UV-resonance Raman thermal unfolding study of Trp-cage shows that it is not a simple two-state miniprotein

Journal of the American Chemical Society

Volumn 127, Issue 31, 2005, Pages 10943-10950

  Ahmed, Zeeshan ^a   Beta, Ilir A ^a,b   Mikhonin, Aleksandr V ^a   Asher, Sanford A ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

^b KANSAS STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL BONDS; MELTING; PROTEINS; RAMAN SPECTROSCOPY; REACTION KINETICS; RESONANCE; SPECTRUM ANALYSIS; SYNTHESIS (CHEMICAL); THERMAL EFFECTS;

AMIDE BONDS; THERMAL MELTING; THERMAL UNFOLDING; ULTRAVIOLET RESONANCE RAMAN SPECTROSCOPY (UVRS);

POLYPEPTIDES;

POLYPEPTIDE; TRYPTOPHAN;

ALPHA HELIX; ARTICLE; CHEMICAL BOND; CHEMICAL REACTION KINETICS; MELTING POINT; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; RAMAN SPECTROMETRY; TEMPERATURE DEPENDENCE; ULTRAVIOLET SPECTROSCOPY;

AMINO ACID SEQUENCE; MOLECULAR SEQUENCE DATA; PEPTIDES; PROLINE; SPECTRUM ANALYSIS, RAMAN; TEMPERATURE; ULTRAVIOLET RAYS;

EID: 23744503388     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja050664e     Document Type: Article

References (89)

