Two-dimensional fluorescence resonance energy transfer as a probe for protein folding: A theoretical study

Journal of Chemical Physics

Volumn 128, Issue 11, 2008, Pages

  Ting, Christina L ^a,b   Makarov, Dmitrii E ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL DYNAMICS; FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET);

CONFORMATIONS; FLUORESCENCE; MARKOV PROCESSES; MATHEMATICAL MODELS; PROTEIN FOLDING; RESONANCE;

ENERGY TRANSFER;

DIAGNOSTIC AGENT;

ARTICLE; CHEMICAL STRUCTURE; FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; METHODOLOGY; MOLECULAR PROBE; PROBABILITY; PROTEIN FOLDING; STATISTICS; THEORETICAL MODEL;

FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; MARKOV CHAINS; MODELS, MOLECULAR; MODELS, THEORETICAL; MOLECULAR PROBES; PROTEIN FOLDING; STOCHASTIC PROCESSES;

EID: 41049090271     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2835611     Document Type: Article

References (82)

1. S. Weiss, Science SCIEAS 0036-8075 10.1126/science.283.5408.1676 283, 1676 (1999).
2. X. Zhuang and M. Rief, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/S0959-440X(03)00011-3 13, 88 (2003).
3. W. Min, B. P. English, G. Luo, B. J. Cherayil, S. C. Kou, and X. S. Xie, Acc. Chem. Res. ACHRE4 0001-4842 10.1021/ar040133f 38, 923 (2005).
4. W. E. Moerner, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0610081104 104, 12596 (2007).
5. P. V. Cornish and T. Ha, ACS Chem. Biol. 2, 53 (2007).
6. B. Chan, K. Weidemaier, W.-T. Yip, P. F. Barbara, and K. Musier-Forsyth, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.96.2.459 96, 459 (1999).
7. 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. U.S.A. PNASA6 0027-8424 10.1073/pnas.96.7.3670 96, 3670 (1999).
8. 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. U.S.A. PNASA6 0027-8424 10.1073/pnas.090104997 97, 5179 (2000).
9. A. A. Deniz, T. A. Laurence, M. Dahan, D. S. Chemla, P. G. Schultz, and S. Weiss, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 10.1146/annurev.physchem.52.1. 233 52, 233 (2001).
10. Y. Jia, D. S. Talaga, W. L. Lau, H. S. M. Lu, W. F. DeGrado, and R. M. Hochstrasser, Chem. Phys. CMPHC2 0301-0104 10.1016/S0301-0104(99)00127-5 247, 747 (1999).
11. E. V. Kuzmenkina, C. D. Heyes, and G. U. Nienhaus, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0507728102 102, 15471 (2005).
12. G. Cosa, Y. Zeng, H. W. Liu, C. F. Landes, D. E. Makarov, K. Musier-Forsyth, and P. F. Barbara, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp054189i 110, 2419 (2006).
13. J. A. Hanson, K. Duderstadt, L. P. Watkins, S. Bhattacharyya, J. Brokaw, J. W. Chu, and H. Yang, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0708600104 104, 18055 (2007).
14. C. Bai, C. Wang, X. S. Xie, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.96.20.11075 96, 11075 (1999).
15. J. Wang and P. Wolynes, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.74.4317 74, 4317 (1995).
16. Y. Jung, E. Barkai, and R. J. Silbey, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1521157 117, 10980 (2002).
17. Y. Jung, E. Barkai, and R. J. Silbey, Adv. Chem. Phys. ADCPAA 0065-2385 10.1002/0471231509.ch4 123, 199 (2002).
18. J. B. Witkoskie and J. Cao, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1785784 121, 6373 (2004).
19. J. B. Witkoskie and J. Cao, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1785783 121, 6361 (2004).
20. O. Flomenbom and R. J. Silbey, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0604546103 103, 10907 (2006).
21. I. V. Gopich and A. Szabo, J. Chem. Phys. JCPSA6 0021-9606 122, 14707 (2005).
22. I. V. Gopich and A. Szabo, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2180770 124, 154712 (2006).
