Quantitative single-molecule conformational distributions: A case study with poly-(L-proline)

Journal of Physical Chemistry A

Volumn 110, Issue 15, 2006, Pages 5191-5203

  Watkins, Lucas P ^a   Chang, Hauyee ^a   Yang, Haw ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL REACTIVITY; FÖRSTER TYPE RESONANCE ENERGY TRANSFER (FRET); POLY-(L-PROLINE);

AMINO ACIDS; MACROMOLECULES; MATHEMATICAL MODELS; ORGANIC POLYMERS; REACTION KINETICS;

MOLECULAR DYNAMICS;

BIOTIN; DRUG DERIVATIVE; FLUORESCENT DYE; PEPTIDE; POLYPROLINE;

ALGORITHM; ARTICLE; CHEMISTRY; CONFORMATION; FLUORESCENCE POLARIZATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; INSTRUMENTATION; METHODOLOGY; MOLECULAR WEIGHT;

ALGORITHMS; BIOTIN; FLUORESCENCE POLARIZATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; MOLECULAR CONFORMATION; MOLECULAR WEIGHT; PEPTIDES;

EID: 33646416480     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp055886d     Document Type: Article

References (70)

1. Weiss, S. Science 1999, 283, 1676-1683.
2. Moerner, W.; Orrit, M. Science 1999, 283, 1670-1676.
3. Xie, X. S.; Trautman, J. K. Annu. Rev. Phys. Chem. 1998, 49, 441-480.
4. Jung, Y.; Barkai, E.; Silbey, R. J. Chem. Phys. 2002, 117 (24), 10980-10995.
5. Lippitz, M.; Kulzer, F.; Orrit, M. ChemPhysChem 2005, 6, 770-789.
6. Watkins, L. P.; Yang, H. Biophys. J. 2004, 86, 4015-4029.
7. Watkins, L. P.; Yang, H. J. Phys. Chem. B 2005, 109, 617-628.
8. Scott, D. W. Biometrika 1979, 66 (3), 605-610.
9. Silverman, B. W. Density Estimation for Statistics and Data Analysis; Chapman & Hall/CRC: New York, 1998.
10. Jaynes, E. T. Proc. IEEE 1982, 70 (9), 939-952.
11. Schuler, B.; Lipman, E. A.; Steinbach, P. J.; Kumke, M.; Eaton, W. A. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2754-2759.
12. Lee, N. K.; Kapanidis, A. N.; Wang, Y.; Michalet, X.; Mukhopadhay, J.; Ebright, R. H.; Weiss, S. Biophys. J. 2005, 88, 2939-2953.
13. Sabanayagam, C. R.; Eid, J. S.; Meller, A. J. Chem. Phys. 2005, 122, 061103.
14. Gornick, F.; Mandelkern, L.; Diorio, A. F.; Roberts, D. E. J. Am. Chem. Soc. 1971, 93, 1769-1777.
15. Mattice, W. L.; Mandelkern, L. J. Am. Chem. Soc. 1971, 93, 1769-1777.
16. Kay, B. K.; Williamson, M. P.; Sudol, M. FASEB 2000, 14 (2), 231-241.
17. Fries, J. R.; Brand, L.; Eggeling, C.; Köllner, M.; Seidel, C. A. M. J. Phys. Chem. A 1998, 102, 6601-6613.
18. Novikov, E.; Hofkens, J.; Cotlet, M.; Maus, M.; De Schryver, F. C.; Boens, N. Spectrochim. Acta 2001, 57 (11), 2109-2133.
19. Enderlein, J.; Sauer, M. J. Phys. Chem. A 2001, 105, 48-53.
20. Yang, H.; Xie, X. S. J. Chem. Phys. 2002, 117, 10965-10979.
21. Barsegov, V.; Mukamel, S. J. Chem. Phys. 2002, 116, 9802-9810.
22. Schröder, G. F.; Grubmüller, H. J. Chem. Phys. 2003, 119, 7830-7834.
23. Andrec, M.; Levy, R. M.; Talaga, D. S. J. Phys. Chem. A 2003, 107 (38), 7454-7464.
24. Laurence, T. A.; Kapanidis, A. N.; Kong, X.; Chemla, D. S.; Weiss, S. J. Phys. Chem. B 2004, 108, 3051-3067.
25. Witkoskie, J. B.; Cao, J. S. J. Chem. Phys. 2004, 121, 6361-6372.
26. Witkoskie, J. B.; Cao, J. S. J. Chem. Phys. 2004, 121, 6373-6379.
27. Enderlein, J.; Goodwin, P. M.; van Orden, A.; Ambrose, W. P.; Erdmann, R.; Keller, R. A. Chem. Phys, Lett. 1997, 270, 464-470.
28. Gopich, I.; Szabo, A. J. Chem. Phys. 2005, 122, 014707.
29. Gopich, I.; Szabo, A. J. Phys. Chem. B 2005, 109, 6845-6848.
30. Harrington, W. F.; Sela, M. Biochim. Biophys. Acta 1958, 27, 24-41.
31. Steinberg, I. Z.; Harrington, W. F.; Berger, A.; Sela, M.; Katchalski, E. J. Am. Chem. Soc. 1960, 82, 5263-5279.
