Molecular Motor System Research Articles

Azo-dye Antibacterial with Nanotube-[SiO2(OH)2]9 System for Drug Delivery Investigation

Azo dye, [SiO2(OH)2]9 molecular ring, and single-walled carbon nanotubes (4,4) SWCNT were considered like an axle, a wheel, and stoppers, respectively. The combination of the azo dye on the [SiO2(OH)2]9 molecular ring with (4,4) SWCNTs may be thought of as a non-covalent system in UV light-isomer- machine. A new molecular motor system that runs like a hinge motion is demonstrated like light-powered molecular hinges. A new molecular motor system that acts as a hinge motion has been demonstrated and introduced as light-moving molecular hinges. By emitting various ultraviolet, visible lights, the [SiO2 (OH)2]9 molecular ring in the system can be reversed with the various dumb-bell size on one side attached halogens and fixing it on the other side of the (4,4) SWCNTs surface, a variety of systems in a wide variety of ultraviolet sensors can be designated to a better model of molecular machines and can be used for drug delivery of some antibiotics that are difficult to administer by straight injection. Molecular machines containing a wide variety of ultraviolet sensors have been designed with the combination of azo derivatives formed by replacing different halogens with hydrogen in the azo dye on the [SiO2(OH)2]9 molecular ring to the (4,4) SWCNTs surface.

Physical requirements for scaling up network-based biocomputation

The high energy consumption of electronic data processors, together with physical challenges limiting their further improvement, has triggered intensive interest in alternative computation paradigms. Here we focus on network-based biocomputation (NBC), a massively parallel approach where computational problems are encoded in planar networks implemented with nanoscale channels. These networks are explored by biological agents, such as biological molecular motor systems and bacteria, benefitting from their energy efficiency and availability in large numbers. We analyse and define the fundamental requirements that need to be fulfilled to scale up NBC computers to become a viable technology that can solve large NP-complete problem instances faster or with less energy consumption than electronic computers. Our work can serve as a guide for further efforts to contribute to elements of future NBC devices, and as the theoretical basis for a detailed NBC roadmap.

PyUNIxMD: A Python-based excited state molecular dynamics package.

Theoretical/computational description of excited state molecular dynamics is nowadays a crucial tool for understanding light‐matter interactions in many materials. Here we present an open‐source Python‐based nonadiabatic molecular dynamics program package, namely PyUNIxMD, to deal with mixed quantum‐classical dynamics for correlated electron‐nuclear propagation. The PyUNIxMD provides many interfaces for quantum chemical calculation methods with commercial and noncommercial ab initio and semiempirical quantum chemistry programs. In addition, the PyUNIxMD offers many nonadiabatic molecular dynamics algorithms such as fewest‐switch surface hopping and its derivatives as well as decoherence‐induced surface hopping based on the exact factorization (DISH‐XF) and coupled‐trajectory mixed quantum‐classical dynamics (CTMQC) for general purposes. Detailed structures and flows of PyUNIxMD are explained for the further implementations by developers. We perform a nonadiabatic molecular dynamics simulation for a molecular motor system as a simple demonstration.

Modeling and analyzing a photo-driven molecular motor system: Ratchet dynamics and non-linear optical spectra.

A light-driven molecular motor system is investigated using a multi-state Brownian ratchet model described by a single effective coordinate with multiple electronic states in a dissipative environment. The rotational motion of the motor system is investigated on the basis of wavepacket dynamics. A current determined from the interplay between a fast photochemical isomerization (photoisomerization) process triggered by pulses and a slow thermal isomerization (thermalization) process arising from an overdamped environment is numerically evaluated. For this purpose, we employ the multi-state low-temperature quantum Smoluchowski equations that allow us to simulate the fast quantum electronic dynamics in the overdamped environment, where conventional approaches, such as the Zusman equation approach, fail to apply due to the positivity problem. We analyze the motor efficiency by numerically integrating the equations of motion for a rotator system driven by repeatedly impulsive excitations. When the time scales of the pulse repetition, photoisomerization, and thermalization processes are separated, the average rotational speed of the motor is determined by the time scale of thermalization. In this regime, the average rotational current can be described by a simple equation derived from a rate equation for the thermalization process. When laser pulses are applied repeatedly and the time scales of the photoisomerization and pulse repetition are close, the details of the photoisomerization process become important to analyze the entire rotational process. We examine the possibility of observing the photoisomerization and the thermalization processes associated with stationary rotating dynamics of the motor system by spectroscopic means, e.g., pump-probe, transient absorption, and two-dimensional electronic spectroscopy techniques.

