T-jump infrared study of the folding mechanism of coiled-coil GCN4-p1

Biophysical Journal

Volumn 89, Issue 6, 2005, Pages 4180-4187

  Wang, Ting ^a   Lau, Wai Leung ^a   DeGrado, William F ^a   Gai, Feng ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LEUCINE ZIPPER PROTEIN;

ARTICLE; CIRCULAR DICHROISM; CROSS LINKING; INFRARED SPECTROSCOPY; PEPTIDE SYNTHESIS; PROTEIN FOLDING; TEMPERATURE;

EID: 28544431572     PISSN: 00063495     EISSN: 00063495     Source Type: Journal    
DOI: 10.1529/biophysj.105.068809     Document Type: Article

References (46)

1. Sanchez, I. E., and T. Kiefhaber. 2003. Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding. J. Mol. Biol. 325:367-376.
2. Daggett, V., and A. Fersht. 2003. The present view of the mechanism of protein folding. Nat. Rev. Mol. Cell Biol. 4:497-502.
3. Kamagata, K., M. Arai, and K. Kuwajima. 2004. Unification of the folding mechanisms of non-two-state and two-state proteins. J. Mol. Biol. 339:951-965.
4. Bai, Y. 2003. Hidden intermediates and Levinthal paradox in the folding of small proteins. Biochem. Biophys. Res. Commun. 305:785-788.
5. Bai, Y., T. R. Sosnick, L. Mayne, and S. W. Englander. 1995. Protein folding intermediates: native-state hydrogen exchange. Science. 269:192-197.
6. Takei, J., W. Pei, D. Vu, and Y. Bar. 2002. Populating partially unfolded forms by hydrogen exchange-directed protein engineering. Biochemistry. 41:12308-12312.
7. Huang, C-Y., Z. Getahun, Y. Zhu, J. W. Klemke, W. F. DeGrado, and F. Gai. 2002. Helix formation via conformation diffusion search. Proc. Natl. Acad. Sci. USA. 99:2788-2793.
8. Wang, T., Y. Zhu, Z. Getahun, D. Du, C.-Y. Huang, W. F. DeGrado, and F. Gai. 2004. Length-dependent helix-coil transition kinetics of nine alanine-based peptides. J. Phys. Chem. B. 108:15301-15310.
9. Hagen, S. J. 2003. Exponential decay kinetics in "downhill" protein folding. Proteins. 50:1-4.
10. O'Shea, E. K., J. D. Klemm, P. S. Kim, and T. Alber. 1991. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science. 254:539-544.
11. Wendt, H., A. Baici, and H. R. Bosshard. 1994. Mechanism of assembly of a leucine zipper domain. J. Am. Chem. Soc. 116:6973-6974.
12. Wendt, H., C. Berger, A. Baici, R. M. Thomas, and H. R. Bosshard. 1995. Kinetics of folding of leucine zipper domains. Biochemistry. 34:4097-4107.
13. Sosnick, T. R., S. Jackson, R. R. Wilk, S. W. Englander, and W. F. DeGrado. 1996. The role of helix formation in the folding of a fully α-helical coiled coil. Proteins. 24:427-432.
14. α NMR chemical shifts and local unfolding curves. Biophys. J. 73:1031-1041.
15. Moran, L. B., J. P. Schneider, A. Kentsis, G. A. Reddy, and T. R. Sosnick. 1999. Transition-state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking. Proc. Natl. Acad. Sci. USA. 96:10699-10704.
16. Jia, Y., D. S. Talaga, W. L. Lau, H. S. M. Lu, W. F. DeGrado, and R. M. Hochstrasser. 1999. Folding dynamics of single GCN4 peptides by fluorescence resonant energy transfer confocal microscopy. Chem. Phys. 247:69-83.
17. Myers, J. K., and T. G. Oas. 1999. Reinterpretation of GCN4-p1 folding kinetics: partial helix formation precedes dimerization in coiled coil folding. J. Mol. Biol. 289:205-209.
18. Mohanty, D., A. Kolinski, and J. Skolnick. 1999. De novo simulations of the folding thermodynamics of the GCN4 leucine zipper. Biophys. J. 77:54-69.
19. Zitzewitz, J. A., B. Ibarra-Molero, D. R. Fishel, K. L. Terry, and C. R. Matthews. 2000. Preformed secondary structure drives the association reaction of GCN4-p1, a model coiled-coil system. J. Mol. Biol. 296:1105-1116.
20. Ibarra-Molero, B., G. I. Makhatadze, and C. R. Matthews. 2001. Mapping the energy surface for the folding reaction of the coiled-coil peptide GCN4-p1. Biochemistry. 40:719-731.
21. Dragan, A. I., and P. L. Privalov. 2002. Unfolding of a leucine zipper is not a simple two-state transition. J. Mol. Biol. 321:891-908.
22. Krantz, B. A., and T. R. Sosnick. 2001. Engineered metal binding sites map the heterogeneous folding landscape of a coiled coil. Nat. Struct. Biol. 8:1042-1047.
