Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism

Journal of the American Chemical Society

Volumn 129, Issue 23, 2007, Pages 7346-7353

  O'Brien, Edward P ^a,b   Dima, Ruxandra I ^c   Brooks, Bernard ^b   Thirumalai, D ^a,b  

^a University of Maryland   (United States)

^b NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^c UNIVERSITY OF CINCINNATI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; HYDROGEN BONDS; HYDROPHOBICITY; MOLECULAR DYNAMICS; PROTEIN FOLDING; UREA;

GUANIDINIUM CHLORIDE; IONIC SOLUTES; PROTEIN DENATURATION;

IONS;

CARBONYL DERIVATIVE; GUANIDINE; ION; UREA; WATER;

AQUEOUS SOLUTION; ARTICLE; CHEMICAL STRUCTURE; ELECTRICITY; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR DYNAMICS; PROTEIN DENATURATION; SOLUTE;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; GUANIDINE; HYDROGEN BONDING; HYDROPHOBICITY; IONS; MICE; PROTEIN DENATURATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOLUTIONS; UREA; WATER;

EID: 34250869055     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja069232+     Document Type: Article

References (49)

1. Schellman, J. A. Biophys. Chem. 2002, 96, 91-101.
2. Tanford, C. Adv. Protein Chem. 1970, 24, 1-95.
3. Nozaki, Y.; Tanford, C. J. Biol. Chem. 1963, 238, 4074-4081.
4. Greene, R. F.; Pace, C. N. J. Biol. Chem. 1974, 249, 5388-5393.
5. Nozaki, Y.; Tanford, C. J. Biol. Chem. 1970, 245, 1648-1652.
6. Pace, C. N. Methods Enzymol. 1986, 131, 266-280.
7. Zuo, Q.; Habermann-Rottinghaus, S. M.; Murphy, K. P. Proteins: Struct., Funct., Genet. 1998, 31, 107-115.
8. Tobi, D.; Elber, R.; Thirumalai, D. Biopolymers 2003, 68, 359-369.
9. Wallqvist, A.; Covell, D. G.; Thirumalai, D. J. Am. Chem. Soc. 1998, 120, 427-428.
10. Robinson, D. R.; Jencks, W. P. J. Am. Chem. Soc. 1965, 87, 2462-2469.
11. Caflisch, A.; Karplus, M. Struct. Folding Des. 1999, 7, 477-488.
12. Tirado-Rives, J.; Orozco, M.; Jorgensen, W. L. Biochemistry 1997, 36, 7313-7329.
13. Bennion, B. J.; Daggett, V. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 5142-5147.
14. Collins, K. D. Biophys. J. 1997, 72, 65-76.
15. Timasheff, S. N. Adv. Protein Chem. 1998, 51, 355-432.
16. Mountain, R. D.; Thirumalai, D. J. Am. Chem. Soc. 2003, 125, 1950-1957.
17. Cacace, M. G.; Landau, E. M.; Ramsden, J. J. Q. Rev. Biophys. 1997, 30, 241-277.
18. Baldwin, R. L. Biophys. J. 1996, 71, 2056-2063.
19. Ikeguchi, M.; Nakamura, S.; Shimizu, K. J. Am. Chem. Soc. 2001, 123, 677-682.
20. Vanzi, F.; Madan, B.; Sharp, K. J. Am. Chem. Soc. 1998, 120, 10748-10753.
21. Pangali, C.; Rao, M.; Berne, B. J. J. Chem. Phys. 1979, 71, 2975-2981.
22. Pratt, L. R.; Chandler, D. J. Chem. Phys. 1977, 67, 3683-3704.
23. Tsai, J.; Gerstein, M.; Levitt, M. J. Chem. Phys. 1996, 104, 9417-9430.
24. Chandler, D. Nature 2005, 437, 640-647.
25. Pratt, L. R. Annu. Rev. Phys. Chem. 2002, 53, 409-436.
26. Shimizu, S.; Chan, H. S. J. Chem. Phys. 2000, 113, 4683-4700.
27. Monera, O. D.; Kay, C. M.; Hodges, R. S. Protein Sci. 1994, 3, 1984-1991.
28. MacKerell, A. D.; et al. J. Phys. Chem. B 1998, 102, 3586-3616.
29. Allen, M. P.; Tildesley, D. J. Computer Simulations of Liquids, 9th ed.; Oxford University Press: Oxford, NY, 1987.
30. Darden, T.; York, D.; Pendersen, L. J. Chem. Phys. 1993, 98, 10089-10092.
31. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802.
32. Ghosh, T.; Karla, A.; Garde, S. J. Phys. Chem. B 2005, 109, 642-651.
33. Kale, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. J. Comput. Phys. 1999, 151, 283-312.
34. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
35. Frenkel, D.; Smit, B. Understanding Molecular Simulation: From Algorithms to Applications, 2nd ed.; Academic Press: San Diego, CA, 2002.
36. Riek, R.; Hornemann, S.; Wider, G.; Billeter, M.; Glockshuber, R.; Wuthrich, K. Nature 1996, 382, 180-182.
37. Liu, A.; Riek, R.; Zahn, R.; Hornemann, S.; Glockshuber, R.; Wuthrich, K. Biopolymers 1999, 51, 145-152.
38. Ziegler, J.; Stichf, H.; Marx, U. C.; Muller, W.; Rosch, P.; Schwarzinger, S. J. Biol. Chem. 2003, 278, 50175-50181.
39. Dima, R.; Thirumalai, D. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15335-15340.
40. Klimov, D.; Thirumalai, D. Structure 2003, 11, 295-307.
41. Vaitheeswaran, S.; Thirumalai, D. J. Am. Chem. Soc. 2006, 128, 13490-13496.
42. Makhatadze, G. I. J. Phys. Chem. B 1999, 103, 4781-4785.
43. Wood, R. H.; Thompson, P. J. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 946-949.
44. Lee, M. E.; van der Vegt, N. F. A. J. Am. Chem. Soc. 2006, 128, 4948-4949.
45. Rezus, Y. L. A.; Bakker, H. J. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 18417-18420.
46. Mountain, R. D.; Thirumalai, D. J. Phys. Chem. B 2004, 108, 6826-6831.
47. Duffy, E. M.; Severance, D. L.; Jorgensen, W. L. Isr. J. Chem. 1993, 33, 323-330.
48. Weerasinghe, S.; Smith, P. E. J. Phys. Chem. B 2003, 107, 3891-3898.
49. Zangi, R.; Berne, B. J. J. Phys. Chem. B 2006, 110, 22736-22741.