Skip to main content

Molecular Machines

  • Chapter
  • First Online:
  • 430 Accesses

Part of the book series: SpringerBriefs in Molecular Science ((BRIEFSMOLECULAR))

Abstract

The ATP hydrolysis cycle is utilized in such processes as the unidirectional movement of myosin along F-actin, assistance in protein folding performed by a chaperonin, transport of diverse substrates across the membrane by an ABC transporter, and rotation of the central subunit within F1-ATPase. On the other hand, the proton motive force is utilized in the functional rotation of the multidrug efflux transporter AcrB. In this chapter, we elucidate the mechanism of these ordering processes. We also argue how the processes are coupled with the ATP hydrolysis cycle or the proton motive force. Like in the self-assembly processes, the key factor is the entropic effect originating from the translational displacement of water molecules in the system.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  1. K. Amano, T. Yoshidome, M. Iwaki, M. Suzuki, M. Kinoshita, J. Chem. Phys. 133, 045103 (2010)

    Article  Google Scholar 

  2. K. Amano, H. Oshima, M. Kinoshita, J. Chem. Phys. 135, 185101 (2011)

    Article  Google Scholar 

  3. T. Yoshidome, Y. Ito, M. Ikeguchi, M. Kinoshita, J. Am. Chem. Soc. 133, 4030 (2011)

    Article  CAS  Google Scholar 

  4. T. Yoshidome, Y. Ito, N. Matubayasi, M. Ikeguchi, M. Kinoshita, J. Chem. Phys. 137, 035102 (2012)

    Article  Google Scholar 

  5. K. Hollenstein, R.J.P. Dawson, K.P. Locher, Curr. Opin. Struct. Biol. 17, 412 (2007)

    Article  CAS  Google Scholar 

  6. H. Mishima, H. Oshima, S. Yasuda, M. Kinoshita, J. Phys. Chem. B 119, 3423 (2015)

    Article  CAS  Google Scholar 

  7. S.M. Block, Biophys. J. 92, 2986 (2007)

    Article  CAS  Google Scholar 

  8. E. Hirakawa, H. Higuchi, Y.Y. Toyoshima, Proc. Natl. Acad. Sci. U.S.A. 99, 2533 (2000)

    Article  Google Scholar 

  9. J.L. Ross, M.Y. Ali, D.M. Warshaw, Curr. Opin. Cell Biol. 20, 41 (2008)

    Article  CAS  Google Scholar 

  10. T. Yanagida, S. Esaki, A.H. Iwane, Y. Inoue, A. Ishijima, K. Kitamura, H. Tanaka, M. Tokunaga, Phil. Trans. R. Soc. Lond. B 355, 441 (2000)

