Molecular motors: a theorist's perspective.

Individual molecular motors, or motor proteins, are enzymatic molecules that convert chemical energy, typically obtained from the hydrolysis of ATP (adenosine triphosphate), into mechanical work and motion. Processive motor proteins, such as kinesin, dynein, and certain myosins, step unidirectionally along linear tracks, specifically microtubules and actin filaments, and play a crucial role in cellular transport processes, organization, and function. In this review some theoretical aspects of motor-protein dynamics are presented in the light of current experimental methods that enable the measurement of the biochemical and biomechanical properties on a single-molecule basis. After a brief discussion of continuum ratchet concepts, we focus on discrete kinetic and stochastic models that yield predictions for the mean velocity, V(F, [ATP], ...), and other observables as a function of an imposed load force F, the ATP concentration, and other variables. The combination of appropriate theory with single-molecule observations should help uncover the mechanisms underlying motor-protein function.

[1]  Denis Tsygankov,et al.  Back-stepping, hidden substeps, and conditional dwell times in molecular motors. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[2]  Samara L. Reck-Peterson,et al.  Single-Molecule Analysis of Dynein Processivity and Stepping Behavior , 2006, Cell.

[3]  J. Joanny,et al.  Collective dynamics of interacting molecular motors. , 2006, Physical review letters.

[4]  M. S. Turner,et al.  A kinetic model describing the processivity of myosin-V. , 2006, Biophysical journal.

[5]  Hideo Higuchi,et al.  Overlapping hand-over-hand mechanism of single molecular motility of cytoplasmic dynein. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Polly M. Fordyce,et al.  Individual dimers of the mitotic kinesin motor Eg5 step processively and support substantial loads in vitro , 2006, Nature Cell Biology.

[7]  M. Fisher,et al.  Vectorial Loading of Processive Motor Proteins: Microtubule buckling experiment revisited , 2006 .

[8]  A. Kolomeisky,et al.  Transport of single molecules along the periodic parallel lattices with coupling. , 2005, The Journal of chemical physics.

[9]  D. Hackney,et al.  The tethered motor domain of a kinesin-microtubule complex catalyzes reversible synthesis of bound ATP. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[10]  K. Neuman,et al.  Statistical determination of the step size of molecular motors , 2005, Journal of physics. Condensed matter : an Institute of Physics journal.

[11]  R. Lipowsky,et al.  Cooperative cargo transport by several molecular motors. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Jianhua Xing,et al.  Making ATP. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Michael E Fisher,et al.  Kinesin crouches to sprint but resists pushing. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[14]  H. Qian Cycle kinetics, steady state thermodynamics and motors—a paradigm for living matter physics , 2005, Journal of physics. Condensed matter : an Institute of Physics journal.

[15]  Michio Homma,et al.  Direct observation of steps in rotation of the bacterial flagellar motor , 2005, Nature.

[16]  J. Spudich,et al.  From the Cover : A force-dependent state controls the coordination of processive myosin V , 2005 .

[17]  Jianhua Xing,et al.  From continuum Fokker-Planck models to discrete kinetic models. , 2005, Biophysical journal.

[18]  J. Sellers,et al.  Load-dependent kinetics of myosin-V can explain its high processivity , 2005, Nature Cell Biology.

[19]  M. Fisher,et al.  Vectorial loading of processive motor proteins: implementing a landscape picture , 2005, Journal of physics. Condensed matter : an Institute of Physics journal.

[20]  R. Cross,et al.  Mechanics of the kinesin step , 2005, Nature.

[21]  Dou Shuo-xing,et al.  Model for processive movement of myosin V and myosin VI , 2005 .

[22]  T. Kapoor,et al.  Monastrol Inhibition of the Mitotic Kinesin Eg5* , 2005, Journal of Biological Chemistry.

[23]  Frank Jülicher,et al.  Theory of mitotic spindle oscillations. , 2005, Physical review letters.

[24]  A. Vilfan Elastic lever-arm model for myosin V. , 2005, Biophysical journal.

[25]  A. Kolomeisky,et al.  Dynamic properties of motor proteins with two subunits , 2005, cond-mat/0503169.

[26]  A. Kolomeisky,et al.  Coupling of two motor proteins: a new motor can move faster. , 2005, Physical review letters.

[27]  Hiroyuki Fujita,et al.  Highly coupled ATP synthesis by F1-ATPase single molecules , 2005, Nature.

[28]  Hitoshi Sakakibara,et al.  Recent progress in dynein structure and mechanism. , 2005, Current opinion in cell biology.

[29]  Sean X. Sun,et al.  Dynamics of myosin-V processivity. , 2005, Biophysical journal.

