Molecular trucks and complementary tracks for bionanotechnological applications

Motility resilience of molecular shuttles against defective motors

Myosin and kinesin are biomolecular motors found in living cells. By propelling their associated cytoskeletal filaments, these biomolecular motors facilitate force generation and material transport in the cells. When extracted, the biomolecular motors are promising candidates for in vitro applications such as biosensor devices, on account of their high operating efficiency and nanoscale size. However, during integration into these devices, some of the motors become defective due to unfavorable adhesion to the substrate surface. These defective motors inhibit the motility of the cytoskeletal filaments which make up the molecular shuttles used in the devices. Difficulties in controlling the fraction of active and defective motors in experiments discourage systematic studies concerning the resilience of the molecular shuttle motility against the impedance of defective motors. Here, we used mathematical modelling to systematically examine the resilience of the propulsion by these molecular shuttles against the impedance of the defective motors. The model showed that the fraction of active motors on the substrate is the essential factor determining the resilience of the molecular shuttle motility. Approximately 40% of active kinesin or 80% of active myosin motors are required to constitute continuous gliding of molecular shuttles in their respective substrates. The simplicity of the mathematical model in describing motility behavior offers utility in elucidating the mechanisms of the motility resilience of molecular shuttles.

Biomolecular interfaces based on self-assembly and self-recognition form biosensors capable of recording molecular binding and release

This research proposed to create the next generation of versatile electrochemical-based biosensors capable of monitoring target capture and release as dictated by molecular binding or unbinding. The biosensor integrates cellular machines (i.e., microtubules, structural elements of cells and kinesin molecular motors involved in cellular transport) as functional units; its assembly is based on molecular self-assembly and self-recognition. Our results demonstrate that the designed biosensor was capable of allowing detection of binding and unbinding events based on redox reactions at user-controlled electrode interfaces. The analysis also showed that the sensitivity of the designed biosensor or its ability to record such events could be user-controlled at any given time by adjusting the energy source that "fuels" the system.

Different Microtubule Structures Assembled by Kinesin Motors

The microtubule-kinesin system is used to form microtubule-based structures via microtubule gliding motility. On the kinesin-coated surface, the microtubules can be easily assembled into stable micro- and nanostructures like circles and microtubule bundles using the streptavidin-biotin system. Furthermore, these microtubules structures can still retain performance with kinesin motor movement in spite of different velocities. Collisions bear responsibility for the majority of events leading to circle formation. By taking advantage of biological substances, some micro- or nanostructures, which are difficult to fabricate by artificial processes, can be easily obtained.

Protein self-assembly onto nanodots leads to formation of conductive bio-based hybrids

The next generation of nanowires that could advance the integration of functional nanosystems into synthetic applications from photocatalysis to optical devices need to demonstrate increased ability to promote electron transfer at their interfaces while ensuring optimum quantum confinement. Herein we used the biological recognition and the self-assembly properties of tubulin, a protein involved in building the filaments of cellular microtubules, to create stable, free standing and conductive sulfur-doped carbon nanodots-based conductive bio-hybrids. The physical and chemical properties (e.g., composition, morphology, diameter etc.) of such user-synthesized hybrids were investigated using atomic and spectroscopic techniques, while the electron transfer rate was estimated using peak currents formed during voltammetry scanning. Our results demonstrate the ability to create individually hybrid nanowires capable to reduce energy losses; such hybrids could possibly be used in the future for the advancement and implementation into nanometer-scale functional devices.

Simulating an Actomyosin in Vitro Motility Assay: Toward the Rational Design of Actomyosin-Based Microtransporters

We present a simulation study of an actomyosin in vitro motility assay. In vitro motility assays have served as an essential element facilitating the application of actomyosin in nanotechnology; such applications include biosensors and biocomputation. Although actomyosin in vitro motility assays have been extensively investigated, some ambiguities remain, as a result of the limited spatio-temporal resolution and unavoidable uncertainties associated with the experimental process. These ambiguities hamper the rational design of nanodevices for practical applications. Here, with the aim of moving toward a rational design process, we developed a 3D computer simulation method of an actomyosin in vitro motility assay, based on a Brownian dynamics simulation. The simulation explicitly included the ATP hydrolysis cycle of myosin. The simulation was validated by the reproduction of previous experimental results. More importantly, the simulation provided new insights that are difficult to obtain experimentally, including data on the number of myosin motors actually binding to actin filaments, the mechanism responsible for the guiding of actin filaments by chemical edges, and the effect of the processivity of motor proteins on the guiding probabilities. The simulations presented here will be useful in interpreting experimental results, and also in designing future nanodevices integrated with myosin motors.

Understanding the guiding of kinesin/microtubule-based microtransporters in microfabricated tracks

Microtransporters using cargo-laden microtubules propelled by kinesin motors are attractive for numerous applications in nanotechnology. To improve the efficiency of transport, the movement of microtubules must be guided by microfabricated tracks. However, the mechanisms of the guiding methods used are not fully understood. Here, using computer simulation, we systematically studied the guiding of such microtransporters by three different types of guiding methods: a chemical boundary, a physical barrier, and their combination. The simulation reproduced the probabilities of guiding previously observed experimentally for the three methods. Moreover, the simulation provided further insight into the mechanisms of guiding, which overturn previous assumptions and models.

Plasma treatment of PDMS for applications of in vitro motility assays

In vitro motility assays are readily used to simplify the complex environments within the cell and in muscle tissue. These assays have afforded considerable insight into the fundamentals of their underlying biophysics, interactions with cargo, intracellular regulation, and motor cooperation/competition. Extension of the standard in vitro motility assay into a more automated and cost-effective fluidic design while providing availability to the scientific community without expertise in lithographic fabrication is critical for the continued advancement of the field. In this work, we utilized a standard plasma cleaner to oxidize the widely prevalent material polydimethylsiloxane (PDMS) to create flow cells that could be used for in vitro motility assays. Our analysis indicated that a 40 min pre-treatment of the PDMS with plasma exposure resulted in optimal bundle motility. This finding was attributed to the condition at which the least amount of oxygen permeates the PDMS slab, enters the motility buffer, and oxidizes the motor proteins. Based on these findings, we developed a method for constructing microfluidic devices from glass and plasma-treated PDMS molds in which motility could be observed.