Millisecond curing time of a molecular adhesive causes velocity-dependent cargo-loading of molecular shuttles

Cooperative cargo transportation by a swarm of molecular machines

Cooperation is a strategy that has been adopted by groups of organisms to execute complex tasks more efficiently than single entities. Cooperation increases the robustness and flexibility of the working groups and permits sharing of the workload among individuals. However, the utilization of this strategy in artificial systems at the molecular level, which could enable substantial advances in microrobotics and nanotechnology, remains highly challenging. Here, we demonstrate molecular transportation through the cooperative action of a large number of artificial molecular machines, photoresponsive DNA-conjugated microtubules driven by kinesin motor proteins. Mechanical communication via conjugated photoresponsive DNA enables these microtubules to organize into groups upon photoirradiation. The groups of transporters load and transport cargo, and cargo unloading is achieved by dissociating the groups into single microtubules. The group formation permits the loading and transport of cargoes with larger sizes and in larger numbers over long distances compared with single transporters. We also demonstrate that cargo can be collected at user-determined locations defined by ultraviolet light exposure. This work demonstrates cooperative task performance by molecular machines, which will help to construct molecular robots with advanced functionalities in the future.

Robotic end-to-end fusion of microtubules powered by kinesin

The active assembly of molecules by nanorobots has advanced greatly since “molecular manufacturing”—that is, the use of nanoscale tools to build molecular structures—was proposed. In contrast to a catalyst, which accelerates a reaction by smoothing the potential energy surface along the reaction coordinate, molecular machines expend energy to accelerate a reaction relative to the baseline provided by thermal motion and forces. Here, we design a nanorobotics system to accelerate end-to-end microtubule assembly by using kinesin motors and a circular confining chamber. We show that the mechanical interaction of kinesin-propelled microtubules gliding on a surface with the walls of the confining chamber results in a nonequilibrium distribution of microtubules, which increases the number of end-to-end microtubule fusion events 20-fold compared with microtubules gliding on a plane. In contrast to earlier nanorobots, where a nonequilibrium distribution was built into the initial state and drove the process, our nanorobotic system creates and actively maintains the building blocks in the concentrated state responsible for accelerated assembly through the adenosine triphosphate–fueled generation of force by kinesin-1 motor proteins. This approach can be used in the future to develop biohybrid or bioinspired nanorobots that use molecular machines to access nonequilibrium states and accelerate nanoscale assembly.

Controlling the length of self-assembled microtubes through mechanical stress-induced scission

We demonstrate that mechanical stress-induced scission is an effective strategy to control the length of self-assembled microtubes. By applying mechanical stress with variable magnitude and mode, the length of microtubes can be tightly regulated. We have succeeded in reducing the average length of microtubes ∼twenty-fold through stretching and compression. The mechanical stress-induced scission of self-assembled, long microtubes into smaller fragments has no adverse effect on the functionality of the microtubes. This work will foster the applications of length-controlled, self-assembled microtubes in various fields.

Synchronous operation of biomolecular engines

Biomolecular motor systems are the smallest natural machines with an ability to convert chemical energy into mechanical work with remarkably high efficiency. Such attractive features enabled biomolecular motors to become classic tools in soft matter research over the past decade. For designing suitably engineered biomimetic systems, the biomolecular motors can potentially be used as molecular engines that can transform energy and ensure great advantages for the construction of bio-nanodevices and molecular robots. From the optimization of their prolonged lifetime to coordinate them into highly complex and ordered structures, enormous efforts have been devoted to make them useful in the synthetic environment. Synchronous operation of the biomolecular engines is one of the key criteria to coordinate them into certain different patterns, which depends on the local interaction of biomolecular motors. Utilizing chemical and physical stimuli, synchronization of biomolecular motor systems has become possible, which allows them to coordinate into different higher ordered patterns with different modes of functionality. Recently, programmed synchronous operation of the biomolecular engines has also been demonstrated, using a smart biomaterial to build up swarms reminiscent of nature. Here, we review the recent progress in the synchronized operation of biomolecular motors in engineered systems to explicitly program their interaction and further their applications. Such developments in the coordination of biomolecular motors have opened a broad way to explore the construction of future autonomous molecular machines and robots based on synchronization of biomolecular engines.

