Kinetics are probe-dependent during downhill folding of an engineered λ6-85 protein

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

Volumn 102, Issue 7, 2005, Pages 2283-2287

  Ma, Hairong ^a   Gruebele, Martin ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Amide band; Fluorescence; Helix bundle; Infrared; Landscape roughness

Indexed keywords

ALANINE; AMIDE; GLUCOSE; GLUTAMINE; GLYCINE; MUTANT PROTEIN; PROTEIN; PROTEIN LAMBDA[6-85]; TRYPTOPHAN; TYROSINE; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO ACID SUBSTITUTION; ARTICLE; ENERGY; FLUORESCENCE; INFRARED SPECTROSCOPY; KINETICS; MOLECULAR PROBE; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN FOLDING; SIMULATION; TEMPERATURE; VISCOSITY;

KINETICS; MUTAGENESIS, SITE-DIRECTED; PROTEIN DENATURATION; PROTEIN ENGINEERING; PROTEIN FOLDING; RECOMBINANT PROTEINS; SPECTROMETRY, FLUORESCENCE; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; TEMPERATURE; THERMODYNAMICS; VISCOSITY;

MUS;

EID: 14044258768     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0409270102     Document Type: Article

References (38)

1. Bryngelson, J. D., Onuchic, J. N., Socci, N. D. & Wolynes, P. G. (1995) Proteins Struct. Funct. Genet. 21, 167-195.
2. Kubelka, J., Hofrichter, J. & Eaton, W. A. (2004) Curr. Opinion. Struct. Biol. 14, 76-88.
3. Jones, C. M., Henry, E. R., Hu, Y., Chan, C., Luck, S. D., Bhuyan, A., Roder, H., Hofrichter, J. & Eaton, W. A. (1993) Proc. Natl. Acad. Sci. USA 90, 11860-11864.
4. Phillips, C. M., Mizutani, Y. & Hochstrasser, R. M. (1995) Proc. Natl. Acad. Sci. USA 92, 7292-7296.
5. Williams, S., Causgrove, T. P., Gilmanshin, R., Fang, K. S., Callender, R. H., Woodruff, W. H. & Dyer, R. B. (1996) Biochemistry 35, 691-697.
6. Ballew, R. M., Sabelko, J. & Gruebele, M. (1996) Proc. Natl. Acad. Sci. USA 93, 5759-5764.
7. Sabelko, J., Ervin, J. & Gruebele, M. (1999) Proc. Natl. Acad. Sci. USA 96, 6031-6036.
8. Osváth, S., Sabelko, J. & Gruebele, M. (2003) J. Mol. Biol. 333, 187-199.
9. Yang, W. Y. & Gruebele, M. (2003) Nature 423, 193-197.
10. Yang, W. & Gruebele, M. (2004) Biophys. J. 87, 596-608.
11. Portman, J. J., Takada, S. & Wolynes, P. G. (1998) Phys. Rev. Lett. 81, 5237-5240.
12. Hagen, S. J., Hofrichter, J., Szabo, A. & Eaton, W. A. (1996) Proc. Natl. Acad. Sci. USA 93, 11615-11617.
13. Chang, I. J., Lee, J. C., Winkler, J. R. & Gray, H. B. (2003) Proc. Natl. Acad. Sci. USA 100, 3838-3840.
14. Camacho, C. J. & Thirumalai, D. (1995) J. Physique I 5, 1457-1467.
15. Pogorelov, T. V. & Luthey-Schulten, Z. (2004) Biophys. J. 87, 207-214.
16. Yang, W. Y. & Gruebele, M. (2004) J. Am. Chem. Soc. 126, 7758-7759.
17. Burton, R. E., Huang, G. S., Daugherty, M. A., Calderone, T. L. & Oas, T. G. (1997) Nat. Struct. Biol. 4, 305-310.
18. Ghaemmaghami, S., Word, J. M., Burton, R. E., Richardson, J. S. & Oas, T. G. (1998) Biochemistry 37, 9179-9185.
19. Myers, J. M. & Oas, T. G. (1999) Biochemistry 38, 6761-6768.
20. Ervin, J., Sabelko, J. & Gruebele, M. (2000) J. Photochem. Photobiol. B54, 1-15.
21. Ma, H., Ervin, J. & Gruebele, M. (2003) Rev. Sci. Instrum. 75, 486-491.
22. Ballew, R. M., Sabelko, J., Reiner, C. & Gruebele, M. (1996) Rev. Sci. Instrum. 67, 3694-3699.
23. Yang, W. Y. & Gruebele, M. (2004) Biochemistry 43, 13018-13025.
24. Jackson, S. E. & Fersht, A. R. (1991) Biochemistry 30, 10428-10435.
25. Berne, B. J. (1993) in Activated Barrier Crossing: Applications in Physics, Chemistry, and Biology, eds. Hänggi, P. & Fleming, G. R. (World Scientific, Singapore), pp. 82-119.
26. Zwanzig, R. (1988) Proc. Natl. Acad. Sci. USA 85, 2029-2030.
27. Klimov, D. K. & Thirumalai, D. (2002) J. Comput. Chem. 23, 161-165.
28. Garcia-Mira, M. M., Sadqi, M., Fischer, N., Sanchez-Ruiz, G. M. & Mun̄oz, V. (2002) Science 298, 2191-2195.
29. Mayor, U., Guydosh, N. R., Johnson, C. M., Grossmann, J. G., Sato, S., Jas, G. S., Freund, S. M., Alonso, D. O., Daggett, V. & Fersht, A. R. (2003) Nature 421, 863-867.
30. Bai, Y. W. (2003) Biochem. Biophys. Res. Comm. 305, 785-788.
31. Onuchic, J. N., Nymeyer, H., Garcia, A. E., Chahine, J. & Socci, N. D. (2000) Adv. Protein Chem. 53, 87-152.
32. Bryngelson, J. D. & Wolynes, P. G. (1987) Proc. Natl. Acad. Sci. USA 84, 7524-7528.
33. Shea, J. & Brooks, C. L. (2001) Annu. Rev. Phys. Chem. 52, 499-535.
34. Cheung, M. S., Chavez, L. L. & Onuchic, J. N. (2003) Polymer 45, 547-555.
35. Skorobogatiy, M., Guo, H. & Zuckerman, M. (1998) J. Chem. Phys. 109, 2528-2535.
36. Nymeyer, H., García, A. E. & Onuchic, J. N. (1998) Proc. Natl. Acad. Sci. USA 95, 5921-5928.
37. Metzler, R., Klafter, J. & Jortner, J. (1999) Proc. Natl. Acad. Sci. USA 96, 11085-11089.
38. Volk, M., Kholodenko, Y., Lu, H. S. M., Gooding, E. A., DeGrado, W. F. & Hochstrasser, R. M. (1997) J. Phys. Chem. 101, 8607-8616.