Motility of an autonomous protein-based artificial motor that operates via a burnt-bridge principle.

Inspired by biology, great progress has been made in creating artificial molecular motors. However, the dream of harnessing proteins - the building blocks selected by nature - to design autonomous motors has so far remained elusive. Here we report the synthesis and characterization of the Lawnmower, an autonomous, protein-based artificial molecular motor comprised of a spherical hub decorated with proteases. Its "burnt-bridge" motion is directed by cleavage of a peptide lawn, promoting motion towards unvisited substrate. We find that Lawnmowers exhibit directional motion with average speeds of up to 80 nm/s, comparable to biological motors. By selectively patterning the peptide lawn on microfabricated tracks, we furthermore show that the Lawnmower is capable of track-guided motion. Our work opens an avenue towards nanotechnology applications of artificial protein motors.

"Turbo-Charged" DNA Motors with Optimized Sequence Enable Single-Molecule Nucleic Acid Sensing.

DNA motors that consume chemical energy to generate processive mechanical motion mimic natural motor proteins and have garnered interest due to their potential applications in dynamic nanotechnology, biosensing, and drug delivery. Such motors translocate by a catalytic cycle of binding, cleavage, and rebinding between DNA "legs" on the motor body and RNA "footholds" on a track. Herein, we address the well-documented trade-off between motor speed and processivity and investigate how these parameters are controlled by the affinity between DNA legs and their complementary footholds. Specifically, we explore the role of DNA leg length and GC content in tuning motor performance by dictating the rate of leg-foothold dissociation. Our investigations reveal that motors with 0 % GC content exhibit increased instantaneous velocities of up to 150 nm/sec, three-fold greater than previously reported DNA motors and comparable to the speeds of biological motor proteins. We also demonstrate that the faster speed and weaker forces generated by 0 % GC motors can be leveraged for enhanced capabilities in sensing. We observe single-molecule sensitivity when programming the motors to stall in response to the binding of nucleic acid targets. These findings offer insights for the design of high-performance DNA motors with promising real-world biosensing applications.

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.

Waiting Time Distributions in Hybrid Models of Motor-Bead Assays: A Concept and Tool for Inference.

In single-molecule experiments, the dynamics of molecular motors are often observed indirectly by measuring the trajectory of an attached bead in a motor-bead assay. In this work, we propose a method to extract the step size and stalling force for a molecular motor without relying on external control parameters. We discuss this method for a generic hybrid model that describes bead and motor via continuous and discrete degrees of freedom, respectively. Our deductions are solely based on the observation of waiting times and transition statistics of the observable bead trajectory. Thus, the method is non-invasive, operationally accessible in experiments and can, in principle, be applied to any model describing the dynamics of molecular motors. We briefly discuss the relation of our results to recent advances in stochastic thermodynamics on inference from observable transitions. Our results are confirmed by extensive numerical simulations for parameters values of an experimentally realized F1-ATPase assay.

Rotary biomolecular motor-powered supramolecular colloidal motor.

Cells orchestrate the motion and force of hundreds of protein motors to perform various mechanical tasks over multiple length scales. However, engineering active biomimetic materials from protein motors that consume energy to propel continuous motion of micrometer-sized assembling systems remains challenging. Here, we report rotary biomolecular motor-powered supramolecular (RBMS) colloidal motors that are hierarchically assembled from a purified chromatophore membrane containing FOF1-ATP synthase molecular motors, and an assembled polyelectrolyte microcapsule. The micro-sized RBMS motor with asymmetric distribution of FOF1-ATPases can autonomously move under light illumination and is collectively powered by hundreds of rotary biomolecular motors. The propulsive mechanism is that a transmembrane proton gradient generated by a photochemical reaction drives FOF1-ATPases to rotate for ATP biosynthesis, which creates a local chemical field for self-diffusiophoretic force. Such an active supramolecular architecture endowed with motility and biosynthesis offers a promising platform for intelligent colloidal motors resembling the propulsive units in swimming bacteria.

Site-Directed Cross-Linking Between Bacterial Flagellar Motor Proteins In Vivo.

The bacterial flagellum employs a rotary motor embedded on the cell surface. The motor consists of the stator and rotor elements and is driven by ion influx (typically H+ or Na+) through an ion channel of the stator. Ion influx induces conformational changes in the stator, followed by changes in the interactions between the stator and rotor. The driving force to rotate the flagellum is thought to be generated by changing the stator-rotor interactions. In this chapter, we describe two methods for investigating the interactions between the stator and rotor: site-directed in vivo photo-crosslinking and site-directed in vivo cysteine disulfide crosslinking.