Tunable seat belt behavior in nanocomposite interfaces inspired from bacterial adhesion pili

A challenging problem in designing nanocomposites is to engineer nanoparticle interfaces that have tunable cohesive strength and rate-responsive behavior, for which inspiration can be taken from biological systems. An exemplary bio-interface is the Chaperone-Usher (CU) pili, such as type 1 expressed by bacteria Escherichia coli. The pili have unique biomechanical properties that enhance the ability of bacteria to sustain attachment to surfaces under large stresses, such as constant force extensibility, logarithmic velocity-uncoiling force dependence, and adhesive tips with catch bond behavior that exhibit longer bond life-times at greater force levels. Although biophysics of the pili under strain or stress is well-studied for anti-infective applications that aim to compromise pili adhesion, utilizing the biomechanical properties of the pili in material design applications is yet to be explored. In this work, we modeled the elongation of a single CU pilus with catch bond tip adhesin and examined its toughness response using Monte Carlo simulations. We showed that the pilus can act as a "molecular seat belt" that exhibits low toughness when pulled slowly and high toughness when pulled rapidly. Furthermore, we found that systematically varying the catch bond and shaft parameters leads to tunable seat belt behavior at the interface, where the sharpness of the transition from the low toughness to the high toughness regime and the velocity at the start of the transition can be dictated by molecular design parameters. Lastly, we tested the performance of CU pilus in slowing down a fast particle, and reveal that pili can effectively stop micron size projectiles with high initial velocities. The molecular seat belt mechanism presented here provides insight into how nanocomposite interfaces can be engineered to create molecular networks with linkers that switch on or off depending on strain rate.

Polymer surface properties control the function of heavy meromyosin in dynamic nanodevices

The actin-myosin system, responsible for muscle contraction, is also the force-generating element in dynamic nanodevices operating with surface-immobilized motor proteins. These devices require materials that are amenable to micro- and nano-fabrication, but also preserve the bioactivity of molecular motors. The complexity of the protein-surface systems is greatly amplified by those of the polymer-fluid interface; and of the structure and function of molecular motors, making the study of these interactions critical to the success of molecular motor-based nanodevices. We measured the density of the adsorbed motor protein (heavy meromyosin, HMM) using quartz crystal microbalance; and motor bioactivity with ATPase assay, on a set of model surfaces, i.e., nitrocellulose, polystyrene, poly(methyl methacrylate), and poly(butyl methacrylate), poly(tert-butyl methacrylate). A higher hydrophobicity of the adsorbing material translates in a higher total number of HMM molecules per unit area, but also in a lower uptake of water, and a lower ratio of active per total HMM molecules per unit area. We also measured the motility characteristics of actin filaments on the model surfaces, i.e., velocity, smoothness and deflection of movement, determined via in vitro motility assays. The filament velocities were found to be controlled by the relative number of active HMM per total motors, rather than their absolute surface density. The study allowed the formulation of the general engineering principles for the selection of polymeric materials for the manufacturing of dynamic nanodevices using protein molecular motors.

Molecular wear of microtubules propelled by surface-adhered kinesins

Wear is the progressive loss of material from a body caused by contact and relative movement and is a major concern in both engineering and biology. Advances in nanotechnology have allowed the origins of wear processes to be studied at the atomic and molecular scale, but also demand that wear in nanoscale systems can be predicted and controlled. Biomolecular systems can undergo a range of active movements at the nanoscale, which are enabled by the transduction of chemical energy into mechanical work by polymerization processes and motor proteins. The active movements are accompanied by dissipative processes that can be conceptually understood as 'protein friction'. Here, we show that wear also occurs in an in vitro system consisting of microtubules gliding across a surface coated with kinesin-1 motor proteins, and that energetic considerations suggest a molecule-by-molecule removal of tubulin proteins. The rates of removal show a complex dependence on sliding velocity and kinesin density, which, in contrast to the friction behaviour between microtubules and kinesin-8, cannot be explained by simple chemical reaction kinetics.

