Entropy rectifies the Brownian steps of kinesin

Abstract

Kinesin is a stepping motor that successively produces forward and backward 8-nm steps along microtubules. Under physiological conditions, the steps powering kinesin's motility are biased in one direction and drive various biological motile processes. The physical mechanism underlying the unidirectional bias of the kinesin steps is not fully understood. Here we explored the mechanical kinetics and thermodynamics of forward and backward kinesin steps by analyzing their temperature and load dependence. Results show that the frequency asymmetry between forward and backward steps is produced by entropy. Furthermore, the magnitude of the entropic asymmetry is 6 kBT, more than three times greater than expected from a current model, in which a mechanical conformational change within the kinesin molecular structure directly biases the kinesin steps forward. We propose that the stepping direction of kinesin is preferably caused by an entropy asymmetry resulting from the compatibility between the kinesin and microtubule interaction based on their polar structures.

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Figure 1: Nanometry of single kinesin molecules.
Figure 2: Load dependence of the proportion (mean ± s.e.m.) of forward steps (pf, blue), backward steps (pb, red) and detachments (pd, green).
Figure 3: Dwell time at various loads and temperatures.
Figure 4: Kinetic analysis for kinesin steps.
Figure 5: Thermodynamic analysis for kinesin steps (a) Free-energy landscape for kinesin steps.
Figure 6: A model for the rectifying mechanism of stepping direction.

References

  1. 1

    Vale, R.D. & Milligan, R.A. The way things move: looking under the hood of molecular motor proteins. Science 288, 88–95 (2000).

    CAS  Article  Google Scholar 

  2. 2

    Howard, J. Molecular motors: structural adaptations to cellular functions. Nature 389, 561–567 (1997).

    CAS  PubMed  Google Scholar 

  3. 3

    Cross, R.A. The kinetic mechanism of kinesin. Trends Biochem. Sci. 29, 301–309 (2004).

    CAS  PubMed  Google Scholar 

  4. 4

    Endow, S. Kinesin motors as molecular machines. Bioessays 25, 1212–1219 (2003).

    CAS  PubMed  Google Scholar 

  5. 5

    Svoboda, K., Schmidt, C.F., Schnapp, B.J. & Block, S.M. Direct observation of kinesin stepping by optical trapping interferometry. Nature 365, 721–727 (1993).

    CAS  PubMed  Google Scholar 

  6. 6

    Carter, N.J. & Cross, R.A. Mechanics of the kinesin step. Nature 435, 308–312 (2005).

    CAS  PubMed  Google Scholar 

  7. 7

    Hua, W., Young, E.C., Fleming, M.L. & Gelles, J. Coupling of kinesin steps to ATP hydrolysis. Nature 388, 390–393 (1997).

    CAS  PubMed  Google Scholar 

  8. 8

    Schnitzer, M.J. & Block, S.M. Kinesin hydrolyses one ATP per 8-nm step. Nature 388, 386–390 (1997).

    CAS  PubMed  Google Scholar 

  9. 9

    Nishiyama, M., Higuchi, H. & Yanagida, T. Chemomechanical coupling of the forward and backward steps of single kinesin molecules. Nat. Cell Biol. 4, 790–797 (2002).

    CAS  PubMed  Google Scholar 

  10. 10

    Hackney, D.D. Evidence for alternating head catalysis by kinesin during microtubule-stimulated ATP hydrolysis. Proc. Natl. Acad. Sci. USA 91, 6865–6869 (1994).

    CAS  PubMed  Google Scholar 

  11. 11

    Kaseda, K., Higuchi, H. & Hirose, K. Alternate fast and slow stepping of a heterodimeric kinesin molecule. Nat. Cell Biol. 5, 1079–1082 (2003).

    CAS  PubMed  Google Scholar 

  12. 12

    Yildiz, A., Tomishige, M., Vale, R.D. & Selvin, P.R. Kinesin walks hand-over-hand. Science 303, 676–678 (2004).

