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Conformational Structure and Dynamics from Single-Molecule FRET

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Energy Transfer Dynamics in Biomaterial Systems

Part of the book series: Springer Series in Chemical Physics ((CHEMICAL,volume 93))

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Abstract

Various ways of extracting information on the conformational structure, dynamics and correlations between them from single-molecule measurements of orescence resonance energy transfer are surveyed. The information obtained via those various ways is then analyzed in detail in the case of an off-lattice model of a two-stranded coiled-coil polypeptide that follows Langevin dynamics. The analysis includes a consideration of the cases of a freely diffusing and surface-immobilized polypeptide as well as the effect of different types of surface and denaturation conditions.

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References

  1. Fersht, A. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding; Freeman and Company: New York, 1998.

    Google Scholar 

  2. Bloomfield, V. A.; Crothers, D. M.; Tinoco, I. Nucleic Acids: Structures, Properties, and Functions; University Science Books: Sausalito CA, 2000.

    Google Scholar 

  3. Edman, L.; Mets, Ü.; Rigler, R. Proc. Natl. Acad. Sci. USA 1996, 93, 6710.

    Article  CAS  Google Scholar 

  4. Nie, S.; Zare, R. N. Annu. Rev. Biophys. Struct 1997, 26, 567.

    Article  CAS  Google Scholar 

  5. Jia, Y.; Sytnik, A.; Li, L.; Vladimirov, S.; Cooperman, B. S.; Hochstrasser, R. M. Proc. Natl. Acad. Sci. USA 1997, 94, 7932.

    Article  CAS  Google Scholar 

  6. Bopp, M. A.; Jia, Y.; haran, G.; Morlino, E. A.; Hochstrasser, R. M. App. Phys. Lett. 1998, 73, 7.

    Article  CAS  Google Scholar 

  7. Xie, X. S.; Trautman, J. K. Ann. Rev. Phys. Chem. 1998, 49, 441.

    Article  CAS  Google Scholar 

  8. Geva, E.; Skinner, J. L. Chem. Phys. Lett. 1998, 288, 225.

    Article  CAS  Google Scholar 

  9. Lu, H. P.; Xun, L.; Xie, X. S. Science 1998, 282, 1877.

    Article  CAS  Google Scholar 

  10. Weiss, S. Science 1999, 283, 1676.

    Article  CAS  Google Scholar 

  11. Dahan, M.; Deniz, A. A.; Ha, T.; Chemla, D. S.; Schultz, P. G.; Weiss, S. Chem. Phys. 1999, 247, 85.

    Article  CAS  Google Scholar 

  12. Hu, D.; Yu, J.; Wong, K.; Bagchi, B.; Rossky, P.; Barabara, P. F. Nature 2000, 405, 1030.

    Article  CAS  Google Scholar 

  13. Moerner, W. E. J. Phys. Chem. B 2002, 106, 910.

    Article  CAS  Google Scholar 

  14. Russel, R.; Zhuang, X. W.; Babcock, H. P.; Millet, I. S.; Doniach, S.; Chu, S.; Herschlag, D. Proc. Natl. Acad. Sci. USA 2002, 99, 155.

    Article  Google Scholar 

  15. Yang, H.; Luo, G.; Karnchanaphanurach, P.; Louie, T.; Rech, I.; Cova, S.; Xun, L.; Xie, X. S. Science 2003, 302, 262.