Bacteriorhodopsin-Inspired Light-Driven Artificial Molecule Motors for Transmembrane Mass Transportation.

In nature, biological machines and motors can selectively transport cargoes across the lipid membranes to efficiently perform various physiological functions via ion channels or ion pumps. It is interesting and challengeable to develop artificial motors and machines of nanodimensions to controllably regulate mass transport in compartmentalized systems. In this work, we show a system of artificial molecular motors that uses light energy to perform transmembrane molecule transport through synthetical nanochannels. After functionalizing the polymer nanochannels with azobenzene derivatives, these nanomachines exhibit autonomous selective transport behavior over a long distance upon simultaneous irradiation with UV (365 nm) and visible (430 nm) light. With new strategies or suitable materials for directed molecular movement, such device can be regarded as a precursor of artificial light-driven molecular pumps.

Bacteriorhodopsin‐Inspired Light‐Driven Artificial Molecule Motors for Transmembrane Mass Transportation

AbstractIn nature, biological machines and motors can selectively transport cargoes across the lipid membranes to efficiently perform various physiological functions via ion channels or ion pumps. It is interesting and challengeable to develop artificial motors and machines of nanodimensions to controllably regulate mass transport in compartmentalized systems. In this work, we show a system of artificial molecular motors that uses light energy to perform transmembrane molecule transport through synthetical nanochannels. After functionalizing the polymer nanochannels with azobenzene derivatives, these nanomachines exhibit autonomous selective transport behavior over a long distance upon simultaneous irradiation with UV (365 nm) and visible (430 nm) light. With new strategies or suitable materials for directed molecular movement, such device can be regarded as a precursor of artificial light‐driven molecular pumps.

Supramolecularly directed rotary motion in a photoresponsive receptor

Stimuli-controlled motion at the molecular level has fascinated chemists already for several decades. Taking inspiration from the myriad of dynamic and machine-like functions in nature, a number of strategies have been developed to control motion in purely synthetic systems. Unidirectional rotary motion, such as is observed in ATP synthase and other motor proteins, remains highly challenging to achieve. Current artificial molecular motor systems rely on intrinsic asymmetry or a specific sequence of chemical transformations. Here, we present an alternative design in which the rotation is directed by a chiral guest molecule, which is able to bind non-covalently to a light-responsive receptor. It is demonstrated that the rotary direction is governed by the guest chirality and hence, can be selected and changed at will. This feature offers unique control of directional rotation and will prove highly important in the further development of molecular machinery.

Traffic control inside the cell: microtubule-based regulation of cargo transport

The cell relies on an intricate system of molecular highways and motors to transport proteins, organelles and other vesicular cargoes to their proper locations. Microtubules, long filaments that form a network throughout the cell, act as highways. The motor proteins kinesin and dynein associate with cargoes and transport them along microtubules. Rather than simply acting as passive tracks, microtubules contain signals that regulate kinesin and dynein to target cargoes to specific locations in the cell. These signals include the organization of the microtubule network, chemical modifications that alter the microtubule surface properties and mechanics, and microtubuleassociated proteins that modulate the motility of motor proteins and microtubule polymerization.

Theory of nanobubble formation and induced force in nanochannels.

This paper presents a fundamental theory of nanobubble formation and induced force in confined nanochannels. It is shown that nanobubble formation between hydrophobic plates can be predicted from their surface tension and geometry, with estimated values for the surface free energy and the force acting on the plates in good agreement with the results of molecular dynamics simulation and experimentation. When a bubble is formed between two plates, vertical attractive force and horizontal retract force due to the shifted plates are applied to the plates. The net force exerted on the plates is not dependent on the distance between them. The short-range force between hydrophobic surfaces due to hydrophobic interaction appears to correspond to the force estimated by our theory. We compared between experimental and theoretical values for the binding energy of a molecular motor system to validate our theory. The tendency that the binding energy increases as the size of the protein increases is consistent with the theory.

Segregation of diffusible and directionally moving particles on a polar filament.

