Folding kinetics of a naturally occurring helical peptide: Implication of the folding speed limit of helical proteins

Journal of Physical Chemistry B

Volumn 112, Issue 30, 2008, Pages 9146-9150

  Mukherjee, Smita ^a   Chowdhury, Pramit ^a   Bunagan, Michelle R ^a   Gai, Feng ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; BACTERIOLOGY; CONCENTRATION (PROCESS); CONTROL THEORY; INFRARED SPECTROSCOPY; PEPTIDES; PROTEINS; RELAXATION PROCESSES; SOLUTIONS; SPECTROSCOPIC ANALYSIS; SPEED;

AQUEOUS SOLUTIONS; BACILLUS STEAROTHERMOPHILUS; CONCENTRATION RANGES; FOLDING KINETICS; FOLDING MECHANISMS; FOLDING RATES; HELICAL PROTEINS; HELICAL SEGMENTS; HIGH HELICITY; MODEL SYSTEMS; PROTEIN FOLDING PROBLEMS; RELAXATION KINETICS; RELAXATION RATES; RELAXATION TIME CONSTANTS; RIBOSOMAL PROTEIN; SIDE CHAINS; SIDE-CHAIN INTERACTIONS; SPEED LIMITS;

PROTEIN FOLDING;

EID: 49349096539     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp801721p     Document Type: Article

References (62)