    Article  CAS  Google Scholar 

  16. Bartley, L. E.; Zhuang, X. W.; Das, R.; Chu, S.; Herschlag, D. J. Mol. Biol 2003, 6, 923.

    Google Scholar 

  17. Zhuang, X. W.; Reif, M. Curr. Opin. Struct. Biol. 2003, 13, 88.

    Article  CAS  Google Scholar 

  18. Chu, S. Phil. Trans. R. Soc. Lond. A 2003, 361, 689.

    Article  CAS  Google Scholar 

  19. Haran, G.; Vöhringer, P. ChemPhysChem 2005, 6, 755.

    Article  Google Scholar 

  20. Sherman, E.; Haran, G. Proc. Natl. Acad. Sci. USA 2006, 103, 11539.

    Article  CAS  Google Scholar 

  21. Ha, T. Biochemistry 2004, 43, 4055.

    Article  CAS  Google Scholar 

  22. Kubelka, J.; Hofrichter, J.; Eaton, W. A. Curr. Opin. Struct. Biol. 2004, 14, 76.

    Article  CAS  Google Scholar 

  23. Fernandez, J. M.; Li, H. Chem. Phys. 2004, 303, 1674.

    CAS  Google Scholar 

  24. Boukobza, E.; Sonnenfeld, A.; Haran, G. J. Phys. Chem. B 2001, 105, 12165.

    Article  CAS  Google Scholar 

  25. Xie, Z.; Srividya, N.; Sosnick, T. R.; Pan, T.; Scherer, N. F. Proc. Natl. Acad. Sci. USA 2004, 101, 534.

    Article  CAS  Google Scholar 

  26. Ha, T.; Enderle, T.;.; Oglertee, D. F.; Chemla, D. S.; Selvin, P. R.; Weiss, S. Proc. Natl. Acad. Sci. USA 1996, 93, 6264.

    Article  CAS  Google Scholar 

  27. Ha, T.; Ting, A. Y.; Liang, J.; Denize, A. A.; Chemla, D. S.; Schultz, P. G.; Weiss, S. Chem. Phys. 1999, 247, 107.

    Article  CAS  Google Scholar 

  28. Ha, T.; Ting, A. Y.; Liang, J.; Caldwell, D. B.; Denize, A. A.; Chemla, D. S.; Schultz, P. G.; Weiss, S. Proc. Natl. Acad. Sci. USA 1999, 96, 893.

    Article  CAS  Google Scholar 

  29. Ha, T.; Zhuang, X.; Kim, H. D.; Orr, J. W.; Williamson, J. R.; Chu, S. Proc. Natl. Acad. Sci. USA 1999, 96, 9077.

    Article  CAS  Google Scholar 

  30. Jia, Y.; Talaga, D. S.; Lau, W. L.; Lu, H. S. M.; DeGrado, W. F.; Hochstrasser, R. M. Chem. Phys. 1999, 247, 69.

    Article  CAS  Google Scholar 

  31. Deniz, A. A.; Dahan, M.; Grunwell, J. R.; Ha, T.; Faulhaber, A. E.; Chemla, D. S.; Weiss, S.; Schultz, P. G. Proc. Natl. Acad. Sci. USA 1999, 96, 3670.

    Article  CAS  Google Scholar 

  32. Ishii, Y.; Yoshida, T.; Funatsu, T.; Wazawa, T.; Yanagida, T. Chem. Phys. 1999, 247, 163.

    Article  CAS  Google Scholar 

  33. Talaga, D. S.; Lau, W. L.; Roder, H.; Tang, J.; Jia, Y.; DeGrado, W. F.; Hochstrasser, R. M. Proc. Natl. Acad. Sci. USA 2000, 97, 13021.

    Article  CAS  Google Scholar 

  34. Deniz, A. A.; Laurence, T. A.; Beligere, G. S.; Dahan, M.; Martin, A. B.; Chemla, D. S.; Dawson, P. E.; Schultz, P. G.; Weiss, S. Proc. Natl. Acad. Sci. USA 2000, 97, 5179.

