Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 3, 2005, Pages 612-617

  Chung, Hoi Sung ^a   Khalil, Munira ^a,b   Smith, Adam W ^a   Ganim, Ziad ^a   Tokmakoff, Andrei ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Nonlinear IR spectroscopy; Protein folding dynamics; Temperature jump

Indexed keywords

UBIQUITIN;

ARTICLE; BETA SHEET; BINDING KINETICS; CONFORMATIONAL TRANSITION; EQUILIBRIUM CONSTANT; HYDROPHOBICITY; INFRARED SPECTROSCOPY; NONHUMAN; NONLINEAR SYSTEM; PRIORITY JOURNAL; PROTEIN FOLDING; STEADY STATE; TIME; VIBRATION;

KINETICS; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; TEMPERATURE; TIME; UBIQUITIN;

MUS;

EID: 14144250238     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0408646102     Document Type: Article

References (49)

1. Onuchic, J. N., Luthey-Schulten, Z. & Wolynes, P. G. (1997) Annu. Rev. Phys. Chem. 48, 545-600.
2. Dobson, C. M., Sali, A. & Karplus, M. (1998) Angew. Chem. Int. Ed. 37, 868-893.
3. Dill, K. A. (1999) Protein Sci. 8, 1166-1180.
4. Snow, C. D., Nguyen, H., Pande, V. S. & Gruebele, M. (2002) Nature 420, 102-106.
5. Snow, C. D., Qiu, L., Du, D., Gai, F., Hagen, S. J. & Pandc, V. S. (2004) Proc. Natl. Acad. Sci. USA 101, 4077-4082.
6. Sabelko, J., Ervin, J. & Gruebele, M. (1999) Proc. Natl Acad. Sci. USA 96, 6031-6036.
7. Leeson, D. T., Gai, F., Rodriguez, H. M., Gregoret, L. M. & Dyer, R. B. (2000) Proc. Natl. Acad. Sci. USA 97, 2527-2532.
8. Yang, W. Y. & Gruebele, M. (2004) Biophys. J. 87, 596-608.
9. Huang, C.-Y., Getahun, Z., Zhu, Y., Klemke, J. W., DeGrado, W. F. & Gai, F. (2002) Proc. Natl. Acad. Sci. USA 99, 2788-2793.
10. Eaton, W. A., Muñoz, V., Hagen, S. J., Jas, G. S., Lapidus, L. J., Henry, E. R. & Hofrichter, J. (2000) Annu. Rev. Biophys. Biomol. Struct. 29, 327-359.
11. Gruebele, M., Sabelko, J., Ballew, R. & Ervin, J. (1998) Ace. Chem. Res. 31, 699-707.
12. Goldbeck, R. A., Thomas, Y. G., Chen, E., Esquerra, R. M. & Kliger, D. S. (1999) Proc. Natl. Acad. Sci. USA 96, 2782-2787.
13. Yamamoto, K., Mizutani, Y. & Kitagawa, T. (2000) Biophys. J. 79, 485-495.
14. Dyer, R. B., Gai, F., Woodruff, W. H., Gilmanshin, R. & Callender, R. H. (1998) Acc. Chem. Res. 31, 709-716.
15. Callender, R. H., Dyer, R. B., Gilmanshin, R. & Woodruff, W. H. (1998) Annu. Rev. Phys. Chem. 49, 173-202.
16. Phillips, C. M., Mizutani, Y. & Hochstrasser, R. M. (1995) Proc. Natl. Acad. Sci. USA 92, 7292-7296.
17. Gilmanshin, R., Williams, S., Callender, R. H., Woodruff, W. H. & Dyer, R. B. (1997) Proc. Natl. Acad. Sci. USA 94, 3709-3713.
18. Williams, S., Causgrove, T. F., Gilmanshin, R, Fang, K. S., Callender, R. H. & Woodruff, W. H. (1996) Biochemistry 35, 691-697.