    Article  CAS  Google Scholar 

  11. T. Okada, H. Tanaka, A.H. Iwane, K. Kitamura, M. Ikebe, T. Yanagida, Biochem. Biophys. Res. Commun. 354, 379 (2007)

    Article  CAS  Google Scholar 

  12. Y. Okada, N. Hirokawa, Science 283, 1152 (1999)

    Article  CAS  Google Scholar 

  13. K. Kitamura, M. Tokunaga, A.H. Iwane, T. Yanagida, Nature 397, 129 (1999)

    Article  CAS  Google Scholar 

  14. K. Kitamura, M. Tokunaga, S. Esaki, A.H. Iwane, T. Yanagida, Biophysics 1, 1 (2005)

    Article  CAS  Google Scholar 

  15. D. Beglov, B. Roux, J. Chem. Phys. 103, 360 (1995)

    Article  CAS  Google Scholar 

  16. M. Ikeguchi, J. Doi, J. Chem. Phys. 103, 5011 (1995)

    Article  CAS  Google Scholar 

  17. M. Kinoshita, J. Chem. Phys. 116, 3493 (2002)

    Article  CAS  Google Scholar 

  18. T. Kodama, Physiol. Rev. 65, 467 (1985)

    CAS  Google Scholar 

  19. T. Katoh, F. Morita, J. Biochem. 120, 189 (1996)

    Article  CAS  Google Scholar 

  20. P. Coureux, A.L. Wells, J. Menetrey, C.M. Yengo, C.A. Morris, H.L. Sweeney, A. Houdusse, Nature 425, 419 (2003)

    Article  CAS  Google Scholar 

  21. P. Coureux, H.L. Sweeney, A. Houdusse, EMBO J. 23, 4527 (2004)

    Article  CAS  Google Scholar 

  22. R. Ananthakrishnan, A. Ehrlichter, Int. J. Biol. Sci. 3, 303 (2007)

    Article  CAS  Google Scholar 

  23. H. Noji, R. Yasuda, M. Yoshida, K. Kinosita Jr., Nature 386, 299 (1997)

    Article  CAS  Google Scholar 

  24. A.L. Horwich, W.A. Fenton, E. Chapman, G.W. Farr, Annu. Rev. Cell Dev. Biol. 23, 115 (2007)

    Article  CAS  Google Scholar 

  25. T.K. Chaudhuri, V.K. Verma, A. Maheshwari, Prog. Biophys. Mol. Biol. 99, 42 (2009)

    Article  CAS  Google Scholar 

  26. S. Tanaka, Y. Kawata, G. Otting, N.E. Dixon, K. Matsuzaki, M. Hoshino, Biochim. Biophys. Acta 1804, 866 (2010)

    Article  CAS  Google Scholar 

  27. H. Mishima, H. Oshima, S. Yasuda, K. Amano, M. Kinoshita, J. Chem. Phys. 139, 205102 (2013)

    Article  Google Scholar 

  28. M.A. Seeger, K. Diederichs, T. Eicher, L. Brandstätter, A. Schiefner, F. Verrey, K.M. Pos, Curr. Drug Targets 9, 729 (2008)