1. Anfinsen, C. B. Science 1973, 181, 4096, 223-230.
2. Chan, H. S.; Dill, K. A. Proteins: Struct, Funct. Genet. 1998, 30, 2-33.
3. Dill, K. A. Biochemistry 1990, 29, 7133-7155.
4. Jewett, A. I.; Pande, V. S.; Plaxco, K. W. J. Mol. Biol. 2003, 326, 247-253.
5. Hardin, C.; Eastwood, M. P.; Prentiss, M.; Luthey-Schulten, Z.; Wolynes, P. G. J. Comput. Chem. 2002, 23, 138-146.
6. Cleland, J. Protein folding: in vivo and in vitro: American Chemical Society: Washington, DC, 1993.
7. Dill, K. A.; Alonso, D. O.; Hutchinson, K. Biochemistry 1989, 28, 5439-5449.
8. th ed.; Springer: New York, 2000.
9. Alm, E.; Baker, D. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11305- 11310.
10. Wolynes, P. G.; Onuchic, J. N.; Thirumalai, D. Science 1995, 267, 5204, 1619-1620.
11. Pappu, R. V.; Srinivasan, R.; Rose, G. D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 23, 12565-12570.
12. Myers, J. K.; Oas, T. G. Annu. Rev. Biochem. 2002, 71, 783-815.
13. Shortle, D. Curr. Opin. Struct. Biol. 1993, 3, 66-74.
14. Bryngelson, J. D.; Wolynes, P. G. J. Phys. Chem. 1989, 93, 6902-6915.
15. Hao, M.; Scheraga, H. A. J. Phys. Chem. 1994, 98, 9882-9893.
16. Dobson, C. M.; Salij, A.; Karplus, M. Angew. Chem., Int. Ed. 1998, 37, 868-893.
17. Muñoz, V.; Thompson, P. A.; Hofrichter, J.; Eaton, W. A. Nature 1997, 390, 196-199.
18. Eaton, W. A.; Muñoz, V.; Thompson, P. A.; Henry, E. R.; Hofrichter, J. Acc. Chem. Res. 1998, 31, 745-753.
19. Muñoz, V.; Henry, E. R.; Hofrichter, J.; Eaton. W. A. Proc. Natl. Acad. Sci. U.S.A 1998, 95, 5872-5879.
20. Dinner, A. R.; Lazaridis, T.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9068-9073.
21. Thompson, P.; Eaton, W. A.; Hofrichter, J. Biochemistry 1997, 36, 9200-9210.
22. Lednev, I. K.; Karnoup, Anton S.; Sparrow, M. C.; Asher, S. A. J. Am. Chem. Soc. 1999, 121, 8074-8086.
23. Bolin, K. A.; Millhauser, G. L. Acc. Chem. Res. 1999, 32, 1027-1033.
24. Garcia, A. E.; Sanbonmatsu, K. Y. Proc. Natl. Acad Sci. U.S.A. 2002, 99, 5, 2782-2787.
25. Andrew, C. D.; Warwicker, J.; Jones, G. R.; Doig, A. J. Biochemistry 2002, 41, 1897-1905.
26. Lednev, I. K.; Karnoup, A. S.; Sparrow, M. C.; Asher, S. A. J. Am. Chem. Soc. 2001, 123, 2388-2392.
27. Woutersen, S.; Hamm, P. J. Chem. Phys. 2001, 114, 2727.
28. Clarke, D. T.; Doig, A. J.; Stapley, B. J.; Jones, G. R. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 7232-7237.
29. Williams, S.; Causgrove, T. P.; Gilmanshin, R.; Fang, K. S.; Callender, R. H.; Woodruff, W. H.; Dyer, R. B. Biochemistry 1996, 35, 691-697.
30. Ianoul, A.; Mikhonin, A.; Lednev, I. K.; Asher, S. A. J. Phys. Chem. A 2002, 106, 3621-3624.
31. Asher, S. A.; Mikhonin, A. V.; Bykov, S. V. J. Am. Chem. Soc. 2004, 126, 27, 8433-8440.
32. Tiffany, M. L.; Krimm, S. Biopolymers 1968, 6, 1379-1382.
33. Neidigh, J. W.; Fesinmeyer, R. M.; Andersen, N. H. Nat. Struct. Biol. 2002, 9, 6, 425-430.
34. Gellman, S. H.; Woolfson, D. N. Nat. Struct. Biol. 2002, 9, 6, 408-410.
35. Qiu, L.; Pabit, S. A.; Roitberg, A. E.; Hagen, S. J. J. Am. Chem. Soc. 2002, 124, 12952-12953.
36. Hagen, S. J.; Hofrichter, L.; Szabo, A.; Eaton, W. A. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 11615-11617.
37. Pascher, T.; Chesick, J. P.; Winkler, J. R.; Gray, H. B. Science 1996, 27, 5255, 1558-1560.
38. Kubelka, J.; H., James; Eaton, W. A. Curr. Opin. Struct. Biol. 2004, 14, 1, 76-88.
39. Hagen, S. J.; Hofrichter, L.; Eaton, W. A. J. Phys. Chem. B 1997, 101, 2325-2365.
40. Kubelka, J.; Eaton, W. A.; Hofrichter, J. J. Mol. Biol. 2003, 329, 625-630.
41. Simmerling, C.; Strockbine, B.; Roitberg, A. E. J. Am. Chem. Soc. 2002, 124, 11258-11259.
42. Roitberg, A. E. Personal communication.
43. Snow, C. D.; Zagrovic, B.; Pande, V. S. J. Am. Chem. Soc. 2002, 124, 14548-14549.
