Protein folding, protein collapse, and Tanford's transfer model: Lessons from single-molecule FRET

Journal of the American Chemical Society

Volumn 131, Issue 8, 2009, Pages 2942-2947

  Ziv, Guy ^a   Haran, Gilad ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ACID SOLVATION; CHEMICAL DENATURANTS; COLLAPSE TRANSITIONS; CONCENTRATION OF; CONFORMATIONAL ENTROPY; DENATURANT CONCENTRATION; DENATURED STATE; ENTROPIC CONTRIBUTIONS; FOLDED STATE; FOLDING REACTIONS; LINEAR DEPENDENCE; PROTEIN COLLAPSE; SINGLE MOLECULE; TRANSFER MODELS;

AMINES; AMINO ACIDS; CONFORMATIONS; DENATURATION; FREE ENERGY; ORGANIC ACIDS; SOLVATION;

PROTEIN FOLDING;

AMINO ACID; PROTEIN;

ARTICLE; CHEMICAL MODEL; COMPETITION; CONCENTRATION (PARAMETERS); CONFORMATION; ENERGY TRANSFER; ENTHALPY; ENTROPY; FLUORESCENCE RESONANCE ENERGY TRANSFER; MEASUREMENT; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN TRANSPORT; SOLVATION; THERMODYNAMICS; CHEMICAL STRUCTURE; CHEMISTRY; METHODOLOGY; PROTEIN CONFORMATION;

ENTROPY; FLUORESCENCE RESONANCE ENERGY TRANSFER; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 67749142097     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja808305u     Document Type: Article

References (51)