1. Williams, S.; Causgrove, T. P.; Gilmanshin. R.; Fang, K. S.; Callender, R. H.; Woodruff, W. H.; Dyer, R. B. Biochemistry 1996, 35, 691.
2. Thompson. P. A.; Eaton, W. A.; Hofrichter, J. Biochemistry 1997, 36, 9200.
3. Volk, M.; Kholodenko, Y.; Lu, H. S. M.; Gooding, E. A.; DeGrado, W. F.; Hochstrasser, R. M. J. Phys. Chem. B 1997, 101, 8607.
4. Clarke, D. T.; Doig, A. J.; Stapley, B. J.; Jones. G. R. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 7232.
5. Lednev, I. K.; Karnoup, A. S.; Sparrow, M. C.; Asher. S. A. J. Am. Chem. Soc. 1999, 121, 8074.
6. Huang, C.-Y.; Getahun, Z.; Wang, T.; DeGrado, W. F.; Gai, F. J. Am. Chem. Soc 2001, 123, 12111.
7. Huang, C.-Y.; Klemke, J. W.; Getahun, Z.; DeGrado. W. F.; Gai, F. J. Am. Chem. Soc. 2001, 123, 9235.
8. Jas, G. S.; Eaton, W. A.; Hofrichter, J. J. Phys. Chem. B 2001, 105, 261.
9. Werner, J. H.; Dyer, R. B.; Fesinmeyer, R. M.; Andersen, N. H. J. Phys. Chem. B 2002, 106, 487.
10. Huang, C.-Y.; Getahun, Z.; Zhu, Y.; Klemke, J. W.; DeGrado, W. F.; Gai, F. Proc. Natl Acad. Sci. U.S.A. 2002, 99, 2788.
11. Wang, T.; Du, D.; Gai, F. Chem. Phys. Lett. 2003, 370, 842.
12. Wang, T.; Zhu, Y.; Getahun, Z.; Du, D.; Huang, C.-Y.; DeGrado, W. F.; Gai, F. J. Phys. Chem. B 2004, 108, 15301.
13. Bredenbeck, J.; Helbing, J.; Kumita, J. R.; Woolley, G. A.; Hamm, P. Proc. Natl Acad. Sci. U.S.A. 2005, 102, 2379.
14. Gooding, E. A.; Ramajo, A. P.; Wang, J. W.; Palmer, C.; Fouts, E.; Volk, M. Chem. Commun. 2005, 48, 5985.
15. Ramajo, A. P.; Petty, S. A.; Volk, M. Chem. Phys. 2006, 323, 11.
16. Balakrishnan, G.; Hu, Y.; Bender, G. M.; Getahun, Z.; DeGrado, W. F.; Spiro, T. G. J. Am. Chem. Soc. 2007, 129, 12801.
17. Du, D.; Bunagan, M. R.; Gai, F. Biophys. J. 2007, 93, 4076.
18. Hummer, G.; Garcia, A. E.; Garde, S. Proteins 2001, 42, 77.
19. Sorin, E. J.; Pande, V. S. Biophys. J. 2005, 88, 2472.
20. van Giessen, A. E.; Straub, J. E. J. Chem. Theor. Comp. 2006, 2, 674.
21. Scott, K. A.; Alonso, D. O. V.; Pan, Y.; Daggett, V. Biochemistry 2006, 45, 4153.
22. Fersht, A. R. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 10869.
23. Kim, P. S.; Baldwin, R. L. Annu. Rev. Biochem. 1982, 51, 459.
24. Daggett, V.; Fersht, A. R. Trends Biochem. Sci. 2003, 28, 18.
25. Kuhlman, B.; Yang, H. Y.; Boice, J. A.; Fairman, R.; Raleigh, D. P. J. Mol. Biol. 1997, 270, 640.
26. Zhou, H.-X. Phys. Biol. 2005, 2, R1.
27. Yang, W. Y.; Gruebele, M. Nature 2003, 423, 193.
28. Chang, I. J.; Lee, J. C.; Winkler, J. R.; Gray, H. B. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 3838.
29. Kubelka, J.; Hofrichter, J.; Eaton, W. A. Curr. Opin. Struct. Biol. 2004, 14, 76.
30. Dyer, R. B. Curr. Opin. Struct. Biol. 2007, 17, 38.
31. Dill, K. A.; Ozkan, S. B.; Weikl, T. R.; Chodera, J. D.; Voelz, V. A. Curr. Opin. Struct. Biol. 2007, 17, 342.
32. Mayor, U.; Johnson, C. M.; Daggett, V.; Fersht, A. R. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 13518.
33. Zhu, Y.; Alonso, D. O. V.; Maki, K.; Huang, C.-Y.; Lahr, S. J.; Daggett, V.; Roder, H.; DeGrado, W. F.; Gai, F. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 15486.
34. Kubelka, J.; Eaton, W. A.; Hofrichter, J. J. Mol. Biol. 2003, 329, 625.
35. Zhu, Y.; Fu, X.; Wang, T.; Tamura, A.; Takada, S.; Saven, J. G.; Gai, F. Chem. Phys. 2004, 307, 99.
36. Bunagan, M. R.; Yang, X.; Saven, J. G.; Gai, F. J. Phys. Chem. B 2006, 110, 3759.
37. Luo, P.; Baldwin, R. L. Biochemistry 1997, 36, 8413.
38. Manas, E. S.; Getahun, Z.; Wright. W. W.; DeGrado, W. F.; Vanderkooi, J. M. J. Am. Chem. Soc. 2000, 122, 9883.
39. Mukherjee, S.; Chowdhury, P.; Gai, F. J. Phys. Chem. B 2007, 111, 4596.
40. Mitsutake, A.; Okamoto, Y. J. Chem. Phys. 2000, 112, 10638.
41. Buchete, N.-V.; Straub, J. E. J. Phys. Chem. B 2001, 105, 6684.
42. Wu, X.; Wang, S. J. Phys. Chem. B 2001, 105, 2227.
43. Levy, Y.; Jortner, J.; Becker, O. M. Proc Natl Acad. Sci. U.S.A. 2001, 98, 2188.
44. Daggett, V.; Levitt, M. J. Mol. Biol. 2002, 223, 1121.
45. Margulis, C. J.; Stern, H. A.; Berne, B. J. J. Phys. Chem. B 2002, 106, 10748.
46. Chowdhury, S.; Zhang, W.; Wu, C.; Xiong, G.; Duan, Y. Biopolymers 2003, 68, 63.
47. Peng, Y.; Hansmann, U. H. E.; Alves, N. A. J. Chem. Phys. 2003, 118, 2374.
48. Takano, M.; Nakamura, H. K.; Nagayama, K.; Suyama, A. J. Chem. Phys. 2003, 118, 10312.
49. Baumketner, A.; Shea, J. E. Phys. Rev. E 2003, 68, 051901/1.
50. Nguyen, H. D.; Marchut, A. J.; Hall, C. K. Protein Sci. 2004, 13, 2909.
51. Doshi, U. R.; Munoz, V. J. Phys. Chem. B 2004, 108, 8497.
52. Gnanakaran, S.; Garcia, A. E. Proteins 2005, 59, 773.
53. Couch, V. A.; Cheng, N.; Nambiar, K.; Fink, W. J. Chem. Phys. 2006, 110, 3410.
54. Morozov, A. N.; Lin, S. H. J. Phys. Chem. B 2006, 110, 20555.
55. Yang, S.; Cho, M. J. Phys. Chem. B 2007, 111, 605.
56. Kim, S.; Roitberg, A. E. J. Phys. Chem. B 2008, 112, 1525.
57. Chakrabartty, A.; Doig, A. J.; Baldwin, R. L. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 11332.
58. Viguera, A. R.; Serrano, L. Protein Sci. 1999, 8, 1733.
59. Kumar, S.; Nussinov, R. J. Mol Biol. 1999, 293, 1241.
60. Fersht, A. R. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding; W. H. Freeman and Company: New York, NY, 1999; p 11.
61. Maness, S. J.; Franzen, S.; Gibbs, A. C.; Causgrove, T. P.; Dyer, R. B. Biophys. J. 2003, 84, 3874.
62. Du, D.; Gai, F. Biochemistry 2006, 45, 13131.