Directed transport in living cells relies on the action of motor proteins. These enzymes can transform chemical energy into mechanical work and move directionally along filamentous tracks. At the same time, these filaments serve as a substrate for the binding of proteins performing other functions, but that also obstruct the motors' motion. Motivated by the mobile cross-linker Ase1, we theoretically study a system of molecular motors in the presence of diffusible particles. Both the motors and the obstacles shuttle between the filament and its surrounding. Numerical simulations of this system show a segregation between motors and obstacles if the filament ends act as diffusion barriers for the obstacles. A phenomenological mean-field theory captures the essential effects observed in the simulations.

A modified active Brownian dynamics model using asymmetric energy conversion and its application to the molecular motor system

We consider a modified energy depot model in the overdamped limit using an asymmetric energy conversion rate, which consists of linear and quadratic terms in an active particle's velocity. In order to analyze our model, we adopt a system of molecular motors on a microtubule and employ a flashing ratchet potential synchronized to a stochastic energy supply. By performing an active Brownian dynamics simulation, we investigate effects of the active force, thermal noise, external load, and energy-supply rate. Our model yields the stepping and stalling behaviors of the conventional molecular motor. The active force is found to facilitate the forwardly processive stepping motion, while the thermal noise reduces the stall force by enhancing relatively the backward stepping motion under external loads. The stall force in our model decreases as the energy-supply rate is decreased. Hence, assuming the Michaelis-Menten relation between the energy-supply rate and the an ATP concentration, our model describes ATP-dependent stall force in contrast to kinesin-1.

An elastic-diffusion model for myosin Ⅵ molecular motor in a periodic potential field

Because of the special structure and intracellular functions of myosin Ⅵ molecular motor, its dynamic principle has become a research focus. Starting from its structure and experimental phenomenon, the elastic-diffusion model of myosin Ⅵ in a periodic potential field is established, and the stochastic dynamics of the molecular motors, which conform to the Langevin equation, is analyzed by Monte Carlo simulations. By means of the environmental noise, myosin Ⅵ molecular motors could take stable stepping motion and effective transport according to its elastic potential energy and periodic potential of track, and a load can weaken the transportation power of the molecular motor system. For a given elastic coefficient, the longer the elastic chain of myosin Ⅵ, the lower the average velocity of it. By selecting a reasonable size of elasticity coefficient, the average velocity can be the maximum for a given elastic chain. In addition, the load can increase exponentially the mean dwelling time of myosin Ⅵ at the connection site.

The single-direction energy transition model of molecular motor based on the control of adenosine triphosphate

The dynamic principle of molecular motor transport in overdamped solution remains unclear. Starting from the transport characteristics and phenomenon of the molecular motor system, the single-direction energy transition model is established, which conforms to the Langevin equation, and the stochastic dynamics of molecular motors is analyzed by Monte Carlo simulations. Results show that with the right transition energy, molecular motors could take a stable stepping motion and effective transport by means of the environment noise, and the load force can weaken material transportation of the molecular motor system. The potential field between a molecular motor and its orbit can affect the magnitude of the velocity of motor, but cannot change the direction of the velocity, the direction of motion of the molecular motor therefore is adjusted by the transition energy of the motor. In addition, although the average velocity is not zero for different noise intensities, the efficient transport of a molecular motor system indicates that the system is selective for the noise intensity.

Self-Organized Cell Motility from Motor-Filament Interactions

Cell motility is driven primarily by the dynamics of the cell cytoskeleton, a system of filamentous proteins and molecular motors. It has been proposed that cell motility is a self-organized process, that is, local short-range interactions determine much of the dynamics that are required for the whole-cell organization that leads to polarization and directional motion. Here we present a mesoscopic mean-field description of filaments, motors, and cell boundaries. This description gives rise to a dynamical system that exhibits multiple self-organized states. We discuss several qualitative aspects of the asymptotic states and compare them with those of living cells.

Walking motion of an overdamped active particle in a ratchet potential.

An active particle can convert its internal energy into mechanical work. We study a generalized energy-depot model of an overdamped active particle in a ratchet potential. Using well-known biological parameters for kinesin-1 and modeling ATP influx as a pulsed energy supply, we apply our model to the molecular motor system. We find that our simple model can capture the essential properties of the kinesin motor such as forward stepping, stalling, backward stepping, dependence on ATP concentration, and stall force. Our model might be quite universal in the sense that it is able to describe dynamics of various types of motors as long as realistic parameters for each motor species are adopted.