19. Werner, J. H., Dyer, R. B., Fesinmeyer, R. M. & Andersen, N. H. (2002) J. Phys. Chem. B 106, 487-494.
20. Bredenbeck, J., Helbing, J., Sieg, A., Schrader, T., Zinth, W., Renner, C., Behrendth, R., Moroder, L., Wachtveitl, J. & Hamm, P. (2003) Proc. Natl. Acad. Sci. USA 100, 6452-6457.
21. Krimm, S. & Bandekar, J. (1986) Adv. Protein Chem. 38, 181-364.
22. Hamm, F., Lim, M. & Hochstrasser, R. M. (1998) J. Phys. Chem. B 102, 6123-6138.
23. Torii, H. & Tasumi, M. (1992) J. Chem. Phys. 95, 3379-3387.
24. Khalil, M., Demirdöven, N. & Tokmakoff, A. (2003) J. Phys. Chem. A 107, 5258-5279.
25. Cheatum, C. M., Tokmakoff, A. & Knoester, J. (2004) J. Chem. Phys. 120, 8201-8215.
26. Demirdöven, N., Cheatum, C. M., Chung, H. S., Khalil, M., Knoester, J. & Tokmakoff, A. (2004) J. Am. Chem. Soc. 126, 7981-7990.
27. Chung, H. S., Khalil, M. & Tokmakoff, A. (2004) J. Phys. Chem. B 108, 15332-15342.
28. Byler, D. M. & Susi, H. (1986) Biopolymers 25, 469-487.
29. Miyazawa, T. (1960) J. Chem. Phys. 32,1647-1652.
30. Vijay-Kumar, S., Bugg, C. E. & Cook, W. J. (1987) J. Mol. Biol. 194, 531-544.
31. Jourdan, M. & Searle, M. S. (2000) Biochemistry 39, 12355-12364.
32. Harding, M. M., Williams, D. H. & Woolfson, D. N. (1991) Biochemistry 30, 3120-3128.
33. Cox, J. P. L., Evans, P. A., Packman, L. C, Williams, D. H. & Woolfson, D. N. (1993) J. Mol. Biol. 234, 483-492.
34. Stockman, B. J., Euvrard, A. & Scahill,T. A. (1993) J. Biomol. NMR 3,285-296.
35. Alonso, D. O. V. & Daggett, V. (1995) J. Mol. Biol. 247, 501-520.
36. Socci, N. D., Onuchic, J. N. & Wolynes, P. G. (1998) Proteins 32, 136-158.
37. Gruebele, M. (1999) Annu. Rev. Phys. Chem. 50, 485-516.
38. Hagen, S. J., Hofrichter, J., Szabo, A. & Eaton, W. A. (1996) Proc. Natl. Acad. Sci. USA 93, 11615-11617.
39. Kubelka, J., Hofrichter, J. & Eaton, W. A. (2004) Curr. Opin. Struct. Biol. 14, 76-88.
40. Yang, W. Y. & Gruebele, M. (2003) Nature 423, 193-197.
41. Wang, T., Zhu, Y. & Gai, F. (2004) J. Phys. Chem. B 108, 3694-3697.
42. Bredenbeck, J., Helbing, J., Behrendt, R., Renner, C., Moroder, L., Wachtveitl, J. & Hamm, P. (2003) J. Phys. Chem. B 107, 8654-8660.
43. Briggs, M. S. & Roder, H. (1992) Proc. Natl. Acad. Sci. USA 89, 2017-2021.
44. Khorasanizadeh, S., Peters, I. D. & Roder, H. (1996) Nat. Struct. Biol. 3, 193-205.
45. Krantz, B. A. & Sosnick, T. R. (2000) Biochemistry 39, 11696-11701.
46. Gladwin, S. T. & Evans, P. A. (1996) Folding Des. 1, 407-417.
47. Qin, Z., Ervin, J., Larios, E., Gruebele, M. & Kihara, H. (2002) J. Phys. Chem. B 106, 13040-13046.
48. Larios, E., Li, J. S., Schulten, K., Kihara, H. & Gruebele, M. (2004) J. Mol. Biol. 340, 115-125.
49. Ham, S. & Cho, M. (2003) J. Chem. Phys. 118, 6915-6922.