[30]  Anatoly B Kolomeisky,et al.  Understanding mechanochemical coupling in kinesins using first-passage-time processes. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[31]  Pengye Wang,et al.  Model for processive movement of myosin V and myosin VI , 2003, q-bio/0312044.

[32]  Paul R Selvin,et al.  Myosin VI Steps via a Hand-over-Hand Mechanism with Its Lever Arm Undergoing Fluctuations when Attached to Actin* , 2004, Journal of Biological Chemistry.

[33]  P. Selvin,et al.  Nanometer localization of single green fluorescent proteins: evidence that myosin V walks hand-over-hand via telemark configuration. , 2004, Biophysical journal.

[34]  Shin'ichi Ishiwata,et al.  Mechanochemical coupling of two substeps in a single myosin V motor , 2004, Nature Structural &Molecular Biology.

[35]  M. Sheetz,et al.  A force-dependent switch reverses type IV pilus retraction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[36]  T. Lohman,et al.  Effects of temperature and ATP on the kinetic mechanism and kinetic step-size for E.coli RecBCD helicase-catalyzed DNA unwinding. , 2004, Journal of molecular biology.

[37]  J. Baker,et al.  Myosin V processivity: multiple kinetic pathways for head-to-head coordination. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Steven M Block,et al.  Forward and reverse motion of single RecBCD molecules on DNA. , 2004, Biophysical journal.

[39]  E. M. De La Cruz,et al.  Relating biochemistry and function in the myosin superfamily. , 2004, Current opinion in cell biology.

[40]  R. Vale,et al.  Kinesin Walks Hand-Over-Hand , 2004, Science.

[41]  Masasuke Yoshida,et al.  Mechanically driven ATP synthesis by F1-ATPase , 2004, Nature.

[42]  Steven M. Block,et al.  Kinesin Moves by an Asymmetric Hand-OverHand Mechanism , 2003 .

[43]  Howard C. Berg,et al.  E. coli in Motion , 2003 .

[44]  G. Charvin,et al.  Single-molecule study of DNA unlinking by eukaryotic and prokaryotic type-II topoisomerases , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[45]  R. Kanada,et al.  Theoretical model for motility and processivity of two-headed molecular motors. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[46]  Gerald R. Smith,et al.  RecBCD enzyme is a DNA helicase with fast and slow motors of opposite polarity , 2003, Nature.

[47]  Yale E. Goldman,et al.  Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization , 2003, Nature.

[48]  Ronald D Vale,et al.  The Molecular Motor Toolbox for Intracellular Transport , 2003, Cell.

[49]  Joshua W. Shaevitz,et al.  Probing the kinesin reaction cycle with a 2D optical force clamp , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[50]  Anatoly B Kolomeisky,et al.  A simple kinetic model describes the processivity of myosin-v. , 2002, Biophysical journal.

[51]  K. Hirose,et al.  Coordination of kinesin's two heads studied with mutant heterodimers , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Toshio Yanagida,et al.  Chemomechanical coupling of the forward and backward steps of single kinesin molecules , 2002, Nature Cell Biology.

[53]  Ronald D Vale,et al.  Conversion of Unc104/KIF1A Kinesin into a Processive Motor After Dimerization , 2002, Science.

[54]  Joshua W Shaevitz,et al.  An automated two-dimensional optical force clamp for single molecule studies. , 2002, Biophysical journal.

[55]  Z. Koza General relation between drift velocity and dispersion of a molecular motor , 2002, cond-mat/0207203.

[56]  Carlos Bustamante,et al.  Supplemental data for : The Bacteriophage ø 29 Portal Motor can Package DNA Against a Large Internal Force , 2001 .

[57]  A. Kolomeisky Exact results for parallel-chain kinetic models of biological transport , 2001 .

[58]  H. Sweeney,et al.  Kinetic Mechanism and Regulation of Myosin VI* , 2001, The Journal of Biological Chemistry.

[59]  R J Baskin,et al.  Structural changes in the neck linker of kinesin explain the load dependence of the motor's mechanical cycle. , 2001, Journal of theoretical biology.

[60]  A. Kolomeisky,et al.  Simple mechanochemistry describes the dynamics of kinesin molecules , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[61]  A Mehta,et al.  Myosin learns to walk. , 2001, Journal of cell science.

[62]  G. Oster,et al.  The physics of molecular motors. , 2001, Accounts of chemical research.

[63]  J. Howard,et al.  Mechanics of Motor Proteins and the Cytoskeleton , 2001 .

[64]  R. Lipowsky,et al.  Universal aspects of the chemomechanical coupling for molecular motors. , 2000, Physical review letters.

[65]  P. Reimann Brownian motors: noisy transport far from equilibrium , 2000, cond-mat/0010237.