32. Luong, A. K.; Gradinaru, C. C.; Chandler, D. W.; Hayden, C. C. J. Phys. Chem. B 2005, 109 (33), 15691-15698.
33. Ha, T.; Rasnik, I.; Cheng, W.; Babcock, H. P.; Gauss, G. H.; Lohman, T. M.; Chu, S. Nature 2002, 419, 638-641.
34. Okumus, B.; Wilson, T. J.; Lilley, D. M. J.; Ha, T. Biophys. J. 2004, 87, 2798-2806.
35. Pal, P.; Lesoine, J. F.; Lieb, M. A.; Novotny, L.; Knauf, P. A. Biophys. J. 2005, in press.
36. dos Remedies, C. G.; Moens, P. D. J. J. Struct. Biol. 1995, 115, 175-185.
37. Budzien, J.; Raphael, C.; Ediger, M. D.; de Pablo, J. J. J. Chem. Phys. 2002, 116, 8209-8217.
38. He, Y.; Lutz, T. R.; Ediger, M. D.; Ayyagari, C.; Bedrov, R.; Smith, G. D. Macromolecules 2004, 37, 5032-5039.
39. Zwanzig, R.; Ailawadi, N. K. Phys. Rev. 1969, 182, 280-283.
40. Magde, D.; Elson, E.; Webb, W. W. Phys. Rev. Lett. 1972, 29, 705-708.
41. Xie, Z.; Srividya, N.; Sosnick, T. R.; Pan, T.; Scherer, N. F. Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (2), 534-539.
42. Schuler, B.; Lipman, E. A.; Eaton, W. A. Nature 2002, 419 (6908), 743-747.
43. Talaga, D. S.; Lau, W. L.; Roder, H.; Tang, J. Y.; Jia, Y. W.; DeGrado, W. F.; Hochstrasser, R. M. Proc. Natl. Acad. Sci. U.S.A. 2000, 97(24), 13021-13026.
44. Brasselet, S.; Peterman, E. J. G.; Miyawaki, A.; Moerner, W. E. J. Phys. Chem. B 2000, 104 (15), 3676-3682.
45. Yang, H.; Luo, G.; Karnchanaphanurach, P.; Louie, T.-M.; Xun, L.; Xie, X. S. Science 2003, 302, 262-266.
46. Slaughter, B. D.; Unruh, J. R.; Allen, M. W.; Urbauer, R. J. B.; Johnson, C. K. Biochemistry 2005, 44 (10), 3694-3707.
47. Margittai, M.; Widengren, J.; Schweinberger, E.; Schröder, G. F.; Felekyan, S.; Haustein, E.; König, M.; Fasshauer, D.; Grubmüller, H.; Jahn, R.; Seidel, C. A. M. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (26), 15516-15521.
48. Lee, M.; Tang, J. Y.; Hochstrasser, R. M. Chem. Phys. Lett. 2001, 344, 501-508.
49. Lee, M.; Kim, J.; Tang, J.; Hochstrasser, R. M. Chem. Phys. Lett. 2002, 359, 412-419.
50. Jaynes, E. T. Phys. Rev. 1957, 106, 620-630.
51. Jaynes, E. T. Phys. Rev. 1957, 108, 171-190.
52. Jia, Y.-w.; Sytnik, A.; Li, L.; Vladimirov, S.; Cooperman, B. S.; Hochstrasser, R. M. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 7932-7936.
53. Geva, E.; Skinner, J. L. Chem. Phys. Lett. 1998, 288 (2-4), 225-229.
54. Edman, L.; Mets, U.; Rigler, R. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 6710-6715.
55. Buschmann, V.; Weston, K. D.; Sauer, M. Bioconjugate Chem. 2003, 14, 195-204.
56. Dale, R. E.; Eisinger, J.; Blumberg, W. E. Biophys. J. 1979, 26, 161-194.
57. Cowan, P. M.; McGavin, S. Nature 1955, 176, 501-503.
58. Stryes, L.; Haugland, R. P. Proc. Natl. Acad. Sci. U.S.A. 1967, 58, 719-726.
59. Schimmel, P. R.; Flroy, P. J. Proc. Natl. Acad. Sci. U.S.A. 1967, 58, 52-59.
60. Brant, D. A.; Flory, P. J. J. Am. Chem. Soc. 1965, 87, 2788-2791.
61. Brant, D. A.; Flory, P. J. J. Am. Chem. Soc. 1965, 87, 2791-2800.
62. Flory, P. J. Statistical Mechanics of Chain Molecules; John Wiley & Sons: New York, 1969.
63. Bhattacharjee, J. K.; Thirumalai, D.; Bryngelson, J. D. arXiv: cond-mat/9709345, 1997.
64. Grosberg, A., Ed. Theoretical and Mathematical Models in Polymer Research; Academic Press: New Yrok, 1998.
65. Yamakawa, H. Annu. Rev. Phys. Chem. 1984, 35, 23-47.
66. Harnau, L.; Winkler, R. G.; Reineker, P. Europhys. Lett. 1999, 45, 488-494.
67. Jacob, J.; Baker, B.; Bryant, R. G.; Cafiso, D. S. Biophys. J. 1999, 77, 1086-1092.
68. Tanaka, S.; Scheraga, H. A. Macromolecules 1975, 8, 623-631.
69. Efron, B. Ann. Stat. 1979, 7, 1-26.
70. Efron, B.; Gong, G. Am. Stat. 1983, 37, 36-48.