Minimum requirements for the actin-like treadmilling motor system

Actin is one of the most abundant proteins in eukaryote cells, which forms a double stranded filament. The actin filament is not only a main component of the cytoskeleton, but also acts as a motor protein which moves toward one specific end, the barbed end, driven by polymerization at the barbed end and depolymerization at the other end, the pointed end, without any associated proteins. This motor activity is referred to as “treadmilling” and it represents the simplest motor system known, consisting of only one 42 kDa protein, actin. Here we report the minimum requirements of the actin-like motor system elucidated by computer simulations: (1) Nucleotide binding and ATPase activity in the filament; (2) Polarity in the rates of polymerization and depolymerization between the two ends; and (3) The dependence of the subunit-subunit interactions on the bound nucleotide. These requirements are simple and this knowledge should facilitate the development of artificial molecular motor systems in the future.

Providing Positional Information with Active Transport on Dynamic Microtubules

Microtubules (MTs) are dynamic protein polymers that change their length by switching between growing and shrinking states in a process termed dynamic instability. It has been suggested that the dynamic properties of MTs are central to the organization of the eukaryotic intracellular space, and that they are involved in the control of cell morphology, but the actual mechanisms are not well understood. Here, we present a theoretical analysis in which we explore the possibility that a system of dynamic MTs and MT end-tracking molecular motors is providing specific positional information inside cells. We compute the MT length distribution for the case of MT-length-dependent switching between growing and shrinking states, and analyze the accumulation of molecular motors at the tips of growing MTs. Using these results, we show that a transport system consisting of dynamic MTs and associated motor proteins can deliver cargo proteins preferentially to specific positions within the cell. Comparing our results with experimental data in the model organism fission yeast, we propose that the suggested mechanisms could play important roles in setting length scales during cellular morphogenesis.

Biologically inspired molecular machines driven by light. Optimal control of a unidirectional rotor

We investigate the extent to which unidirectional intramolecular torsional motion can be created in an oriented bicyclic model system driven solely by laser light. We apply the machinery of quantum control via specifically tailored laser pulses to induce such motion, eliminating the need for the thermally constrained steps conventionally used in molecular motor systems. Our approach does not rely on specific details of the potential surfaces to create a preferred direction. Rather, we use matter–field interaction and the tools of coherent optimal control to create a wave packet with nonzero angular momentum among unbound torsional states on an excited electronic surface. Analysis of the results of the control algorithm provides general insight into when and how optimal control theory can find solutions that could not be generated through simple intuitive schemes. We find that, under constrained polarization, the control algorithm reduces to a simple intuitive coherent control strategy wherein a first IR pulse creates a non-stationary wave packet on the ground surface and a subsequent UV pulse transfers it to the excited state. Allowing for polarization shaping, however, we find new control routes that go beyond the intuitive scheme.

Transportation of Drug-(Polystyrene Bead) Conjugate by Actomyosin Motor System

The Nanorobotics and cargo transportation application of molecular motors is of recent intent. The present study explores the transportation of Mesalamine/5-aminosalicylic acid/5-ASA drug by molecular motors. Mesalamine is an anti-inflammatory drug used to treat Crohn's disease and ulcerative colitis. Conjugate of mesalamine and polystyrene (Dia.: 3 microm) beads was prepared by amide linkage between amine (-NH2) group of drug and carboxyl (-COOH) group of the bead. In Fourier Transform Infrared spectra, peaks were observed at 3428.1 and 1654.0 cm(-1) for N-H and C=O stretching bond respectively confirming the amide bond formation between drug and microbeads. Quantification of 5-ASA attached to polystyrene bead was done by UV-vis spectroscopy and it was ascertained that 93% of 5-ASA was loaded on polystyrene beads. Conjugate of drug-polystyrene beads were then covalently attached to actin filaments. Velocity of actin filaments attached to drug loaded beads in in-vitro motility assay reduced to 0.89 microm/s as compared to free actin velocity (4.64 microm/s). This further ascertains the microcomposites formation. The present study provides an insight into the actin-myosin based molecular motor systems for an efficient tool for drug transportation.

3P183 Information-heat engine as a model system of molecular motors(Molecular motor,The 48th Annual Meeting of the Biophysical Society of Japan)

3P183 Information-heat engine as a model system of molecular motors(Molecular motor,The 48th Annual Meeting of the Biophysical Society of Japan)