Motor potential profile and a robust method for extracting it from time series of motor positions

Journal of Theoretical Biology

Volumn 242, Issue 4, 2006, Pages 908-921

  Wang, Hongyun ^a  

^a University of California   (United States)

Author keywords

Fokker Planck equations; Molecular motors; Stochastic processes; Time series analysis

Indexed keywords

MOLECULAR MOTOR;

CHEMICAL REACTION; EXPERIMENTAL STUDY; EXTRACTION METHOD; FORCE;

ARTICLE; DATA ANALYSIS; EXPERIMENTATION; MATHEMATICAL ANALYSIS; MEASUREMENT; METHODOLOGY; MOLECULAR SIZE; MOLECULE; PHYSICS; PRIORITY JOURNAL; SIMULATION; TIME SERIES ANALYSIS;

ANIMALS; CHEMISTRY, PHYSICAL; MODELS, CHEMICAL; MOLECULAR MOTOR PROTEINS; MOTION; STOCHASTIC PROCESSES; VISCOSITY;

EID: 33748447640     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2006.04.005     Document Type: Article

References (53)

1. Abbondanzieri E.A., Greenleaf W.J., Shaevitz J.W., Landick R., and Block S.M. Direct observation of base-pair stepping by RNA polymerase. Nature 438 (2005) 460-465
2. 1-ATPase from bovine heart mitochondria. Nature 370 (1994) 621-628
3. Astumian R. Thermodynamics and kinetics of a Brownian motor. Science 276 (1997) 917-922
4. Astumian R.D., and Derenyi I. Fluctuation driven transport and models of molecular motors and pumps. Eur. J. Biophys. 27 (1998) 474-489
5. Berg H.C. Random Walks in Biology (1993), Princeton University Press, Princeton, N.J
6. Berg H.C. The rotary motor of bacterial flagella. Ann. Rev. Biochem. 72 (2003) 19-54
7. Block S.M., and Berg H.C. Successive incorporation of force-generating units in the bacterial rotary motor. Nature 309 (1984) 470-473
8. Block S.M., Asbury C.L., Shaevitz J.W., and Lang M.J. Probing the kinesin reaction cycle with a 2D optical force clamp. Proc. Natl Acad. Sci. USA 100 (2003) 2351-2356
9. Boyer P. The binding change mechanism for ATP synthase-some probabilities and possibilities. Biochim. Biophys. Acta 1140 (1993) 215-250
10. Boyer P. The ATP synthase-a splendid molecular machine. Ann. Rev. Biochem. 66 (1997) 717-749
11. Brockwell P.J., and Davis R.A. Time Series: Theory and Methods (1998), Springer, New York
12. Coppin C., Pierce D., Hsu L., and Vale R. The load dependence of kinesin's mechanical cycle. Proc. Natl. Acad. Sci. USA 94 (1997) 8539-8544
13. Dimroth P., Wang H., Grabe M., and Oster G. Energy transduction in the sodium F-ATPase of propionigenium modestum. Proc. Natl Acad. Sci. USA 96 (1999) 4924-4929
14. Doering C., Horsthemke W., and Riordan J. Nonequilibrium fluctuation-induced transport. Phys. Rev. Lett. 72 (1994) 2984-2987
15. Elston T., Wang H., and Oster G. Energy transduction in ATP synthase. Nature 391 (1998) 510-514
16. Fan J., and Yao Q. Nonlinear Time Series: Nonparametric and Parametric Methods (2005), Springer, New York
17. Fisher R.A. On the mathematical foundations of theoretical statistics. Philos. Trans. R. Soc. London Ser. A 222 (1922) 309-368
18. Fletcher R., and Reeves C.M. Function minimization by conjugate gradients. Comput. J. 7 (1964) 148-154
19. Gardiner C. Handbook of Stochastic Methods. second ed. (1985), Springer, New York
20. Harris J.W., and Stocker H. Handbook of Mathematics and Computational Science (1988), Springer, New York
21. 1 motor by external force. Proc. Natl Acad. Sci. USA 120 (2005) 4288-4293