23. S. A. McKinney, C. Joo, and T. Ha, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.106.082487 91, 1941 (2006).
24. J. Shang and E. Geva, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp067657c 111, 4220 (2007).
25. J. B. Witkoskie and J. Cao, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp061471w 110, 19009 (2006).
26. L. P. Watkins and H. Yang, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp0467548 109, 617 (2005).
27. L. P. Watkins and H. Yang, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.103.037739 86, 4015 (2004).
28. F. L. Brown, Acc. Chem. Res. ACHRE4 0001-4842 10.1021/ar050028l 39, 363 (2006).
29. F. L. Brown, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.90. 028302 90, 028302 (2003).
30. Y. Peng, Y. Zheng, and F. L. Brown, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2567235 126, 104303 (2007).
31. Y. Zheng and F. L. Brown, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1772754 121, 3238 (2004).
32. Y. Zheng and F. L. Brown, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.90.238305 90, 238305 (2003).
33. A. Gaiduk, R. Kuhnemuth, S. Felekyan, M. Antonik, W. Becker, V. Kudryavtsev, C. Sandhagen, and C. A. Seidel, Microsc. Res. Tech. MRTEEO 1059-910X 10.1002/jemt.20430 70, 433 (2007).
34. V. Kudryavtsev, S. Felekyan, A. K. Wozniak, M. Konig, C. Sandhagen, R. Kuhnemuth, C. A. Seidel, and F. Oesterhelt, Anal. Bioanal. Chem. ABCNBP 1618-2642 10.1007/s00216-006-0917-0 387, 71 (2007).
35. M. Heilemann, P. Tinnefeld, G. Sanehez Mosteiro, M. Garcia Parajo, N. F. Van Hulst, and M. Sauer, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja049351u 126, 6514 (2004).
36. S. Hohng, C. Joo, and T. Ha, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.104.043935 87, 1328 (2004).
37. J. P. Clamme and A. A. Deniz, ChemPhysChem CPCHFT 1439-4235 10.1002/cphc.200400261 6, 74 (2005).
38. M. Heilemann, R. Kasper, P. Tinnefeld, and M. Sauer, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja065585x 128, 16864 (2006).
39. N. K. Lee, A. N. Kapanidis, H. R. Koh, Y. Korlann, S. O. Ho, Y. Kim, N. Gassman, S. K. Kim, and S. Weiss, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.106.093211 92, 303 (2007).
40. X. Zhuang, L. E. Bartley, H. P. Babcock, R. Russell, T. Ha, D. Herschlag, and S. Chu, Science SCIEAS 0036-8075 10.1126/science.288.5473.2048 288, 2048 (2000).
41. B. Schuler, E. A. Lipman, and W. A. Eaton, Nature (London) NATUAS 0028-0836 10.1038/nature01060 419, 743 (2002).
42. B. Schuler, E. A. Lipman, P. J. Steinbach, M. Kumke, and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0408164102 102, 2754 (2005).
43. E. Sherman and G. Haran, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0601395103 103, 11539 (2006).
44. D. S. Talaga, W. L. Lau, H. Roder, J. Tang, Y. Jia, W. F. DeGrado, and R. M. Hochstrasser, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.97.24.13021 97, 13021 (2000).
45. S. Weiss, Nat. Struct. Biol. NSBIEW 1072-8368 10.1038/78941 7, 724 (2000).
46. E. R. McCarney, J. H. Werner, S. L. Bernstein, I. Ruczinski, D. E. Makarov, P. M. Goodwin, and K. W. Plaxco, J. Mol. Biol. JMOBAK 0022-2836 10.1016/j.jmb.2005.07.015 352, 672 (2005).
47. D. Nettels, I. V. Gopich, A. Hoffmann, and B. Schuler, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0611093104 104, 2655 (2007).
48. H. Yang, G. Luo, P. Karnchanaphanurach, T. M. Louie, I. Rech, S. Cova, L. Xun, and X. S. Xie, Science SCIEAS 0036-8075 10.1126/science.1086911 302, 262 (2003).
49. A. J. Berglund, A. C. Doherty, and H. Mabuchi, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.89.068101 89, 068101 (2002).
50. Z. S. Wang and D. E. Makarov, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp034285o 107, 5617 (2003).