Sample solution constraints on motor-driven diagnostic nanodevices

The last decade has seen appreciable advancements in efforts towards increased portability of lab-on-a-chip devices by substituting microfluidics with molecular motor-based transportation. As of now, first proof-of-principle devices have analyzed protein mixtures of low complexity, such as target protein molecules in buffer solutions optimized for molecular motor performance. However, in a diagnostic work-up, lab-on-a-chip devices need to be compatible with complex biological samples. While it has been shown that such samples do not interfere with crucial steps in molecular diagnostics (for example antibody-antigen recognition), their effect on molecular motors is unknown. This critical and long overlooked issue is addressed here. In particular, we studied the effects of blood, cell lysates and solutions containing genomic DNA extracts on actomyosin and kinesin-microtubule-based transport, the two biomolecular motor systems that are most promising for lab-on-a-chip applications. We found that motor function is well preserved at defined dilutions of most of the investigated biological samples and demonstrated a molecular motor-driven label-free blood type test. Our results support the feasibility of molecular-motor driven nanodevices for diagnostic point-of-care applications and also demonstrate important constraints imposed by sample composition and device design that apply both to kinesin-microtubule and actomyosin driven applications.

Modeling negative cooperativity in streptavidin adsorption onto biotinylated microtubules

The nanoscale architecture of binding sites can result in complex binding kinetics. Here, the adsorption of streptavidin and neutravidin to biotinylated microtubules is found to exhibit negative cooperativity due to electrostatic interactions and steric hindrance. This behavior is modeled by a newly developed kinetic analogue of the Fowler-Guggenheim adsorption model. The complex adsorption kinetics of streptavidin to biotinylated structures needs to be considered when these intermolecular bonds are employed in self-assembly and nanobiotechnology.

Superhydrophobic alkanethiol-coated microsubmarines for effective removal of oil

We demonstrate the use of artificial nanomachines for effective interaction, capture, transport, and removal of oil droplets. The simple nanomachine-enabled oil collection method is based on modifying microtube engines with a superhydrophobic layer able to adsorb oil by means of its strong adhesion to a long chain of self-assembled monolayers (SAMs) of alkanethiols created on the rough gold outer surface of the device. The resultant SAM-coated Au/Ni/PEDOT/Pt microsubmarine displays continuous interaction with large oil droplets and is capable of loading and transporting multiple small oil droplets. The influence of the alkanethiol chain length, polarity, and head functional group and hence of the surface hydrophobicity upon the oil-nanomotor interaction and the propulsion is examined. No such oil-motor interactions were observed in control experiments involving both unmodified microengines and microengines coated with SAM layers containing a polar terminal group. These results demonstrate that such SAM-Au/Ni/PEDOT/Pt micromachines can be useful for a facile, rapid, and efficient collection of oils in water samples, which can be potentially exploited for other water-oil separation systems. The integration of oil-sorption properties into self-propelled microengines holds great promise for the remediation of oil-contaminated water samples and for the isolation of other hydrophobic targets, such as drugs.

Selective control of gliding microtubule populations

First lab-on-chip devices based on active transport by biomolecular motors have been demonstrated for basic detection and sorting applications. However, to fully employ the advantages of such hybrid nanotechnology, versatile spatial and temporal control mechanisms are required. Using a thermo-responsive polymer, we demonstrate the selective starting and stopping of modified microtubules gliding on a kinesin-1-coated surface. This approach allows the self-organized separation of multiple microtubule populations and their respective cargoes.

Nanoscale transport enables active self-assembly of millimeter-scale wires

Active self-assembly processes exploit an energy source to accelerate the movement of building blocks and intermediate structures and modify their interactions. A model system is the assembly of biotinylated microtubules partially coated with streptavidin into linear bundles as they glide on a surface coated with kinesin motor proteins. By tuning the assembly conditions, microtubule bundles with near millimeter length are created, demonstrating that active self-assembly is beneficial if components are too large for diffusive self-assembly but too small for robotic assembly.