    Article  CAS  Google Scholar 

  29. X.-Z. Li, H. Nikaido, Drugs 69, 1555 (2009)

    Article  CAS  Google Scholar 

  30. K.M. Pos, Biochim. Biophys. Acta 1794, 782 (2009)

    Article  CAS  Google Scholar 

  31. T. Hayashi, S. Chiba, Y. Kaneta, T. Furuta, M. Sakurai, J. Phys. Chem. B 118, 12612 (2014)

    Article  CAS  Google Scholar 

  32. F. Takagi, N. Koga, S. Takada, Proc. Natl. Acad. Sci. U.S.A. 100, 11367 (2003)

    Article  CAS  Google Scholar 

  33. W. Xu, J. Wang, W. Wang, Proteins 61, 777 (2005)

    Article  CAS  Google Scholar 

  34. K.L. Nielsen, N. Mclennan, M. Masters, N.J. Cowan, J. Bacteriol. 181, 5871 (1999)

    CAS  Google Scholar 

  35. R. Hara, K. Amano, M. Kinoshita, A. Yoshimori, J. Chem. Phys. 144, 105103 (2016)

    Article  Google Scholar 

  36. A. Ward, C.L. Reyes, J. Yu, C.B. Roth, G. Chang, Proc. Natl. Acad. Sci. U.S.A. 104, 19005 (2007)

    Article  CAS  Google Scholar 

  37. L. Vaccaro, K.A. Scott, M.S.P. Sansom, Biophys. J. 95, 5681 (2008)

    Article  CAS  Google Scholar 

  38. S. Murakami, R. Nakashima, E. Yamashita, T. Matsumoto, A. Yamaguchi, Nature 443, 173 (2006)

    Article  CAS  Google Scholar 

  39. S. Murakami, Curr. Opin. Struct. Biol. 18, 459 (2008)

    Article  CAS  Google Scholar 

  40. T. Imai, N. Miyashita, Y. Sugita, A. Kovalenko, F. Hirata, A. Kidera, J. Phys. Chem. B 115, 8288 (2011)

    Article  CAS  Google Scholar 

  41. J.P. Abrahams, A.G. Leslie, R. Lutter, J.E. Walker, Nature 370, 621 (1994)

    Article  CAS  Google Scholar 

  42. D. Okuno, R. Fujisawa, R. Iino, Y. Hirono-Hara, H. Imamura, H. Noji, Proc. Natl. Acad. Sci. U.S.A. 105, 20722 (2008)

    Article  CAS  Google Scholar 

  43. H. Sieladd, H. Rennekamp, S. Engelbrecht, W. Junge, Biophys. J. 95, 4979 (2008)

    Article  Google Scholar 

  44. T. Masaike, F. Koyama-Horibe, K. Oiwa, M. Yoshida, T. Nishizaka, Nat. Struct. Mol. Biol. 15, 1326 (2008)

    Article  CAS  Google Scholar 

  45. R. Yasuda, H. Noji, K. Kinosita Jr., M. Yoshida, Cell 93, 1117 (1998)

    Article  CAS  Google Scholar 

  46. K. Adachi, K. Oiwa, T. Nishizaka, S. Furuike, H. Noji, H. Itoh, M. Yoshida, M. Kinosita Jr., Cell 130, 309 (2007)

    Article  CAS  Google Scholar 

  47. Y. Ito, M. Ikeguchi, J. Comput. Chem. 31, 2175 (2010)

    Article  CAS  Google Scholar 

  48. M.W. Bowler, M.G. Montgomery, A.G.W. Leslie, J.E. Walker, J. Biol. Chem. 282, 14238 (2007)

    Article  CAS  Google Scholar 

  49. S. Adinolfi, M. Nair, A. Politou, E. Bayer, S. Martin, P. Temussi, A. Pastore, Biochemistry 43, 6511 (2004)

    Article  CAS  Google Scholar 

  50. J. Ma, T.C. Flynn, Q. Cui, A.G.W. Leslie, J.E. Walker, M. Karplus, Structure 10, 921 (2002)

    Article  CAS  Google Scholar 

  51. K.Y. Hara, H. Noji, D. Bald, R. Yasuda, K. Kinosita Jr., M. Yoshida, J. Biol. Chem. 275, 14260 (2000)

    Article  CAS  Google Scholar 

  52. T. Uchihashi, R. Iino, T. Ando, H. Noji, Science 333, 755 (2011)

    Article  CAS  Google Scholar 

  53. V. Koronakis, A. Sharff, E. Koronakis, B. Luisi, C. Hughes, Nature 405, 914 (2000)

    Article  CAS  Google Scholar 

  54. S. Murakami, R. Nakashima, E. Yamashita, T. Matsumoto, A. Yamaguchi, Nature 443, 173 (2006)

    Article  CAS  Google Scholar 

  55. M.A. Seeger, A. Schiefner, T. Eicher, F. Verrey, K. Diederichs, K.M. Pos, Science 313, 1295 (2006)

    Article  CAS  Google Scholar 

  56. G. Sennhauser, P. Amstutz, C. Briand, O. Storchenegger, M. Grütter, PLOS Biol. 5, e7(0106) (2007)

    Google Scholar 

  57. T. Yamane, S. Murakami, M. Ikeguchi, Biochemistry 52, 7648 (2013)

    Article  CAS  Google Scholar 

  58. P.G. Kusalik, G.N. Patey, J. Chem. Phys. 88, 7715 (1988)

    Article  CAS  Google Scholar 

  59. P.G. Kusalik, G.N. Patey, Mol. Phys. 65, 1105 (1988)

    Article  CAS  Google Scholar 

  60. Y. Harano, M. Kinoshita, Biophys. J. 89, 2701 (2005)

    Article  CAS  Google Scholar 

  61. M. Kinoshita, J. Chem. Phys. 128, 024507 (2008)

    Article  Google Scholar 

  62. S. Yasuda, H. Oshima, M. Kinoshita, J. Chem. Phys. 137, 135103 (2012)

    Article  Google Scholar 

  63. J.-P. Hansen, L.R. McDonald, Theory of Simple Liquids, 3rd edn. (Academic, London, 2006)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Masahiro Kinoshita .

Rights and permissions

Reprints and permissions

Copyright information

© 2016 The Author(s)

About this chapter

Cite this chapter

Kinoshita, M. (2016). Molecular Machines. In: Mechanism of Functional Expression of the Molecular Machines. SpringerBriefs in Molecular Science. Springer, Singapore. https://doi.org/10.1007/978-981-10-1486-4_3

Download citation

Publish with us

Policies and ethics