In silico design and testing of guiding tracks for molecular shuttles powered by kinesin motors.

We present an extended computer simulation method which allows in silico design and testing of guiding tracks for molecular shuttles powered by kinesin motors. The simulation reproduced molecular shuttle movements under external forces and dissociation of shuttles from guiding track surfaces. The simulation was validated by comparing the simulation results with the corresponding experimental ones. Using the simulation, track designers can change guiding track designs, choose guiding methods, tune the strength of external forces, and test the module performance. This simulation would significantly reduce the effort expended in designing guiding tracks for molecular shuttles powered by kinesin motors.

[1]  Taesung Kim,et al.  Active alignment of microtubules with electric fields. , 2007, Nano letters.

[2]  K. Oiwa,et al.  Behaviors of microtubules (MTs) driven by biological motors (dynein c) at collisions against micro-fabricated tracks and mts for potential nano-bio-machines. , 2009, Journal of nanoscience and nanotechnology.

[3]  C. Dekker,et al.  Microtubule curvatures under perpendicular electric forces reveal a low persistence length , 2008, Proceedings of the National Academy of Sciences.

[4]  T Kanayama,et al.  Controlling the direction of kinesin-driven microtubule movements along microlithographic tracks. , 2001, Biophysical journal.

[5]  Y Y Toyoshima,et al.  Fluctuation in the microtubule sliding movement driven by kinesin in vitro. , 1996, Biophysical journal.

[6]  D V Nicolau,et al.  Actin motion on microlithographically functionalized myosin surfaces and tracks. , 1999, Biophysical journal.

[7]  Yuichi Hiratsuka,et al.  Three approaches to assembling nano-bio-machines using molecular motors , 2006 .

[8]  Li-Jing Cheng,et al.  Highly efficient guiding of microtubule transport with imprinted CYTOP nanotracks. , 2005, Small.

[9]  J A Tuszynski,et al.  Analysis of the migration behaviour of single microtubules in electric fields. , 2002, Biochemical and biophysical research communications.

[10]  Hiroyuki Fujita,et al.  Unidirectional Transport of Kinesin-Coated Beads on Microtubules Oriented in a Microfluidic Device , 2004 .

[11]  L. Montelius,et al.  Actin-Based Molecular Motors for Cargo Transportation in Nanotechnology— Potentials and Challenges , 2005, IEEE Transactions on Advanced Packaging.

[12]  Katsuo Kurabayashi,et al.  Self-contained, biomolecular motor-driven protein sorting and concentrating in an ultrasensitive microfluidic chip. , 2008, Nano letters.

[13]  C. Dinu,et al.  Cellular Motors for Molecular Manufacturing , 2007, Anatomical record.

[14]  Katsuo Kurabayashi,et al.  Efficient designs for powering microscale devices with nanoscale biomolecular motors. , 2006, Small.

[15]  Viola Vogel,et al.  Mechanisms of Microtubule Guiding on Microfabricated Kinesin-Coated Surfaces: Chemical and Topographic Surface Patterns , 2003 .

[16]  Viola Vogel,et al.  Light-Controlled Molecular Shuttles Made from Motor Proteins Carrying Cargo on Engineered Surfaces , 2001 .

[17]  J. V. José,et al.  A dynamical model of kinesin-microtubule motility assays. , 2001, Biophysical journal.

[18]  Frédéric Gibou,et al.  Simulation tools for lab on a chip research: advantages, challenges, and thoughts for the future. , 2008, Lab on a chip.

[19]  Viola Vogel,et al.  Powering nanodevices with biomolecular motors. , 2004, Chemistry.

[20]  Takahiro Nitta,et al.  Dispersion in active transport by kinesin-powered molecular shuttles. , 2005, Nano letters.

[21]  Lars Montelius,et al.  Actin filament guidance on a chip: toward high-throughput assays and lab-on-a-chip applications. , 2006, Langmuir : the ACS journal of surfaces and colloids.