Fatigue failure and molecular machine design

Sophisticated molecular machines have evolved in nature, and the first synthetic molecular machines have been demonstrated. With our increasing understanding of individual operating cycles, the question of how operation can be sustained over many cycles comes to the forefront. In the design of macroscale machines, performance and lifetime are opposing goals. Similarly, the natural evolution of biological nanomachines, such as myosin motor proteins, is likely constrained by lifetime requirements. Rather than bond rupture at high forces, bond fatigue under repeated small stresses may limit the mechanical performance of molecular machines. Here, the effect of cyclic stresses using single and double bonds as simple examples are discussed. Additionally, it is demonstrated that an increase in lifetime requires a reduction in mechanical load and that molecular engineering design features, such as polyvalent bonds capable of rebinding, can extend the bond lifetime dramatically. A universal scaling law for the force output of motors is extrapolated to the molecular scale to estimate the design space for molecular machines.

Polymer-based catch-bonds

Catch-bonds refer to the counterintuitive notion that the average lifetime of a bond has a maximum at a nonzero applied force. They have been found in several ligand-receptor pairs and their origin is still a topic of debate. Here, we use coarse-grained simulations and kinetic theory to demonstrate that a multimeric protein, with self-interacting domain pairs, can display catch-bond behavior. Our model is motivated by one of the largest proteins in the human body, the von Willebrand Factor, which has been found to display this behavior. In particular, our model polymer consists of a series of repeating units that self-interact with their nearest neighbors along the chain. Each of the units mimics a domain of the protein. Apart from the short-range specific interaction, we also include a linker chain that will hold the domains together if unbinding occurs. This linker molecule represents the sequence of unfolded amino acids that connect contiguous domains, as is typically found in multidomain proteins. The units also interact with an immobilized ligand, but the interaction is masked by the presence of the self-interacting neighbor along the chain. Our results show that this model displays all the features of catch-bonds because the average lifetime of a binding event between the polymer and the immobilized receptor has a maximum at a nonzero pulling force of the polymer. The effects of the energy barriers for detaching the masking domain and the ligand from the binding domain, as well as the effects of the properties of the polypeptide chain connecting the contiguous domains, are also studied. Our study suggests that multimeric proteins can engage in catch-bonds if their self-interactions are carefully tuned, and this mechanism presumably plays a major role in the mechanics of extracellular proteins that share a multidomain character. Furthermore, our biomimetic design clearly shows how one could build and tune macromolecules that exhibit catch-bond characteristics.

Cargo loading onto kinesin powered molecular shuttles

Cells have evolved sophisticated molecular machinery, such as kinesin motor proteins and microtubule filaments, to support active intracellular transport of cargo. While kinesins tail domain binds to a variety of cargoes, kinesins head domains utilize the chemical energy stored in ATP molecules to step along the microtubule lattice. The long, stiff microtubules serve as tracks for long-distance intracellular transport. These motors and filaments can also be employed in microfabricated synthetic environments as components of molecular shuttles. In a frequently used design, kinesin motors are anchored to the track surface through their tails, and functionalized microtubules serve as cargo carrying elements, which are propelled by these motors. These shuttles can be loaded with cargo by utilizing the strong and selective binding between biotin and streptavidin. The key components (biotinylated tubulin, streptavidin, and biotinylated cargo) are commercially available. Building on the classic inverted motility assay, the construction of molecular shuttles is detailed here. Kinesin motor proteins are adsorbed to a surface precoated with casein; microtubules are polymerized from biotinylated tubulin, adhered to the kinesin and subsequently coated with rhodamine-labeled streptavidin. The ATP concentration is maintained at subsaturating concentration to achieve a microtubule gliding velocity optimal for loading cargo. Finally, biotinylated fluorescein-labeled nanospheres are added as cargo. Nanospheres attach to microtubules as a result of collisions between gliding microtubules and nanospheres adhering to the surface. The protocol can be readily modified to load a variety of cargoes such as biotinylated DNA, quantum dots or a wide variety of antigens via biotinylated antibodies.