1. Anfinsen, C. B.; Haber, E. J. Biol. Chem. 1961, 236, 1361-1363.
2. Fersht, A. Structure and mechanism in protein science: a guide to enzyme catalysis and protein folding; W. H. Freeman and Company: New York, 1999.
3. Roca, M.; Liu, H.; Messer, B.; Warshel, A. Biochemistry 2007, 46, 15076-15088.
4. Garcia-Alai, M. M.; Gallo, M.; Salame, M.; Wetzler, D. E.; McBride. A. A.; Paci, M.; Cicero, D. O.; de Prat-Gav. G. Structure 2006, 14, 309-319.
5. Chiti, F.; Taddei, N.; Bucciantini. M.; White, P.; Ramponi, G.; Dobson, C. M. EMBO J. 2000, 19, 1441-1449.
6. Whitnev, P. L.; Tanford, C. J. Biol. Chem. 1962, 237, PC 1735-PC1737.
7. Schellman, J. A. Biopolymers 1987, 26, 549-559.
8. Mountain, R. D.; Thiramalai, D. J. Am. Chem. Soc 2003, 125, 1950-1957.
9. Mason, P. E.; Neilson, G. W.; Enderby, J. E.; Saboungi, M. L.; Dempsev, C. E.; MacKerell, A. D.; Brady, J. W. J. Am. Chem. Soc. 2004, 126, 11462-11470.
10. Stumpe, M. C.; Grubmuller, H. J. Phys. Chem. B 2007, 111, 6220-6228.
11. O'Brien, E. P.; Dima, R. I.; Brooks. B.; Thirumalai, D. J. Am. Chem. Soc. 2007, 129, 7346-7353.
12. England, J. L.; Pande, V. S.; Haran, G. J. Am. Chem. Soc 2008, 130, 11854-11855.
13. Jackson, S. E. Folding and Design 1998, 3, R81-R91.
14. Tanford, C. Adp. Protein Chem. 1970, 24, 1-95.
15. Tanford, C. Adp. Protein Chem. 1968, 23, 121-282.
16. Tanford, C. J. Am. Chem. Soc 1964, 86. 2050-2059.
17. Myers, J. K.; Pace, C. N.; Scholtz, J. M. Protein Sci. 1995, 4, 2138-2148.
18. Auton, M.; Holthauzen, L. M. F.; Bolen. D. W. Proc Natl. Acad. Sci USA. 2007, 104, 15317-15322.
19. Park. S. H.; Shastry, M. C.; Roder, H. Nat. Struct. Mol. Biol. 1999, 6, 943-947.
20. Hagen, S. J.; Eaton, W. A. J. Mol. Biol. 2000, 301, 1019-27.
21. Kimura, T.; Uzawa, T.; Ishimori, K.; Morishima, I.; Takahashi, S.; Konno, T.; Akiyama, S.; Fujisawa, T. Proc Natl. Acad. Sci. U.S.A. 2005, 102, 2748-2753.
22. Ziv, G.; Thirumalai. D.; Haran, G. Phys. Chem. Chem. Phys. 2009, 11, 83-91.
23. Schuler, B.; Lipman, E. A.; Eaton, W. A. Nature 2002, 419, 743-747.
24. Laurence. T. A.; Kong. X.; Jager. M.; Weiss, S. Proc. Natl. Acad. Sci. USA. 2005, 102, 17348-17353.
25. Kuzmenkina. E. V.; Heyes, C. D.; Nienhaus, G. U. J. Mol. Biol. 2006, 357, 313-324.
26. Sherman, E.; Haran, G. Proc Natl. Acad. Sci. U.S.A. 2006, 103, 11539-11543.
27. Tezuka-Kawakami, T.; Gell, C.; Brockwell, D. J.; Radford, S. E.; Smith, D. A. Biophys. J. 2006, 91, L42-4.
28. Mukhopadhyav, S.; Krishnan, R.; Lemke. E. A.; Lindquist, S.; Deniz, A. A. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 2649-2654.
29. Merchant, K. A.; Best, R. B.; Louis. J. M.; Gopich, I. V.; Eaton. W. A. Proc Natl. Acad. Sci. U.S.A. 2007, 104, 1528-1533.
30. Hoffmann, A.; Kane, A.; Nettels, D.; Hertzog, D. E.; Baumgartel, P.; Lengefeld, J.; Reichardt, G.; Horsley, D. A.; Seckler, R.; Bakajin, O.; Schuler. B. Proc Natl. Acad. Sci. U.S.A. 2007, 104, 105-110.
31. Huang, F.; Sato, S.; Sharpe. T. D.; Ying, L.; Fersht. A. R. Proc Natl. Acad. Sci. U.S.A. 2007, 104. 123-127.
32. Hofmann. H.; Golbik, R. P.; Ott. M.; Hubner. C. G.; Ulbrich-Hofmann, R. J. Mol. Biol. 2008, 376, 597-605.
33. Flory, P. J. Principles of polymer chemistry: Cornell University Press: New' York, 1953.
34. Sanchez, I. C. Macromolecules 1979, 12, 980-988.
35. Flory, P. J.; Fisk, S. J. Chem. Phys. 1966, 44, 2243.
36. Tran, H. T.; Mao, A.; Pappu, R. V. J. Am. Chem. Soc 2008, 130, 7380-7392.
37. Buscaglia, M.; Schuler, B.; Lapidus, L. J.; Eaton, W. A.; Hofrichter, J. J. Mol. Biol. 2003, 332, 9-12.
38. Chattopadhvay, K.; Elson, E. L.; Frieden, C. Proc Natl. Acad. Sci. UJA. 2005, 102, 2385-2389.
39. Nettels, D.; Gopich, I. V.; Hoffmann, A.; Schuler, B. Proc Natl, Acad. Sci. U.S.A. 2007, 104, 2655-2660.
40. Calmettes, P.; Roux, B.; Durand, D.; Desmadril, M.; Smith, J. C. J. Mol. Biol. 1993, 231, 840-848.
41. Dima, R. I.; Thiramalai, D. J. Phys. Chem. B 2004, 108, 6564-6570.
42. Tran, H. T.; Pappu. R. V. Biophys. J. 2006, 91, 1868-1886.
43. Mok, Y. K.; Kay, C. M.; Kay, L. E.; Forman-Kay, J. J. Mol. Biol. 1999, 289, 619-638.
44. Since only two data sets were measured using urea as denaturant, we use only the proteins denatured with GdmCl here.
45. O'Brien, E. P., Jr.; Brooks, B.; Ziv, G.; Haran, G.; Thirumalai, D. Proc Natl. Acad. Sci. U.S.A. 2008, 105, 13403-13408.
46. Alonso. D. O.; Dill. K. A. Biochemistry 1991, 30, 5974-5985.
47. Guo, Z. Y.; Brooks, C. L. Biopolymers 1997, 42, 745-757.
48. Veitshans, T.; Klimov, D.; Thirumalai, D. Fold Des. 1997, 2, 1-22.
49. Jacob, J.; Dothager, R. S.; Thiyagarajan, P.; Sosnick. T. R. J. Mol. Biol. 2007, 367, 609-615.
50. Jacob, J.; Krantz, B.; Dothager, R. S.; Thivagarajan, P.; Sosnick, T. R. J. Mol. Biol. 2004, 338, 369-382.
51. Plaxco, K. W.; Millett, I. S.; Segel. D. J.; Doniach, S.; Baker, D. Nat. Struct. Mol. Biol. 1999, 6, 554-556.