22. Hoel P.G. Introduction to Mathematical Statistics (1962), Wiley, New York
23. Howard J., Hudspeth A.J., and Vale R.D. Movement of microtubules by single kinesin molecules. Nature 342 (1989) 154-158
24. Hunt A.J., Gittes F., and Howard J. The force exerted by a single kinesin molecule against a viscous load. Biophys. J. 67 (1994) 766-781
25. 1-ATPase Nature 427 (2004) 465-468
26. Julicher F., Ajdari A., and Prost J. Modeling molecular motors. Rev. Mod. Phys. 69 (1997) 1269-1281
27. Landau L.D., Lifshitz E.M., and Pitaevskii L.P. Statistical Physics. third rev. ed. (1980), Pergamon Press, Oxford, New York
28. 1-ATPase with nucleotide bound to all three catalytic sites. implications for the mechanism of rotary catalysis. Cell 106 (2001) 331-341
29. Mogilner A., and Oster G. The polymerization ratchet model explains the force-velocity relation for growing microtubules. Eur. J. Biophys. 28 (1999) 235-242
30. 1-ATPase. Nature 386 (1997) 299-302
31. Oster G., and Wang H. Reverse engineering a protein. the mechanochemistry of ATP synthase. Biochim. Biophys. Acta (Bioenerg.) 1458 (2000) 482-510
32. Oster G., and Wang H. Rotary protein motors. Trends Cell Biol. 13 (2003) 114-121
33. Peskin C.S., Odell G.M., and Oster G. Cellular motions and thermal fluctuations. the Brownian ratchet. Biophys. J. 65 (1993) 316-324
34. Peskin C.S., Ermentrout G.B., and Oster G.F. Mechanochemical Coupling in ATPase Motors (1994), Springer, Les Houches
35. Polak E., and Ribiere G. Note sur la convergence de methode de directions conjuguees. Rev. Fr. Inf. Rech. Oper. 16 (1969) 35-43
36. Prost J., Chauwin J., Peliti L., and Ajdari A. Asymmetric pumping of particles. Phys. Rev. Lett. 72 (1994) 2652-2655
37. Reif F. Fundamentals of Statistical and Thermal Physics (1965), McGraw-Hill, New York
38. Reimann P. Brownian motors. noisy transport far from equilibrium. Phys. Rep. 361 (2002) 57-265
39. Risken H. The Fokker-Planck Equation. second ed (1989), Springer, New York
40. Sabbert D., Engelbrecht S., and Junge W. Intersubunit rotation in active F-ATPase. Nature 381 (1996) 623-625
41. 1). direct observation. Science 286 (1999) 1722-1724
42. Samuel A., and Berg H. Fluctuation analysis of rotational speed of the bacterial flagellar motor. Proc. Natl Acad. Sci. 92 (1995) 3502-3506
43. Schnitzer M.J., and Block S.M. Kinesin hydrolyses one ATP per 8-nm step. Nature 388 (1997) 386-390
44. Vale R. Kinesin: possible biological roles for a new microtubule motor. TIBS 11 (1986) 464-468
45. Visscher K., Schnitzer M., and Block S. Single kinesin molecules studied with a molecular force clamp. Nature 400 (1999) 184-189
46. Walton, D.B., 2002. Analysis of single-molecule kinesin assay data by hidden Markov model filtering. Ph.D. Dissertation, University of Arizona.
47. Wang H. Mathematical theory of molecular motors and a new approach for uncovering motormechanism. IEE Proc. Nanobiotechnol. 150 (2003) 127-133
48. 1 motor of ATP synthase. Nature 396 (1998) 279-282
49. Wang H., and Oster G. The Stokes efficiency for molecular motors and its applications. Europhys. Lett. 57 (2002) 134-140
50. Wang H., Peskin C., and Elston T. A robust numerical algorithm for studying biomolecular transport processes. J. Theor. Biol. 221 (2003) 491-511
51. 1-ATPase. Biochim. Biophys. Acta 1319 (1997) 19-58
52. {ring operator} steps. Cell 93 (1998) 1117-1124
53. 1-ATPase. Nature 410 (2001) 898-904