51. R. L. Baldwin and G. D. Rose, Trends Biochem. Sci. TBSCDB 0167-7640 10.1016/S0968-0004(98)01345-0 24, 77 (1999).
52. H. S. Chan, S. Bromberg, and K. A. Dill, Philos. Trans. R. Soc. London, Ser. B PTRBAE 0962-8436 10.1098/rstb.1995.0046 348, 61 (1995).
53. K. A. Dill, K. M. Fiebig, and H. S. Chan, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.90.5.1942 90, 1942 (1993).
54. D. A. Debe, M. J. Carlson, and W. A. Goddard, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.96.6.2596 96, 2596 (1999).
55. D. A. Debe and W. A. Goddard, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1999.3278 294, 619 (1999).
56. O. V. Galzitskaya and A. V. Finkelstein, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.96.20.11299 96, 11299 (1999).
57. S. A. Islam, M. Karplus, and D. L. Weaver, J. Mol. Biol. JMOBAK 0022-2836 10.1016/S0022-2836(02)00029-3 318, 199 (2002).
58. M. Karplus and D. L. Weaver, Biopolymers BIPMAA 0006-3525 10.1002/bip.1979.360180608 18, 1421 (1979).
59. D. E. Makarov and K. W. Plaxco, Protein Sci. PRCIEI 0961-8368 10.1110/ps.0220003 12, 17 (2003).
60. V. Munoz and W. A. Eaton, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.96.20.11311 96, 11311 (1999).
61. J. K. Myers and T. G. Oas, Nat. Struct. Biol. NSBIEW 1072-8368 10.1038/88626 8, 552 (2001).
62. G. D. Rose, J. Mol. Biol. JMOBAK 0022-2836 10.1016/0022-2836(79)90363-2 134, 447 (1979).
63. Y. Q. Zhou and M. Karplus, Nature (London) NATUAS 0028-0836 10.1038/43937 401, 400 (1999).
64. J. M. Fernandez and H. Li, Science SCIEAS 0036-8075 10.1126/science. 1092497 303, 1674 (2004).
65. R. B. Best and G. Hummer, Science SCIEAS 0036-8075 10.1126/science. 1106969 308, 498 (2005).
66. S. Kirmizialtin, L. Huang, and D. E. Makarov, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1931659 122, 234915 (2005).
67. X. Qi and J. J. Portman, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0609321104 104, 10841 (2007).
68. M. S. Li, D. K. Klimov, and D. Thirumalai, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93.268107 93, 268107 (2004).
69. T. R. Weikl, M. Palassini, and K. A. Dill, Protein Sci. PRCIEI 0961-8368 10.1110/ps.03403604 13, 822 (2004).
70. P. Bruscolini, A. Pelizzola, and M. Zamparo, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2738473 126, 215103 (2007).
71. J. D. Chodera, N. Singhal, and V. S. Pande, K. A. Dill, and W. C. Swope, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2714538 126, 155101 (2007).
72. D. E. Makarov, C. A. Keller, K. W. Plaxco, and H. Metiu, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.052713599 99, 3535 (2002).
73. D. E. Makarov and H. Metiu, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1450123 116, 5205 (2002).
74. K. Eom, P.-C. Li, D. E. Makarov, and G. J. Rodin, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp035178x 107, 8730 (2003).
75. K. Eom, D. E. Makarov, and G. J. Rodin, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.71.021904 71, 021904 (2005).
76. N. G. van Kampen, Stochastic Processes in Physics and Chemistry (Elsevier, New York/North Holland, Amsterdam, 1981).
77. K. W. Plaxco, K. T. Simons, I. Ruczinski, and D. Baker, Biochemistry BICHAW 0006-2960 10.1021/bi000200n 39, 11177 (2000).
78. D. E. Makarov and G. J. Rodin, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.66.011908 66, 011908 (2002).
79. A. Szabo, K. Schulten, and Z. Schulten, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.439715 72, 4350 (1980).
80. I. V. Gopich and A. Szabo, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp027481o 107, 5058 (2003).
81. K. W. Plaxco, K. T. Simons, and D. Baker, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1998.1645 277, 985 (1998).
82. H. S. Chan and K. A. Dill, Proteins 30, 2 (1998).