44. Chowdhury, S.; Lee, M. C.; Xiong, G.; Duan, Y. J. Mol. Biol. 2003, 327, 711-717.
45. Zhou, R. J. Mol. Graphics Modell. 2004, 22, 451-462.
46. Zhou, R. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 23, 13280-13285.
47. Chowdhury, S.; Lee, M. C.; Xiong, G.; Duan, Y. J. Phys. Chem. B 2004, 108, 13855-13865.
48. Pitera, J. W.; Swope, W. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13, 7587-7592.
49. Sweeny, J. A.; Asher, S. A. J. Phys. Chem. 1990, 94, 12, 4784-4791.
50. Ludwig, M.; Asher, S. A. J. Am. Chem. Soc. 1988, 110, 1005-1011.
51. Chi, Z.; Asher, S. A. Biochemistry 1998, 37, 2865-2872.
52. Chi, Z.; Chen, X. G.; Holtz, J. S. W.; Asher, S. A. Biochemistry 1998, 37, 2854-2864.
53. Mirkin, N. G.; Krimm, S. J. Mol. Struct. 1996, 377, 219.
54. Caswell, D. S.; Spiro, T. G. J. Am. Chem. Soc. 1987, 109, 2796-2800.
55. Rippon, W. B.; Koenig, J. L.; Walton, A. G. J. Am Chem. Soc. 1970, 92, 7455-7459.
56. Mayne, L.; Hudson, B. J. Phys. Chem. 1987, 91, 4438-4440.
57. Dorman, D. E.; Torchia, D. A.; Bovey, F. A. Macromolecules 1973, 6, 80-82.
58. Harhay, G. P.; Hudson, B. S. J. Phys. Chem. 1991, 3511-3513.
59. Swenson, C. A. Biopolymers 1970, 10, 2591-2596.
60. Wang, Y.; Purrello, R.; Jordan, T.; Spiro, T. G. J. Am. Chem. Soc. 1991, 113, 6359-6368.
61. Diem, M.; Lee, O.; Roberts, G. M. J. Phys. Chem. 1992, 96, 548.
62. Lee, S. H.; Krimm, S. Biopolymers 1998, 46, 283.
63. Lee, S. H.; Krimm, S. Chem. Phys. 1998, 230, 277.
64. Mikhonin, A. V.; Ahmed, Z.; Ianoul, A.; Asher, S. A. J. Phys. Chem. B 2004, 108, 19020-19028.
65. Overman, S. A.; Thomas, G. J., Jr. Biochemistry 1998, 37, 5654-5665.
66. Torii, H. J. Phys. Chem. A 2004, 108, 7272-7280.
67. Besley, N. A.; Oakley, M. T.; Cowan, A. J.; Hirst, J. D. J. Am. Chem. Soc. 2004, 126, 13502-13511.
68. Triggs, N. E.; Valentini, J. J. J. Phys. Chem. 1992, 96, 6922-6931.
69. Takeuchi, H.; Harada, I. J. Raman Spectrosc. 1990, 21, 509-515.
70. A 6% decrease in absorption would result in a ∼12% decrease in the resonance Raman cross sections (RCS roughly scale as the square of extinction coefficient). In the case of Trp-cage the AmI1′ band intensity decreases by ∼33% between 4 and 70 °C.
71. Cantor, C. R.; Schimmel, P. R. Biophysical Chemistry: Freeman and Compant: San Francisco, CA, 1980: Vol. 1.
72. Asher, S. A.; Ianoul, A.; Mix, G.; Boyden, M. N.; Karnoup, A.; Diem, M.; Schweitzer-Stenner, R. J. Am. Chem. Soc. 2001, 123, 11775-11781.
73. Dudik, J. M.; Johnson, C. R.; Asher, S. A. J. Chem. Phys. 1985, 82, 1732.
74. Boyden, M. N.; Asher, S. A. Biochemistry 2001, 40, 13723-13727.
75. Ahmed, Z.; Asher, S. A. Manuscript in preparation.
76. Chi, Z.; Asher, S. A. J. Phys. Chem. B 1998, 102, 9595-9602.
77. Chi, Z.; Asher, S. A. Biochemistry 1999, 38, 8196-8203.
78. Miura, T.; Takeuchi, H.; Harada, I. Biochemistry 1988, 27, 88-98.
79. Mukerji, I.; Spiro, T. G. Biochemistry 1994, 33, 13132-13139.
80. Rockers, K. R.; Su, C.; Subramaniam, S.; Spiro, T. G. J. Am. Chem. Soc. 1992, 114, 3697-3709.
81. Harada, I.; Miura, T.; Takeuchi, H. Spectrochim. Acta 1986, 42A (2/3), 307-312.
82. Hideo, T.; Nemoto, Y.; Harada, I. Biochemistry 1990, 29, 1572-1579.
83. Kochendoerfer, G. G.; Kaminaka, S.; Mathies, R. A. Biochemistry 1997, 36, 13153-13159.
84. Hasmimoto, S.; Obata, K.; Takeuchi, H.; Needleman, R.; Lanyi, J. K. Biochemistry 1997, 36, 11583- 11590.
85. Miura, T.; Takeuchi, H.; Harada, I. Biochemistry 1988, 27, 88-94.
86. Miura, T.; Takeuchi, H.; Harada, I. J. Raman Spectrosc. 1989, 20, 667-671.
87. Andersen, N. H.; Cort, J. R.; Liu, Z.; Sjoberg, S. J.; Tong, H. J. Am. Chem. Soc. 1996, 118, 42, 10309-10310.
88. Privalov, P. L.; Griko, Y. V.; Venyaminov, S. Y.; Kutyshenko, V. P. J. Mol. Biol. 1986, 190, 487-498.
89. Urry, D. W. J. Phys. Chem. B 1997, 101, 51, 11007-11028.