Direct Observation of Archaellar Motor Rotation by Single-Molecular Imaging Techniques.

Single-molecular techniques have characterized dynamics of molecular motors such as flagellum in bacteria and myosin, kinesin, and dynein in eukaryotes. We can apply these techniques to a motility machine of archaea, namely, the archaellum, composed of a thin helical filament and a rotary motor. Although the size of the motor hinders the characterization of its motor function under a conventional optical microscope, fluorescence-labeling techniques allow us to visualize the architecture and function of the archaellar filaments in real time. Furthermore, a tiny polystyrene bead attached to the filament enables the visualization of motor rotation through the bead rotation and quantification of biophysical properties such as speed and torque produced by the rotary motor imbedded in the cell membrane. In this chapter, I describe the details of the above biophysical method based on an optical microscope.

Renal injury associated with MYH9 disorder with 5773delG mutation: A case report.

A 35-year-old man with persistent urine abnormalities and renal dysfunction was referred to our hospital. May-Hegglin anomaly was suspected, and a renal biopsy showed focal segmental glomerulosclerosis (FSGS) with IgA deposition. Electron microscopy revealed foot process effacements and intense bleb-like morphological changes in podocytes. Nonmuscle myosin heavy chain IIA (NMMHCIIA) staining of granulocytes revealed a localized, type II pattern, and genomic DNA sequencing of MYH9 exon 40 revealed MYH9 5773delG mutation (c.5773delG [p.(Asp1925Thrfs*23)]). Podocytes were significantly stained by an antibody specific for NMMHC-IIA abnormalities associated with this mutation. Colocalization observation of vimentin and NMMHC-IIA demonstrated a diminished form of NMMHC-IIA in podocytes. Taking these observations into account, it was determined that the present case was likely associated with MYH9 disorder. Treatment was started with olmesartan, followed by methylprednisolone pulse therapy 3 times bi-monthly. Finally, the patient began hemodialysis 18 months later. This is the first known report of renal phenotype expression associated with this MYH9 mutation. FSGS can occur in association with MYH9 mutations at the 3' regions, such as exon 40. Abnormal expression or metabolism of NMMHC-IIA in podocytes might be related to the formation of FSGS lesions due to this MYH9 mutation.

Direct identification of the rotary angle of ATP cleavage in F1-ATPase from Bacillus PS3.

F1-ATPase is the world's smallest biological rotary motor driven by ATP hydrolysis at three catalytic ß subunits. The 120° rotational step of the central shaft γ consists of 80° substep driven by ATP binding and a subsequent 40° substep. In order to correlate timing of ATP cleavage at a specific catalytic site with a rotary angle, we designed a new F1-ATPase (F1) from thermophilic Bacillus PS3 carrying ß(E190D/F414E/F420E) mutations, which cause extremely slow rates of both ATP cleavage and ATP binding. We produced an F1 molecule that consists of one mutant ß and two wild-type ßs (hybrid F1). As a result, the new hybrid F1 showed two pausing angles that are separated by 200°. They are attributable to two slowed reaction steps in the mutated ß, thus providing the direct evidence that ATP cleavage occurs at 200° rather than 80° subsequent to ATP binding at 0°. This scenario resolves the long-standing unclarified issue in the chemomechanical coupling scheme and gives insights into the mechanism of driving unidirectional rotation.

Rotations of F-ATPase and V-ATPase analyzed by a torque approach.

F-type ATP synthase (F-ATPase) and vacuolar ATP hydrolase (V-ATPase) are well-known biomolecular motors, which play significant catalytic roles in ATP synthesis and ATP hydrolysis reactions. Their rotational torques are important factors involved in their rotational behavior that can be measured experimentally but with considerable difficulty. To overcome this difficulty and thereby provide an in-depth understanding of their operation mechanism, we herein carry out simple and fast computer modelling to study the two proteins, using our torque approach that relies on interatomic forces and coordinates of unequilibrated configurations taken from brief molecular dynamics (MD) simulations. As predicted by the torque approach, F-ATPase is demonstrated to be a random rotor, but it prefers to rotate in clockwise direction (as seen from the membrane toward the protein) for ATP synthesis, owing to the predominantly negative angle-averaged torques. By contrast, V-ATPase tends to rotate only in counterclockwise direction for ATP hydrolysis, due to the almost uniform averaged positive torques generated by the unidirectional rotation near the three catalytic sites. The rotational behaviors of both proteins are also affected by the surrounding solvent which can promote or hinder the internal rotation. By combining the torque approach with classic force-field MD simulations, the torques of two biomolecular motors can be calculated economically, and are found to agree with previous experiments and theoretical calculations. This work demonstrates that our torque approach can be extended to the field of biology and can help gain a deeper insight into the mechanistic rotation of biomolecular motors with modest computation time.Communicated by Ramaswamy H. Sarma.

