Theory of Single-Molecule FRET Efficiency Histograms

Single Molecule Biophysics: Experiment and Theory

Volumn 146, Issue , 2011, Pages 245-297

  Gopich, Irina V ^a   Szabo, Attila ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

"Slow" conformational dynamics; FRET efficiency histograms; Photon count rates

Indexed keywords

EFFICIENCY; GRAPHIC METHODS;

CONFORMATIONAL DYNAMICS; PHOTON COUNT; SINGLE-MOLECULE FRETS;

FORSTER RESONANCE ENERGY TRANSFER;

EID: 84923218988     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118131374.ch10     Document Type: Chapter

References (69)

1. A. A. Deniz, M. Dahan, J. R. Grunwell, T. Ha, A. E. Faulhaber, D. S. Chemla, S. Weiss, and P. G. Schultz, Proc. Natl. Acad. Sci. USA 96(7), 3670-3675 (1999).
2. A. A. Deniz, T. A. Laurence, G. S. Beligere, M. Dahan, A. B. Martin, D. S. Chemla, P. E. Dawson, P.G. Schultz, and S. Weiss, Proc. Natl. Acad. Sci. USA 97(10), 5179-5184 (2000).
3. B. Schuler, E. A. Lipman, and W. A. Eaton, Nature (London) 419(6908), 743-747 (2002).
4. P. J. Rothwell, S. Berger, O. Kensch, S. Felekyan, M. Antonik, B. M. Wöhrl, T. Restle, R. S. Goody, and C.A. M. Seidel, Proc. Natl. Acad. Sci. USA 100(4), 1655-1660 (2003).
5. E. Rhoades, M. Cohen, B. Schuler, and G. Haran, J. Am. Chem. Soc. 126(45), 14686-14687 (2004).
6. X. Michalet, S. Weiss, and M. Jäger, Chem. Rev. 106(5), 1785-1813 (2006).
7. W. E. Moerner, Proc. Natl. Acad. Sci. USA 104(31), 12596-12602 (2007).
8. J.A. Hanson, K. Duderstadt, L.P. Watkins, S. Bhattacharyya, J. Brokaw, J.W. Chu, and H. Yang, Proc. Natl. Acad. Sci. USA 104(46), 18055 (2007).
9. S. Mukhopadhyay, R. Krishnan, E. A. Lemke, S. Lindquist, and A. A. Deniz, Proc. Natl. Acad. Sci. USA 104(8), 2649-2654 (2007).
10. M. Kinoshita, K. Kamagata, A. Maeda, Y. Goto, T. Komatsuzaki, and S. Takahashi, Proc. Natl. Acad. Sci. USA 104(25), 10453 (2007).
11. A.K. Wozniak, G.F. Schroder, H. Grubmüller, C.A.M. Seidel, and F. Oesterhelt, Proc. Natl. Acad. Sci. USA 105(47), 18337 (2008).
12. B. Schuler and W.A. Eaton, Curr. Opin. Struct. Biol. 18, 16-26 (2008).
13. H. S. Chung and W. A. Louis, J. M. Eaton, Proc. Natl. Acad. Sci. USA 106(29), 11837-11844 (2009).
14. Y. Santoso, C.M. Joyce, O. Potapova, L. Le Reste, J. Hohlbein, J.P. Torella, N.D.F. Grindley, and A.N. Kapanidis, Proc. Natl. Acad. Sci. USA 107(2), 715 (2010).
15. M. Dahan, A. A. Deniz, T. Ha, D. S. Chemla, P. G. Schultz, and S. Weiss, Chem. Phys. 247(1), 85-106 (1999).
16. D. S. Talaga, W. L. Lau, H. Roder, J. Tang, Y. Jia, W. F. DeGrado, and R. M. Hochstrasser, Proc. Natl. Acad. Sci. USA 97(24), 13021-13026 (2000).