    Article  CAS  Google Scholar 

  35. Weiss, S. Nature: Structural Biology 2000, 7, 724.

    Article  CAS  Google Scholar 

  36. Ying, L.; Wallace, M. L.; Balasubramainian, S.; Klenerman, D. J. Phys. Chem. B 2000, 104, 5171.

    Article  CAS  Google Scholar 

  37. Brasselet, S.; Peterman, E. J. G.; Miyawaki, A.; Moerner, W. E. J. Phys. Chem. B 2000, 104, 3676.

    Article  CAS  Google Scholar 

  38. Zhuang, X.; Kim, H.; Pereira, M. J.; Babcock, H. P.; Walter, N. G.; Chu, S. Science 2002, 296, 1473.

    Article  CAS  Google Scholar 

  39. Schuler, B.; Lipman, E. A.; Eaton, W. A. Nature 2002, 419, 743.

    Article  CAS  Google Scholar 

  40. Lipman, E. A.; Schuler, B.; Bakajin, O.; Eaton, W. A. Science 2003, 301, 1233.

    Article  CAS  Google Scholar 

  41. Haran, G. J. Phys.: Condens. Matter 2003, 15, R1291.

    Article  Google Scholar 

  42. Rhoades, E.; Gussakovsky, E.; Haran, G. Proc. Natl. Acad. Sci. USA 2003, 100, 3197.

    Article  CAS  Google Scholar 

  43. Rhoades, E.; Cohen, M.; Schuler, B.; Haran, G. J. Am. Chem. Soc. 2004, 126, 14686.

    Article  CAS  Google Scholar 

  44. Slaughter, B. D.; Allen, M. W.; Unruh, J. R.; Bieber-Urbauer, R. J.; Johnson, C. K. J. Phys. Chem. B 2004, 108, 10388.

    Article  CAS  Google Scholar 

  45. Hodak, J. H.; Downey, C. D.; Fiore, J. L.; Pardi, A.; Nesbitt, D. J. Proc. Natl. Acad. Sci. USA 2005, 102, 10505.

    Article  CAS  Google Scholar 

  46. Sabanayagam, C. R.; Eid, J. S.; Meller, A. J. Chem. Phys. 2005, 123, 224708.

    Article  Google Scholar 

  47. Liu, H.-W.; Cosa, G.; Landes, C. F.; Zeng, Y.; Kovaleski, B. J.; Mullen, D. G.; Barany, G.; Musier-Forsyth, K.; Barbara, P. F. Biophysical Journal 2005, 89, 3470.

