins^20-26. This previous work and considering low-Reynolds-number dynamics and inherent stochasticity^27,28 led us to develop a nanoscale rotary motor built from DNA origami that is driven by ratcheting and whose mechanical capabilities approach those of biological motors such as F₁F₀-ATPase.

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.

Superresolved Motions of Single Molecular Catalysts during Polymerization Show Wide Distributions

The motion of single molecular ruthenium catalysts during and after single turnover events of ring-opening metathesis polymerization is imaged through single-molecule superresolution tracking with a positional accuracy of ±32 nm. This tracking is achieved through the real-time incorporation of spectrally tagged monomer units into active polymer chain ends during living polymerization; thus, by design, only active-catalyst motion is detected and imaged, without convolution by inactive catalysts. The catalysts show diverse individualistic diffusive behaviors with respect to time that persist for up to 20 s. Catalysts occupy three mobility populations: quasi-stationary (23%), intermediate (53%, 65 nm), and large (24%, 145 nm) step sizes. Differences in catalyst mobility populations also exist between individual aggregates (p < 0.001). Such differential motion indicates widely different local catalyst microenvironments during the catalytic turnover. These mobility differences are uniquely observable through single-catalyst microscopy and are not measurable through traditional ensemble analytical techniques for characterizing the behavior of molecular catalysts, such as nuclear magnetic resonance spectroscopy. The measured distributions of active molecular catalyst motions would not be readily predictable through modeling or first-principles, and the range likely impacts individual catalyst turnover rate and selectivity. This range plausibly contributes to property distributions observable in bulk polymers, such as molecular weight polydispersity (e.g., 1.9 in this system), leading to a revised understanding of the mechanistic, microscale origins of macroscale polymer properties.

Darwinian Evolution of Intelligence

Intelligence is often discussed in terms of neural networks in the cerebral cortex, whose evolution has presumably been influenced by Darwinian selection. Here we present molecular evidence that one of the many kinesin motors, KIF14, has evolved to exhibit a special feature in its amino acid sequence that could improve neural networks. The improvement is quantified by comparison of NIF14 sequences for 12 species. The special feature is level sets of synchronized hydrophobic extrema in water wave profiles based on several hydropathic scales. The most effective scale is a new one based on fractals indicative of approach of globular curvatures to self-organized criticality, which summarizes evolutionary trends based on intelligent design.