17. E. Sisamakis, A. Valeri, S. Kalinin, P. J. Rothwell, and C. A. M. Seidel, Methods in Enzymology 475, 455-514 (2010).
18. K. Zhang and H. Yang, J. Phys. Chem. B 109(46), 21930-21937 (2005).
19. I. V. Gopich and A. Szabo, J. Phys. Chem. B 107(21), 5058-5063 (2003).
20. I. Gopich and A. Szabo, J. Chem. Phys. 122(1), 14707-1-18 (2005).
21. I. V. Gopich and A. Szabo, J. Phys. Chem. B 111(44), 12925-12932 (2007).
22. T. Basché, W. E. Moerner, M. Orrit, and H. Talon, Phys. Rev. Lett. 69(10), 1516-1519 (1992).
23. D. Nettels, I. V. Gopich, A. Hoffmann, and B. Schuler, Proc. Natl. Acad. Sci. USA 104(8), 2655-2660 (2007).
24. I. V. Gopich and A. Szabo, J. Chem. Phys. 124(15), 154712-1-21 (2006).
25. I. V. Gopich, D. Nettels, B. Schuler, and A. Szabo, J. Chem. Phys. 131, 095102-1-5 (2009).
26. I. V. Gopich and A. Szabo, Theory of Photon Counting in Single-Molecule Spectroscopy. In: E. Barkai, F. L. H. Brown, and M. Orrit, Eds., Theory and evaluation of single-molecule signals, World Scientific Publishing Co. Inc. 2008, pp. 181-244.
27. A.A. Deniz, T.A. Laurence, M. Dahan, D.S. Chemla, P.G. Schultz, and S. Weiss, Annu. Rev. Phys. Chem 52, 233-53 (2001).
28. A. Baba and T. Komatsuzaki, Proc. Natl. Acad. Sci. USA 104(49), 19297 (2007).
29. C.B. Li, H. Yang, and T. Komatsuzaki, Proc. Natl. Acad. Sci. USA 105(2), 536-541 (2008).
30. F. L. H. Brown, Phys. Rev. Lett. 90(2), 28302-1-4 (2003).
31. E. Barkai, Y.J. Jung, and R. Silbey, Annual Review of Physical Chemistry 55(1), 457-507 (2004).
32. F. L. H. Brown, Acc. Chem. Res. 39(6), 363-373 (2006).
33. I. V. Gopich and A. Szabo, J. Chem. Phys. 118(1), 454-455 (2003).
34. R.L. Graham, D.E. Knuth, and O. Patashnik, Concrete Mathematics: A Foundation for Computer Science. Addison-Wesley Longman Publishing Co., Inc. Boston, MA, 1994.
35. G. Hummer and A. Szabo, Acc. Chem. Res 38(7), 504-513 (2005).
36. A. M. Berezhkovskii, A. Szabo, and G. H. Weiss, J. Chem. Phys. 110(18), 9145-9150 (1999).
37. I. V. Gopich and A. Szabo, J. Phys. Chem. B 114(46), 15221-15226 (2010).
38. H. S. Chung, I. V. Gopich, K. McHale, T. Cellmer, J. M. Louis, and W. A. Eaton, J. Phys. Chem. A, 115(16) 3642-3656 (2011).
39. P. Kask, K. Palo, D. Ullmann, and K. Gall, Proc. Natl. Acad. Sci. USA 96(24), 13756-13761 (1999).
40. Y. Chen, J. D. Muller, P. T. C. So, and E. Gratton, Biophys. J. 77(1), 553-567 (1999).
41. K. Palo, U. Mets, S. Jager, P. Kask, and K. Gall, Biophys. J. 79(6), 2858-2866 (2000).
42. J.D. Muller, Y. Chen, and E. Gratton, Biophys. J. 78(1), 474-486 (2000).
43. T. D. Perroud, B. O. Huang, and R. N. Zare, ChemPhysChem 6(5), 905-912 (2005).
44. J.R. Fries, L. Brand, C. Eggeling, M. Kollner, and C.A.M. Seidel, J. Phys. Chem. A 102(33), 6601-6613 (1998).