Optimal Control of the F1-ATPase Molecular Motor.

F1-ATPase is a rotary molecular motor that in vivo is subject to strong nonequilibrium driving forces. There is great interest in understanding the operational principles governing its high efficiency of free-energy transduction. Here we use a near-equilibrium framework to design a nontrivial control protocol to minimize dissipation in rotating F1 to synthesize adenosine triphosphate. We find that the designed protocol requires much less work than a naive (constant-velocity) protocol across a wide range of protocol durations. Our analysis points to a possible mechanism for energetically efficient driving of F1 in vivo and provides insight into free-energy transduction for a broader class of biomolecular and synthetic machines.

Information flow, gating, and energetics in dimeric molecular motors.

Molecular motors, kinesin and myosin, are dimeric consisting of two linked identical monomeric globular proteins. Fueled by the free energy generated by ATP hydrolysis, they walk on polar tracks (microtubule or filamentous actin) processively, which means that only one head detaches and executes a mechanical step while the other stays bound to the track. One motor head must regulate the chemical state of the other, referred to as "gating", a concept that is still not fully understood. Inspired by experiments, showing that only a fraction of the energy from ATP hydrolysis is used to advance the kinesin motors against load, we demonstrate that the rest of the energy is associated with chemical transitions in the two heads. The coordinated chemical transitions involve communication between the two heads - a feature that characterizes gating. We develop a general framework, based on information theory and stochastic thermodynamics, and establish that gating could be quantified in terms of information flow between the motor heads. Applications to kinesin-1 and Myosin V show that information flow, with positive cooperativity, at external resistive loads less than a critical value, Fc. When force exceeds Fc, effective information flow ceases. Interestingly, Fc, which is independent of the input energy generated through ATP hydrolysis, coincides with the force at which the probability of backward steps starts to increase. Our findings suggest that transport efficiency is optimal only at forces less than Fc, which implies that these motors must operate at low loads under in vivo conditions.

Cooperation and Competition Coexist in Bidirectional Transport by Motor Proteins.

In intracellular transport, the cargo is usually simultaneously carried by two types of motor proteins that move oppositely, widely described as a "tug-of-war". We show theoretically that apart from the apparent competition, there is also a unintuitive cooperation between motors with opposite directionality. The model reproduces the in vivo experimental data with high accuracy. Under certain conditions, the cooperation can significantly increase the transport distance, rationalizing the choice of bidirectional over unidirectional transport in evolution. We further derive the exact analytical solution for the transport distance. Our results pave the road to understanding the physical nature of intracellular transport by motor proteins.

Intrinsically unidirectional chemically fuelled rotary molecular motors.

Biological systems mainly utilize chemical energy to fuel autonomous molecular motors, enabling the system to be driven out of equilibrium1. Taking inspiration from rotary motors such as the bacterial flagellar motor2 and adenosine triphosphate synthase3, and building on the success of light-powered unidirectional rotary molecular motors4-6, scientists have pursued the design of synthetic molecular motors solely driven by chemical energy7-13. However, designing artificial rotary molecular motors operating autonomously using a chemical fuel and simultaneously featuring the intrinsic structural design elements to allow full 360° unidirectional rotary motion like adenosine triphosphate synthase remains challenging. Here we show that a homochiral biaryl Motor-3, with three distinct stereochemical elements, is a rotary motor that undergoes repetitive and unidirectional 360° rotation of the two aryl groups around a single-bond axle driven by a chemical fuel. It undergoes sequential ester cyclization, helix inversion and ring opening, and up to 99% unidirectionality is realized over the autonomous rotary cycle. The molecular rotary motor can be operated in two modes: synchronized motion with pulses of a chemical fuel and acid-base oscillations; and autonomous motion in the presence of a chemical fuel under slightly basic aqueous conditions. This rotary motor design with intrinsic control over the direction of rotation, simple chemical fuelling for autonomous motion and near-perfect unidirectionality illustrates the potential for future generations of multicomponent machines to perform mechanical functions.

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 symmetry1-5. Ratcheting is thought to underpin the function of many natural biological motors, such as the F1F0-ATPase6-8, 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 synthesis9-12. DNA nanotechnology13 has yielded a variety of nanoscale mechanisms, including pivots, hinges, crank sliders and rotary systems14-17, which can adopt different configurations, for example, triggered by strand-displacement reactions18,19 or by changing environmental parameters such as pH, ionic strength, temperature, external fields and by coupling their motions to those of natural motor proteins20-26. This previous work and considering low-Reynolds-number dynamics and inherent stochasticity27,28 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.

