Cosolvent interactions with biomolecules: Relating computer simulation data to experimental thermodynamic data

Journal of Physical Chemistry B

Volumn 108, Issue 48, 2004, Pages 18716-18724

  Smith, Paul E ^a  

^a KANSAS STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULES; COSOLVENTS; PARTIAL MOLAR VOLUMES; PROTEIN DENATURATION;

COMPUTER SIMULATION; CONCENTRATION (PROCESS); DERIVATIVES; ETHANOL; PRESSURE EFFECTS; PROTEINS; SODIUM CHLORIDE; SOLVENTS; THERMODYNAMICS; UREA; VOLUME FRACTION;

MOLECULAR DYNAMICS;

EID: 10444273367     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0474879     Document Type: Article

References (68)

1. Schellman, J. A. Biophys. Chem. 1990, 37, 121-140.
2. Timasheff, S. N. Biochemistry 2002, 41, 13473-13482.
3. Hibbard, L. S.; Tulinsky, A. Biochemistry 1978, 17, 5460-5468.
4. Liepinsh, E.; Otting, G. J. Am. Chem. Soc. 1994, 116, 9670-9674.
5. Chen, L.; Hodgson, K. O.; Doniach, S. J. Mol. Biol. 1996, 261, 658-671.
6. Schwalbe, H.; Fiebig, K. M.; Buck, M.; Jones, J. A.; Grimshaw, S. B.; Spencer, A.; Glaser, S. J.; Smith, L. J.; Dobson, C. M. Biochemistry 1997, 36, 8977-8991.
7. Dunbar, J.; Ynnawar, H. P.; Banerjee, S.; Luo, J.; Farber, G. K. Protein Sci. 1997, 6, 1727-1733.
8. Mande, S. C.; Sobhia, M. E. Protein Eng. 2000, 13, 133-141.
9. Alonso, D. O.; Daggett, V. J. Mol. Biol. 1995, 247, 501-520.
10. Zou, Q.; Bennion, B. J.; Daggett, V.; Murphy, K. P. J. Am. Chem. Soc. 2002, 124, 1192-1202.
11. Tirado-Rives, J.; Orozco, M.; Jorgensen, W. L. Biochemistry 1997, 36, 7313-7329.
12. Caflisch, A.; Karplus, M. J. Mol. Biol. 1995, 252, 672-708.
13. Caflisch, A.; Karplus, M. Structure Fold. Des. 1999, 7, 477-488.
14. Greene, Jr., R. F.; Pace, C. N. J. Biol. Chem. 1974, 249, 5388-5393.
15. Makhatadze, G. I.; Privalov, P. L. J. Mol. Biol. 1992, 226, 491-505.
16. Schellman, J. A. Biopolymers 1994, 34, 1015-1026.
17. Timasheff, S. N. Adv. Protein Chem. 1998, 51, 356-432.
18. Schellman, J. A.; Gassner, N. C. Biophys. Chem. 1996, 59, 259-275.
19. Anderson, C. F.; Courtenay, E. S.; Record, M. T., Jr. J. Phys. Chem. B 2002, 106, 418-433.
20. Baynes, B. M.; Trout, B. L. J. Phys. Chem. B 2003, 107, 14058-1067.
21. Chitra, R.; Smith, P. E. J. Phys. Chem. B 2001, 105, 11513-11522.
22. Weerasinghe, S.; Smith, P. E. J. Chem. Phys. 2003, 118, 5901-5910.
23. Aburi, M.; Smith, P. E. J. Phys. Chem. B 2004, 108, 7382-7388.
24. Tang, K. E. S.; Bloomfield, V. A. Biophys. J. 2002, 82, 2876-2891.
25. Kirkwood, J. G.; Buff, F. P. J. Chem. Phys. 1951, 19, 774-777.
26. Ben-Naim, A. Inversion of Kirkwood-Buff Theory of Solutions and Its Applications. In Advances in Thermodynamics. Fluctuation Theory of Mixtures; Matteoli, E., Mansoori, G. A., Eds.; Taylor & Francis: New York, 1990; Vol. 2, pp 211-226.
27. Newman, K. E. Chem. Soc. Rev. 1994, 23, 31-40.
28. Ben-Naim, A. Statistical Thermodynamics for Chemists and Biochemists; Plenum Press: New York, 1992.