23. O'Shea, E. K., R. Rutkowski, and P. S. Kim. 1989. Evidence that the leucine zipper is a coiled coil. Science. 243:538-542.
24. Lumb, K. J., C. M. Carr, and P. S. Kim. 1994. Subdomain folding of the coiled coil leucine zipper from the bZIP transcriptional activator GCN4. Biochemistry. 33:7361-7367.
25. Kammerer, R. Á., T. Schulthess, R. Landwehr, A. Lustig, J. Engel, U. Aebi, and M. O. Steinmetz. 1998. An autonomous folding unit mediates the assembly of two-stranded coiled coils. Proc. Natl. Acad. Sci. USA. 95:13419-13424.
26. Krimm, S., and J. Bandekar. 1986. Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. Adv. Protein Chem. 38:181-364.
27. Kauppinen, J. K., D. J. Moffatt, H. H. Manisch, and D. G. Cameron. 1981. Fourier self-deconvolution: a method for resolving intrinsically overlapped bands. Appl. Spectrosc. 35:271-276.
28. 3D: a de novo designed three-helix bundle protein. Proc. Natl. Acad. Sci. USA. 100:15486-15491.
29. Zhu, Y., X. Fu, T. Wang, A. Tamura, S. Takada, J. G. Saven, and F. Gai. 2004. Guiding the search for a protein's maximum rate of folding. Chem. Phys. 307:99-109.
30. Walsh, S. T. R., R. P. Cheng, W. W. Wright, D. O. V. Alonso, V. Daggett, J. M. Vanderkooi, and W. F. DeGrado. 2003. The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR. Protein Sci. 12:520-531.
31. Zitzewitz, J. A., O. Bilsel, J. B. Luo, B. E. Jones, and C. R. Matthews. 1995. Probing the folding mechanism of a leucine-zipper peptide by stopped-flow circular-dichroism spectroscopy. Biochemistry. 34:12812-12819.
32. Thompson, K. S., C. R. Vinson, and E. Freire. 1993. Thermodynamic characterization of the structural stability of the coiled-coil region of the bZIP transcription factor GCN4. Biochemistry. 32:5491-5496.
33. Sabelko, J., J. Ervin, and M. Gruebele. 1999. Observation of strange kinetics in protein folding. Proc. Natl. Acad. Sci. USA. 96:6031-6036.
34. Yang, W. Y., and M. Gruebele. 2004. Folding λ-repressor at its speed limit. Biophys. J. 87:596-608.
35. Meisner, W. K., and T. R. Sosnick. 2004. Barrier-limited, microsecond folding of a stable protein measured with hydrogen exchange: implications for downhill folding. Proc. Natl. Acad. Sci. USA. 101:15639-15644.
36. Jemth, P., S. Gianni, R. Day, B. Li, C. M. Johnson, V. Daggett, and A. R. Fersht. 2004. Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and simulation. Proc. Natl. Acad. Sci. USA. 101:6450-6455.
37. Roder, H., K. Maki, H. Cheng, and M. C. R. Shastry. 2004. Rapid mixing methods for exploring the kinetics of protein folding. Methods. 34:15-27.
38. d'Avignon, D. A., G. L. Bretthorst, M. E. Holtzer, and A. Holtzer. 1998. Site-specific thermodynamics and kinetics of a coiled-coil transition by spin inversion transfer NMR. Biophys. J. 74:3190-3197.
39. d'Avignon, D. A., G. L. Bretthorst, M. E. Holtzer, and A. Holtzer. 1999. Thermodynamics and kinetics of a folded-folded′ transition at valine-9 of a GCN4-like leucine zipper. Biophys. J. 76:2752-2759.
40. Klimov, D. K., and D. Thirumalai. 2002. Is there a unique melting temperature for two-state proteins? J. Comput. Chem. 23:161-165.
41. Parker, M. J., J. Spencer, and A. R. Clarke. 1995. An integrated kinetic analysis of intermediates and transition states in protein folding reactions. J. Mol. Biol. 253:771-786.
42. 13C-labeled helical peptides. J. Am. Chem. Soc. 123:12111-12112.
43. Decatur, S. M., and J. Antonic. 1999. Isotope-edited infrared spectroscopy of helical peptides. J. Am. Chem. Soc. 121:11914-11915.
44. Yang, W. Y., J. W. Pitera, W. C. Swope, and M. Gruebele. 2004. Heterogeneous folding of the Trpzip hairpin: full atom simulation and experiment. J. Mol. Biol. 336:241-251.
45. Onuchic, J. N., Z. Luthey-Schulten, and P. G. Wolynes. 1997. Theory of protein folding: the energy landscape perspective. Annu. Rev. Phys. Chem. 48:545-600.
46. Garcia-Mira, M. M., M. Sadqi, N. Fischer, J. M. Sanchez-Ruiz, and V. Munoz. 2002. Experimental identification of downhill protein folding. Science. 298:2191-2195.