[66]  M. Schnitzer,et al.  Force production by single kinesin motors , 2000, Nature Cell Biology.

[67]  Anatoly B. Kolomeisky,et al.  Extended kinetic models with waiting-time distributions: Exact results , 2000, cond-mat/0007455.

[68]  Masasuke Yoshida,et al.  Stepping rotation of F1-ATPase visualized through angle-resolved single-fluorophore imaging. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[69]  Anatoly B. Kolomeisky,et al.  Periodic sequential kinetic models with jumping, branching and deaths , 2000 .

[70]  R. Berry Theories of rotary motors. , 2000, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[71]  C. Bustamante,et al.  The mechanochemistry of molecular motors. , 2000, Biophysical journal.

[72]  N. Hirokawa,et al.  Mechanism of the single-headed processivity: diffusional anchoring between the K-loop of kinesin and the C terminus of tubulin. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[73]  T. Strick,et al.  Stress-induced structural transitions in DNA and proteins. , 2000, Annual review of biophysics and biomolecular structure.

[74]  Roger Cooke,et al.  A structural change in the kinesin motor protein that drives motility , 1999, Nature.

[75]  Anatoly B. Kolomeisky,et al.  Molecular motors and the forces they exert , 1999 .

[76]  Amber L. Wells,et al.  The kinetic mechanism of myosin V. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[77]  P K Hansma,et al.  Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase. , 1999, Biophysical journal.

[78]  Matthias Rief,et al.  Myosin-V is a processive actin-based motor , 1999, Nature.

[79]  Mark J. Schnitzer,et al.  Single kinesin molecules studied with a molecular force clamp , 1999, Nature.

[80]  M. Fisher,et al.  The force exerted by a molecular motor. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[81]  J. Howard,et al.  Kinesin Takes One 8-nm Step for Each ATP That It Hydrolyzes* , 1999, The Journal of Biological Chemistry.

[82]  R M Berry,et al.  The bacterial flagella motor. , 1999, Advances in microbial physiology.

[83]  B. Widom,et al.  A Simplified “Ratchet” Model of Molecular Motors , 1998 .

[84]  Robert Landick,et al.  RNA Polymerase as a Molecular Motor , 1998, Cell.

[85]  T. Elston,et al.  Force generation in RNA polymerase. , 1998, Biophysical journal.

[86]  K. Johnson,et al.  Pathway of ATP hydrolysis by monomeric and dimeric kinesin. , 1998, Biochemistry.

[87]  E. Mandelkow,et al.  The Crystal Structure of Dimeric Kinesin and Implications for Microtubule-Dependent Motility , 1997, Cell.

[88]  F. Jülicher,et al.  Modeling molecular motors , 1997 .

[89]  T C Elston,et al.  Protein turbines. I: The bacterial flagellar motor. , 1997, Biophysical journal.

[90]  Mark J. Schnitzer,et al.  Kinesin hydrolyses one ATP per 8-nm step , 1997, Nature.

[91]  J. Gelles,et al.  Coupling of kinesin steps to ATP hydrolysis , 1997, Nature.

[92]  T. Yanagida,et al.  Kinetics of force generation by single kinesin molecules activated by laser photolysis of caged ATP. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[93]  R J Fletterick,et al.  The design plan of kinesin motors. , 1997, Annual review of cell and developmental biology.

[94]  E. Meyhöfer,et al.  Directional loading of the kinesin motor molecule as it buckles a microtubule. , 1996, Biophysical journal.

[95]  E. Taylor,et al.  Mechanism of microtubule kinesin ATPase. , 1995, Biochemistry.

[96]  C S Peskin,et al.  Coordinated hydrolysis explains the mechanical behavior of kinesin. , 1995, Biophysical journal.

[97]  W. Ebeling Stochastic Processes in Physics and Chemistry , 1995 .

[98]  Steven M. Block,et al.  Force and velocity measured for single kinesin molecules , 1994, Cell.

[99]  S. Leibler,et al.  Porters versus rowers: a unified stochastic model of motor proteins , 1993, The Journal of cell biology.

[100]  E. Taylor,et al.  A kinetic study of the kinesin ATPase. , 1992, The Journal of biological chemistry.

[101]  Dennis Bray,et al.  Cell Movements: From Molecules to Motility , 1992 .

[102]  H. Lodish Molecular Cell Biology , 1986 .

[103]  Bernard Derrida,et al.  Velocity and diffusion constant of a periodic one-dimensional hopping model , 1983 .

[104]  N. Kampen,et al.  Stochastic processes in physics and chemistry , 1981 .

[105]  E. Montroll,et al.  Random walks and generalized master equations with internal degrees of freedom. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[106]  C. Weibull Bacterial Flagella , 1951, Nature.