    Article  CAS  Google Scholar 

  48. Kuzmenkina, E. V.; Heyes, C. D.; Nienhaus, G. U. J. Mol. Biol. 2006, 257, 313.

    Article  Google Scholar 

  49. Srinivas, G.; Yethiraj, A.; Bagchi, B. J. Phys. Chem. B 2001, 105, 2475.

    Article  CAS  Google Scholar 

  50. Srinivas, G.; Bagchi, B. J. Chem. Phys. 2002, 116, 837.

    Article  CAS  Google Scholar 

  51. Srinivas, G.; Bagchi, B. Phys. Chem. Comm. 2002, 5, 59.

    Google Scholar 

  52. Yang, H.; Witkoskie, J. B.; Cao, J. S. J. Chem. Phys. 2002, 117, 11010.

    Article  CAS  Google Scholar 

  53. Gopich, I. V.; Szabo, A. J. Phys. Chem. B 2003, 107, 5058.

    Article  CAS  Google Scholar 

  54. Wang, D.; Geva, E. J. Phys. Chem. B 2005, 109, 1626.

    Article  CAS  Google Scholar 

  55. Shang, J.; Geva, E. J. Phys. Chem. B 2005, 109, 16340.

    Article  CAS  Google Scholar 

  56. Stryer, L.; Haugland, R. P. Proc. Natl. Acad. Sci. USA 1967, 58, 719.

    Article  CAS  Google Scholar 

  57. Haas, E.; Wilchek, M.; Katchalski-Katzir, E.; Steinberg, I. Z. Proc. Natl. Acad. Sci. USA 1975, 72, 1807.

    Article  CAS  Google Scholar 

  58. Selvin, P. R. Meth. Enzymology 1995, 246, 300.

    Article  CAS  Google Scholar 

  59. Andrews, D. L.; Demidov, A. A. Resonance energy transfer; Wiley: New York, 1999.

    Google Scholar 

  60. Selvin, P. R. Nature: Structural Biology 2000, 7, 730.

    Article  CAS  Google Scholar 

  61. Förster, T. Ann. Physik 1948, 2, 55.

    Article  Google Scholar 

  62. Dexter, D. L. J. Chem. Phys. 1953, 21(5), 836.

    Article  CAS  Google Scholar 

  63. Lakowicz, J. R. Principles of fluorescence spectroscopy; Plenum Publishing Corporation: New York, U.S.A., 1999.

    Google Scholar 

  64. Scholes, G. D. Annu. Rev. Phys. Chem. 2003, 54, 57.

    Article  CAS  Google Scholar 

  65. Shang, J.; Geva, E. J. Phys. Chem. B 2007, 111, 4178.

    Article  CAS  Google Scholar 

  66. Shang, J.; Geva, E. J. Phys. Chem. B 2007, 111, 4220.

    Article  CAS  Google Scholar 

  67. Srinivas, G.; Yethiraj, A.; Bagchi, B. J. Chem. Phys. 2001, 114, 9170.

    Article  CAS  Google Scholar 

  68. O’Shea, E. K.; Rutkowski, R.; Kim, P. S. Science 1989, 243, 538.

    Article  Google Scholar 

  69. O’Shea, E. K.; Klemm, J. D.; Kim, P. S.; Alber, T. Science 1991, 254, 539.

    Article  Google Scholar 

  70. Lumb, K. J.; Carr, C. M.; Kim, P. S. Biochemistry 1994, 33, 7361.

    Article  CAS  Google Scholar 

  71. Zitzewitz, J. A.; Bilsel, O.; Luo, J.; Jones, B. E.; Matthews, C. R. Biochemistry 1995, 34, 12812.

    Article  CAS  Google Scholar 

  72. Wendt, H.; Berger, C.; Baici, A.; Thomas, R. M.; Bosshard, H. R. Biochemistry 1995, 34, 4097.

    Article  CAS  Google Scholar 

  73. Jelesarov, I.; Dürr, E.; Thomas, R. M.; Bosshard, H. R. Biochemistry 1998, 37, 7539.

    Article  CAS  Google Scholar 

  74. Sosnick, T. R.; Jackson, S.; Wilk, R. R.; Englander, S. W.; Degrado, W. F. Proteins: Structure, Function, and Genetics 1996, 24, 427-432.

    Article  CAS  Google Scholar 

  75. Ratner, V.; Sinev, M.; Haas, E. J. Mol. Biol. 2000, 299, 1383.

    Article  Google Scholar 

  76. Lee, M.; Tang, J.; Hochstrasser, R. M. Chem. Phys. Lett. 2001, 344, 501.

    Article  CAS  Google Scholar 

  77. Guo, Z.; Thirumalai, D. J. Mol. Biol. 1996, 263, 323-343.

    Article  CAS  Google Scholar 

  78. Klimov, D. K.; Betancourt, M. R.; Thirumalai, D. Folding and Design 1998, 3, 481-496.

    Article  CAS  Google Scholar 

  79. Honeycutt, J. D.; Thirumalai, D. biopolymers 1992, 32, 695.

    Article  CAS  Google Scholar 

  80. Veithans, T.; Klimov, D.; Thirumalai, D. Fol. Des. 1996, 2, 1.

    Article  Google Scholar 

  81. Klimov, D. K.; Thirumalai, D. Phys. Rev. Lett. 1997, 79, 317.

    Article  CAS  Google Scholar 

  82. Walqwist, A.; Covell, D. G.; Thirumalai, D. J. Am. Chem. Soc. 1998, 120, 427.

    Article  Google Scholar 

  83. Durr, E.; Jelesarov, I.; Bosshard, H. R. Biochemistry 1999, 38, 870.

    Article  CAS  Google Scholar 

  84. Makarov, D. E.; Metiu, H. J. Chem. Phys. 1999, 111, 10126.

    Article  CAS  Google Scholar 

  85. de Gennes, P. G. Scaling concepts in polymer physics; Cornell University Press: Cornell, U.S.A., 1979.

    Google Scholar 

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Geva, E., Shang, J. (2009). Conformational Structure and Dynamics from Single-Molecule FRET. In: Burghardt, I., May, V., Micha, D., Bittner, E. (eds) Energy Transfer Dynamics in Biomaterial Systems. Springer Series in Chemical Physics, vol 93. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02306-4_3

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