    CAS  PubMed  Google Scholar 

  13. 13

    Asbury, C.L., Fehr, A.N. & Block, S.M. Kinesin moves by an asymmetric hand-over-hand mechanism. Science 302, 2130–2134 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 14

    Case, R.B., Pierce, D.W., Hom-Booher, N., Hart, C.L. & Vale, R.D. The directional preference of kinesin motors is specified by an element outside of the motor catalytic domain. Cell 90, 959–966 (1997).

    CAS  PubMed  Google Scholar 

  15. 15

    Rice, S. et al. A structural change in the kinesin motor protein that drives motility. Nature 402, 778–784 (1999).

    CAS  PubMed  Google Scholar 

  16. 16

    Rice, S. et al. Thermodynamic properties of the kinesin neck-region docking to the catalytic core. Biophys. J. 84, 1844–1854 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17

    Schnitzer, M.J., Visscher, K. & Block, S.M. Force production by single kinesin motors. Nat. Cell Biol. 2, 718–723 (2000).

    CAS  PubMed  Google Scholar 

  18. 18

    Block, S.M., Asbury, C.L., Shaevitz, J.W. & Lang, M.J. Probing the kinesin reaction cycle with a 2D optical force clamp. Proc. Natl. Acad. Sci. USA 100, 2351–2356 (2003).

    CAS  PubMed  Google Scholar 

  19. 19

    Wang, M. et al. Force and velocity measured for single molecules of RNA polymerase. Science 282, 902–907 (1998).

    CAS  PubMed  Google Scholar 

  20. 20

    Mazumdar, M. & Cross, R.A. Engineering a lever into the kinesin neck. J. Biol. Chem. 273, 29352–29359 (1998).

    CAS  PubMed  Google Scholar 

  21. 21

    Eyring, H. The activated complex in chemical reactions. J. Chem. Phys. 3, 107–115 (1935).

    CAS  Google Scholar 

  22. 22

    Atkins, P.W. Physical Chemistry 3rd edn. Ch. 30, 737–761 (Oxford University Press, Oxford, UK, 1987).

    Google Scholar 

  23. 23

    Yang, W.Y. & Gruebele, M. Folding at the speed limit. Nature 423, 193–197 (2003).

    CAS  PubMed  Google Scholar 

  24. 24

    Kojima, H., Muto, E., Higuchi, H. & Yanagida, T. Mechanics of single kinesin molecules measured by optical trapping nanometry. Biophys. J. 73, 2012–2022 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. 25

    Nishiyama, M. et al. Substeps within the 8-nm step of the ATPase cycle of single kinesin molecules. Nat. Cell Biol. 3, 425–428 (2001).

    CAS  PubMed  Google Scholar 

  26. 26

    Kawaguchi, K. & Ishiwata, S. Temperature dependence of force, velocity, and processivity of single kinesin molecules. Biochem. Biophys. Res. Commun. 272, 895–899 (2000).

    CAS  PubMed  Google Scholar 

  27. 27

    Nishiyama, M., Higuchi, H., Ishii, Y., Taniguchi, Y. & Yanagida, T. Single molecule processes on the stepwise movement of ATP-driven molecular motors. Biosystems 71, 145–156 (2003).

    CAS  PubMed  Google Scholar 

  28. 28

    Böhm, K. et al. Effect of temperature on kinesin-driven microtubule gliding and kinesin ATPase activity. FEBS Lett. 466, 59–62 (2000).

    PubMed  Google Scholar 

  29. 29

    Kawaguchi, K. & Ishiwata, S. Thermal activation of single kinesin molecules with temperature pulse microscopy. Cell Motil. Cytoskeleton 49, 41–47 (2001).

    CAS  PubMed  Google Scholar 

  30. 30

    Fersht, A.R. Structure and Mechanism in Protein Science (W.H. Freeman, New York, 1999).