Biomolecular-motor-based autonomous delivery of lipid vesicles as nano- or microscale reactors on a chip

We aimed to create an autonomous on-chip system that performs targeted delivery of lipid vesicles (liposomes) as nano- or microscale reactors using machinery from biological systems. Reactor-liposomes would be ideal model cargoes to realize biomolecular-motor-based biochemical analysis chips; however, there are no existing systems that enable targeted delivery of cargo-liposomes in an autonomous manner. By exploiting biomolecular-motor-based motility and DNA hybridization, we demonstrate that single-stranded DNA (ssDNA)-labeled microtubules (MTs), gliding on kinesin-coated surfaces, acted as cargo transporters and that ssDNA-labeled cargo-liposomes were loaded/unloaded onto/from gliding MTs without bursting at loading reservoirs/micropatterned unloading sites specified by DNA base sequences. Our results contribute to the development of an alternative strategy to pressure-driven or electrokinetic flow-based microfluidic devices.

Molecular shuttles powered by motor proteins: loading and unloading stations for nanocargo integrated into one device

A central challenge on the way to engineer novel materials and nanodevices comprising active transport by nanomotors is the integration of cargo loading and unloading stations on one chip. Exploiting DNA hybridization in zipping and shearing geometries, we demonstrate spatially distinct cargo pick-up and unload by "molecular shuttles" in an integrated device. With this approach, applications can be realized where motor-driven processes are needed to enable transport and active sorting of analytes and nanosystems, or the reconfiguration or self-repair of materials and devices.

Towards the application of cytoskeletal motor proteins in molecular detection and diagnostic devices

Over the past ten years, great advancements have been made towards using biomolecular motors for nanotechnological applications. In particular, devices using cytoskeletal motor proteins for molecular transport are maturing. First efforts towards designing such devices used motor proteins attached to micro-structured substrates for the directed transport of microtubules and actin filaments. Soon thereafter, the specific capture, transport and detection of target analytes like viruses were demonstrated. Recently, spatial guiding of the gliding filaments was added to increase the sensitivity of detection and allow parallelization. Whereas molecular motor powered devices have not yet demonstrated performance beyond the level of existing detection techniques, the potential is great: Replacing microfluidics with transport powered by molecular motors allows integration of the energy source (ATP) into the assay solution. This opens up the opportunity to design highly integrated, miniaturized, autonomous detection devices. Such devices, in turn, may allow fast and cheap on-site diagnosis of diseases and detection of environmental pathogens and toxins.

Two-stage capture employing active transport enables sensitive and fast biosensors

Nanoscale sensors enable the detection of analytes with improved signal-to-noise ratio but suffer from mass transport limitations. Molecular shuttles, assembled from, e.g., antibody-functionalized microtubules and kinesin motor proteins, can selectively capture analytes from solution and deliver the analytes to a sensor patch. This two-stage process can accelerate mass transport to nanoscale biosensors and facilitate the rapid detection of analytes. Here, the possible increase of the signal-to-noise ratio is calculated, and the optimal layout of a system which integrates active transport is determined.

"Smart dust" biosensors powered by biomolecular motors

The concept of a microfabricated biosensor for environmental and biomedical monitoring applications which is composed of environmentally benign components is presented. With a built-in power source (the biological fuel ATP) and driven by biological motors (kinesin), sensing in the microdevice can be remotely activated and the presence of a target molecule or toxin remotely detected. The multifaceted progress towards the realization of such a device is described.

Biomolecular-motor-based nano- or microscale particle translocations on DNA microarrays

We aimed to create autonomous on-chip systems that perform targeted translocations of nano- or microscale particles in parallel using machinery that mimics biological systems. By exploiting biomolecular-motor-based motility and DNA hybridization, we demonstrate that single-stranded DNA-labeled microtubules gliding on kinesin-coated surfaces acted as cargo translocators and that single-stranded DNA-labeled cargoes were loaded/unloaded onto/from gliding microtubules at micropatterned loading/unloading sites specified by DNA base sequences. Our results will help to create autonomous molecular sorters and sensors.