Impact of noise on the regulation of intracellular transport of intermediate filaments.

Noise affects all biological processes from molecules to cells, organisms and populations. Although the effect of noise on these processes is highly variable, evidence is accumulating which shows natural stochastic fluctuations (noise) can facilitate biological functions. Herein, we investigate the effect of noise on the transport of intermediate filaments in cells by comparing the stochastic and deterministic formalizations of the bidirectional transport of intermediate filaments, long elastic polymers transported along microtubules by antagonistic motor proteins (Dallon et al., 2019; Portet et al., 2019). By numerically exploring discrepancies in timescales and attractors between both formalizations, we characterize the impact of stochastic fluctuations on the individual and ensemble transport. Biologically, we find that noise promotes the collective movement of intermediate filaments and increases the efficiency of its regulation by the biochemical properties of motor-cargo interactions. While stochastic fluctuations reduce the impact of the initial distributions of motor proteins in cells, the number of binding sites and the affinity of motor-cargo interactions are the key parameters controlling transport efficiency and efficacy.

Editorial to the Special Issue "Molecular Motors: From Single Molecules to Cooperative and Regulatory Mechanisms In Vivo".

The Molecular motors or motor proteins are able to generate force and do mechanical work that is used to displace a load or produce relative movements between molecules or macromolecular assembles [...].

Retraction ATPase Motors from Three Orthologous Type IVa Pilus Systems Support Promiscuous Retraction of the Vibrio cholerae Competence Pilus.

Bacterial surface appendages called type IVa pili (T4aP) promote diverse activities, including DNA uptake, twitching motility, and virulence. These activities rely on the ability of T4aP to dynamically extend and retract from the cell surface. Dynamic extension relies on a motor ATPase commonly called PilB. Most T4aP also rely on specific motor ATPases, commonly called PilT and PilU, to dynamically and forcefully retract. Here, we systematically assess whether motor ATPases from three orthologous T4aP can functionally complement Vibrio cholerae mutants that lack their endogenous motors. We found that the PilT and PilU retraction ATPases from the three T4aP systems tested are promiscuous and promote the retraction of the V. cholerae competence T4aP despite a high degree of sequence divergence. In contrast, the orthologous extension ATPases from the same T4aP systems were not able to mediate the extension of the V. cholerae competence T4aP despite exhibiting a similar degree of sequence divergence. Also, we show that one of the PilT orthologs characterized does not support PilU-dependent retraction and provide some data to indicate that the C terminus of PilT is important for PilU-dependent retraction. Together, our data suggest that retraction ATPases may have maintained a high degree of promiscuity for promoting the retraction of T4aP, while extension ATPases may have evolved to become specific for their cognate systems. IMPORTANCE One way in which bacteria interact with their environments is via hair-like appendages called type IVa pili (T4aP). These appendages dynamically extend and retract from the cell surface via the action of distinct ATPase motors. T4aP are present in diverse bacterial species. Here, we demonstrate that retraction motors from three T4aP are promiscuous and capable of promoting the retraction of a heterologous T4aP system. In contrast, the extension ATPase motors from these same T4aP systems are specific and cannot promote the extension of a heterologous T4aP. Thus, these results suggest that T4aP extension may be more tightly regulated than T4aP retraction.

Human HELB is a processive motor protein that catalyzes RPA clearance from single-stranded DNA.

Human DNA helicase B (HELB) is a poorly characterized helicase suggested to play both positive and negative regulatory roles in DNA replication and recombination. In this work, we used bulk and single-molecule approaches to characterize the biochemical activities of HELB protein with a particular focus on its interactions with Replication Protein A (RPA) and RPA­single-stranded DNA (ssDNA) filaments. HELB is a monomeric protein that binds tightly to ssDNA with a site size of ∼20 nucleotides. It couples ATP hydrolysis to translocation along ssDNA in the 5' to 3' direction accompanied by the formation of DNA loops. HELB also displays classical helicase activity, but this is very weak in the absence of an assisting force. HELB binds specifically to human RPA, which enhances its ATPase and ssDNA translocase activities but inhibits DNA unwinding. Direct observation of HELB on RPA nucleoprotein filaments shows that translocating HELB concomitantly clears RPA from ssDNA. This activity, which can allow other proteins access to ssDNA intermediates despite their shielding by RPA, may underpin the diverse roles of HELB in cellular DNA transactions.