    Google Scholar 

  31. 31

    Hirose, K., Lockhart, A., Cross, R.A. & Amos, L.A. Three-dimensional cytoelectron microscopy of dimeric kinesin and ncd motor domains on microtubules. Proc. Natl. Acad. Sci. USA 93, 9539–9544 (1996).

    CAS  PubMed  Google Scholar 

  32. 32

    Hirose, K., Löwe, J., Alonso, M., Cross, R.A. & Amos, L.A. Congruent docking of dimeric kinesin and ncd into three-dimensional electron cryomicroscopy maps of microtubule-motor ADP complexes. Mol. Biol. Cell 10, 2063–2074 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33

    Mandelkow, E. & Hoenger, A. Structures of kinesin and kinesin-microtubule interactions. Curr. Opin. Cell Biol. 11, 34–44 (1999).

    CAS  PubMed  Google Scholar 

  34. 34

    Uemura, S. & Ishiwata, S. Loading direction regulates the affinity of ADP for kinesin. Nat. Struct. Biol. 10, 308–311 (2003).

    CAS  PubMed  Google Scholar 

  35. 35

    Kawaguchi, K., Uemura, S. & Ishiwata, S. Equilibrium and transition between single- and double-headed binding of kinesin as revealed by single-molecule mechanics. Biophys. J. 84, 1103–1113 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. 36

    Ali, M.Y. et al. Unconstrained steps of myosin VI appear longest among known molecular motors. Biophys. J. 86, 3804–3810 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. 37

    Kitamura, K., Tokunaga, M., Esaki, S., Iwane, A.H. & Yanagida, T. Mechanism of muscle contraction based on stochastic properties of single actomyosin motors observed in vitro. Biophysics 1, 1–19 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. 38

    Svoboda, K. & Block, S.M. Force and velocity measured for single kinesin molecules. Cell 77, 773–784 (1994).

    CAS  PubMed  Google Scholar 

  39. 39

    William, H.P., Saul, A.T., William, T.V. & Brian, P.F. Numerical Recipes in C 2nd edn. (Cambridge University Press, New York, 1992).

    Google Scholar 

  40. 40

    Rief, M. et al. Myosin-V stepping kinetics: a molecular model for processivity. Proc. Natl. Acad. Sci. USA 97, 9482–9486 (2000).

    CAS  PubMed  Google Scholar 

  41. 41

    Altman, D., Sweeney, H.L. & Spudich, J.A. The mechanism of myosin VI translocation and its load-induced anchoring. Cell 116, 737–749 (2004).

    CAS  Google Scholar 

  42. 42

    Howard, J. Mechanics of Motor Proteins and the Cytoskeleton (Sinauer Associates, Sunderland, Massachusetts, 2001).

    Google Scholar 

  43. 43

    Kull, F.J. et al. Crystal structure of the kinesin motor domain reveals a structural similarity to myosin. Nature 380, 550–555 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 44

    Tadakuma, H., Yamaguchi, J., Ishihara, Y. & Funatsu, T. Imaging of single fluorescent molecules using video-rate confocal microscopy. Biochem. Biophys. Res. Commun. 287, 323–327 (2001).

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank F. Oosawa, T. Kodama, K. Sekimoto, H. Higuchi, A. Ishijima, H. Kojima, T. Ariga and colleagues at Osaka University and Japan Science and Technology Agency for valuable discussions and P. Karagiannis and J. West for carefully revising the manuscript.

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Correspondence to Toshio Yanagida.

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Supplementary information

Supplementary Fig. 1

Step size and direction of kinesin steps. (PDF 38 kb)

Supplementary Fig. 2

Distribution of dwell times of the forward (blue) and backward (red) steps. T = 35 °C. (PDF 31 kb)

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Taniguchi, Y., Nishiyama, M., Ishii, Y. et al. Entropy rectifies the Brownian steps of kinesin. Nat Chem Biol 1, 342–347 (2005). https://doi.org/10.1038/nchembio741

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