[22]  S. Mashiko,et al.  Control of actin moving trajectory by patterned poly(methylmethacrylate) tracks. , 1997, Biophysical journal.

[23]  Thomas N Jackson,et al.  Microscale Transport and Sorting by Kinesin Molecular Motors , 2004, Biomedical microdevices.

[24]  D. Nicolau,et al.  Protein Linear Molecular Motor-Powered Nanodevices , 2007 .

[25]  Cees Dekker,et al.  Motor Proteins at Work for Nanotechnology , 2007, Science.

[26]  Viola Vogel,et al.  Analysis of Microtubule Guidance in Open Microfabricated Channels Coated with the Motor Protein Kinesin , 2003 .

[27]  H. Hess,et al.  Ratchet patterns sort molecular shuttles , 2002 .

[28]  Frank Jülicher,et al.  Acting on actin: the electric motility assay , 1999, European Biophysics Journal.

[29]  K. Oiwa,et al.  The coordination of protein motors and the kinetic behavior of microtubule--a computational study. , 2007, Biophysical chemistry.

[30]  Takahiro Nitta,et al.  Comparing guiding track requirements for myosin- and kinesin-powered molecular shuttles. , 2008, Nano letters.

[31]  Ashutosh Agarwal,et al.  A smart dust biosensor powered by kinesin motors. , 2009, Nature nanotechnology.

[32]  Viola Vogel,et al.  Motor-protein "roundabouts": microtubules moving on kinesin-coated tracks through engineered networks. , 2004, Lab on a chip.

[33]  Takahiro Nitta,et al.  Simulating molecular shuttle movements: towards computer-aided design of nanoscale transport systems. , 2006, Lab on a chip.

[34]  Cees Dekker,et al.  Molecular Sorting by Electrical Steering of Microtubules in Kinesin-Coated Channels , 2006, Science.

[35]  H. Craighead,et al.  Powering an inorganic nanodevice with a biomolecular motor. , 2000, Science.

[36]  Thomas N Jackson,et al.  Microtubule transport, concentration and alignment in enclosed microfluidic channels , 2007, Biomedical microdevices.

[37]  Viola Vogel,et al.  "Smart dust" biosensors powered by biomolecular motors. , 2009, Lab on a chip.

[38]  Richard Superfine,et al.  Two-Dimensional Manipulation and Orientation of Actin−Myosin Systems with Dielectrophoresis , 2003 .

[39]  Viola Vogel,et al.  Molecular shuttles: directed motion of microtubules along nanoscale kinesin tracks , 1999 .

[40]  Russell J. Stewart,et al.  Toward kinesin-powered microdevices , 2000 .

[41]  Robert R. Ishmukhametov,et al.  Recent developments of bio-molecular motors as on-chip devices using single molecule techniques. , 2007, Lab on a chip.

[42]  Cees Dekker,et al.  High rectifying efficiencies of microtubule motility on kinesin-coated gold nanostructures. , 2005, Nano letters.

[43]  Roland Stracke,et al.  Motor protein-driven unidirectional transport of micrometer-sized cargoes across isopolar microtubule arrays , 2001 .

[44]  Viola Vogel,et al.  Harnessing biological motors to engineer systems for nanoscale transport and assembly. , 2008, Nature nanotechnology.

[45]  Roland Stracke,et al.  Physical and technical parameters determining the functioning of a kinesin-based cell-free motor system , 2000 .

[46]  Mary Elizabeth Williams,et al.  Directing transport of CoFe2O4-functionalized microtubules with magnetic fields. , 2007, Small.

[47]  Ernest F. Hasselbrink,et al.  Biomolecular motor-driven microtubule translocation in the presence of shear flow: analysis of redirection behaviours , 2007 .

[48]  Thomas N. Jackson,et al.  Lithographically patterned channels spatially segregate kinesin motor activity and effectively guide microtubule movements , 2003 .