45. E. Nir, X. Michalet, K. M. Hamadani, T. A. Laurence, D. Neuhauser, Y. Kovchegov, and S. Weiss, J. Phys. Chem. B 110(44), 22103-22124 (2006).
46. H.-X. Zhou and A. Szabo, J. Phys. Chem. 100(7), 2597-2604 (1996).
47. I. V. Gopich, J. Phys. Chem. B 112(19), 6214-6220 (2008).
48. I. V. Gopich and A. Szabo, J. Phys. Chem. B 109(37), 17683-17688 (2005).
49. B. Huan, T. D. Perroud, and R. N. Zare, ChemPhysChem 5(10), 1523-1531 (2004).
50. M. Antonik, S. Felekyan, A. Gaiduk, and C. A. M. Seidel, J. Phys. Chem. B 110(13), 6970-6978 (2006).
51. S. Kalinin, A. Valeri, M. Antonik, S. Felekyan, and C.A.M. Seidel, J. Phys. Chem. B 114(23), 7983-7995 (2010).
52. Y. Santoso, J. P. Torella, and A. N. Kapanidis, ChemPhysChem 11, 2209-2219 (2010).
53. I. V. Gopich and A. Szabo, J. Phys. Chem. B 113(31), 10965-10973 (2009).
54. A. N. Kapanidis, N. K. Lee, T. A. Laurence, S. Doose, E. Margeat, and S. Weiss, Proc. Natl. Acad. Sci. USA 101(24), 8936-8941 (2004).
55. B.W. Van Der Meer, G. Coker, and S.Y.S. Chen, Resonance energy transfer: theory and data. VCH, New York, 1994.
56. B. A. Camley, F. L. H. Brown, and E. A Lipman, J. Chem. Phys. 131(10) 104509 (2009).
57. P. Frantsuzov, M. Kuno, B. Jankó, and R.A. Marcus, Nature Phys. 4(7), 519-522 (2008).
58. R. B. Best, K. A. Merchant, I. V. Gopich, B. Schuler, A. Bax, and W. A. Eaton, Proc. Natl. Acad. Sci. USA 104(48), 18964-18969 (2007).
59. M. Margittai, J. Widengren, E. Schweinberger, G. F. Schröder, S. Felekyan, E. Haustein, M. Konig, D. Fasshauer, H. Grubmuller, R. Jahn, and C. A. M. Seidel, Proc. Natl. Acad. Sci. USA 100(26), 15516-15521 (2003).
60. T. A. Laurence, X. Kong, M. Jäger, and S. Weiss, Proc. Natl. Acad. Sci. USA 102(48), 17348-17353 (2005).
61. K. A. Merchant, R. B. Best, J. M. Louis, I. V. Gopich, and W. A. Eaton, Proc. Natl. Acad. Sci. USA 104(5), 1528-1533 (2007).
62. A. Hoffmann, A. Kane, D. Nettels, D. E. Hertzog, P. Baumgartel, J. Lengefeld, G. Reichardt, D. A. Horsley, R. Seckler, O. Bakajin, and B. Schuler, Proc. Natl. Acad. Sci. USA 104(1), 105-110 (2007).
63. I. Gopich and A. Szabo, J. Phys. Chem. B 109(14), 6845-6848 (2005).
64. D. E. Makarov and K. W. Plaxco, J. Chem. Phys. 131, 085105-1-6 (2009).
65. G. F. Schröder and H. Grubmüller, J. Chem. Phys. 119(18), 9920-9924 (2003).
66. M. Andrec, R. M. Levy, and D. S. Talaga, J. Phys. Chem. A 107(38), 7454-7464 (2003).
67. J. B. Witkoskie and J. Cao, J. Chem. Phys. 121(13), 6373-6379 (2004).
68. S. C. Kou, X. S. Xie, and J. S. Liu, J. Royal Stat. Soc. Series C 54(3), 469 (2005).
69. S.A. McKinney, C. Joo, and T. Ha, Biophys. J. 91(5), 1941-1951 (2006).