29. Friedman, H. L.; Ramanathan, P. S. J. Phys. Chem. 1970, 74, 3756-3765.
30. Kusalik, P. G.; Patey, G. N. J. Chem. Phys. 1987, 86, 5110-5116.
31. Smith, P. E. J. Phys. Chem. B 1999, 103, 525-534.
32. Chitra, R.; Smith, P. E. J. Phys. Chem. B 2002, 706, 1491-1500.
33. Tanford, C. J. Mol. Biol. 1969, 39, 539-544.
34. Wyman, J. J. Adv. Protein Chem. 1964, 19, 223-286.
35. Casassa, E. F.; Eisenberg, H. Adv. Protein Chem. 1964, 19, 287-395.
36. Parsegian, V. A.; Rand, R. P.; Rau, D. C. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 3987-3992.
37. Royer, C. A. Biochim. Biophys. Acta 2002, 1595, 201-209.
38. Herberhold, H.; Royer, C. A.; Winter, R. Biochemistry 2004, 43, 3336-3345.
39. Record Jr., M. T.; Anderson, C. F. Biophys. J. 1995, 68, 786-794.
40. Courtenay, E. S.; Capp, M. W.; Saecker, R. M.; Record, M. T., Jr. Proteins: Struct., Funct., Genet. 2000, S4, 72-85.
41. Shimizu, S. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 1195-1199.
42. Timasheff, S. N.; Xie, G. Biophys. Chem. 2003, 105, 421-448.
43. Rösgen, J.; Pettitt, B. M.; Perkyns, J.; Bolen, D. W. J. Phys. Chem. B 2004, 108, 2048-2055.
44. Makhatadze, G. I.; Fernandez, J.; Freire, E.; Lilley, T. H.; Privalov, P. L. J. Chem. Eng. Data 1993, 38, 83-87.
45. Robinson, R. A.; Stokes, R. H. Electrolyte Solutions; Butterworths: London, 1959.
46. Kawahara, K.; Tanford, C. J. Biol. Chem. 1966, 241, 3228-3232.
47. Rogers, P. S. Z.; Pitzer, K. S. J. Phys. Chem. Ref. Data 1982, 11, 15-81.
48. Pace, C. N.; Shaw, K. L. Proteins: Struct., Funct., Genet. 2000, S4, 1-7.
49. Myers, J. K.; Pace, C. N.; Scholtz, J. M. Protein Sci. 1995, 4, 2138-2148.
50. Buck, M. Q. Rev. Biophys. 1998, 31, 297-355.
51. Loof, H. D.; Nilsson, L.; Rigler, R. J. Am. Chem. Soc. 1992, 114, 4028-4035.
52. van Buuren, A. R.; Berendsen, H. J. C. Biopolymers 1993, 33, 1159-1166.
53. Hong, D. P.; Hoshino, M.; Kuboi, R.; Goto, Y. J. Am. Chem. Soc. 1999, 121, 8427-8433.
54. Jasanoff, A.; Fersht, A. R. Biochemistry 1994, 33, 2129-2135.
55. Chitra, R.; Smith, P. E. J. Chem. Phys. 2001, 114, 426-435.
56. Chitra, R.; Smith, P. E. J. Chem. Phys. 2001, 115, 5521-5530.
57. Sasahara, K.; Sakuri, M.; Nitta, K. J. Mol. Biol. 1999, 291, 693-701.
58. Weerasinghe, S.; Smith, P. E. J. Phys. Chem. B 2003, 107, 3891-3898.
59. Weerasinghe, S.; Smith, P. E. J. Chem. Phys. 2003, 118, 10663-10670.
60. Weerasinghe, S.; Smith, P. E. J. Chem. Phys. 2003, 779, 11342-12349.
61. Trzesniak, D.; van der Vegt, N. F. A.; van Gunsteren, W. F. Phys. Chem. Chem. Phys. 2004, 6, 697-702.
62. Weerasinghe, S.; Pettitt, B. M. Mol. Phys. 1994, 82, 897-912.
63. Matubayasi, N.; Levy, R. M. J. Phys. Chem. 1996, 100, 2681-2688.
64. Anderson, C. F.; Record, M. T. Annu. Rev. Biophys. Biophys. Chem. 1990, 19, 423-465.
65. Pace, C. N. Methods Enzymol. 1986, 131, 266-280.
66. Makhatadze, G. I. J. Phys. Chem. B 1999, 103, 4781-4785.
67. Lee, J. C.; Timasheff, S. N. Biochemistry 1974, 13, 257-265.
68. Tanford, C. Adv. Protein Chem. 1970, 24, 1-95.