Thermodynamics of Protein Hydration Computed by Molecular Dynamics and Normal Modes

Journal of Physical Chemistry B

Volumn 107, Issue 46, 2003, Pages 12820-12828

  Yu, Xin ^a   Park, Jongsoon ^b   Leitner, David M ^a  

^a UNIVERSITY OF NEVADA   (United States)

^b Pusan National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; ENTROPY; GLASS TRANSITION; HYDRATION; HYDROPHILICITY; MOLECULAR DYNAMICS; SPECIFIC HEAT; THERMODYNAMIC PROPERTIES;

ENERGY LANDSCAPE; NORMAL MODE ANALYSIS (NMA);

ENZYMES;

EID: 0345393320     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp035471x     Document Type: Article

References (45)

1. Gregory, R. B., Ed. Protein-Solvent Interactions; Marcel Dekker: New York, 1995.
2. Bizzarri, A. R.; Cannistraro, S. J. Phys. Chem. B 2002, 106, 6617.
3. Merzel, F.; Smith, J. C. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5378.
4. Kunz, I. D.; Kauzmann, W. Adv. Protein Chem. 1973, 28, 239.
5. Rupley, J. A.; Careri, G. Adv. Protein Chem. 1991, 41, 37.
6. Fischer, S.; Smith, J. C.; Verma, C. S. J. Phys. Chem. B 2001, 105, 8050.
7. Yang, P. H.; Rupley, J. A. Biochemistry 1979, 18, 2654.
8. Finney, J. L.; Poole, P. L. Comments Mol. Cell. Biophys. 1984, 2, 129.
9. Gregory, R. B. Protein-Solvent Interactions; Marcel Dekker: New York, 1995; p 191.
10. Angell, C. A. Science 1995, 267, 1924.
11. Steinbach, P. J.; Brooks, B. R. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 9135.
12. Steinbach, P. J.; Brooks, B. R. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 55.
13. Arcangeli, C.; Bizzarri, A. R.; Cannistraro, S. Chem. Phys. Lett. 1998, 291, 7.
14. Berry, R. S.; Beck, T. L.; Davis, H. L.; Jellinek, J. adv. Chem. Phys. 1988, 70, 75.
15. Wales, D. J. Science 1996, 271, 925.
16. Wales, D. J.; Doye, J. P. K.; Miller, M. A.; Mortenson, P. N.; Walsh, T. R. Adv. Chem. Phys. 2000, 115, 1.
17. Mishima, O.; Stanley, H. E. Nature 1998, 396, 329.
18. Velikov, V.; Borick, S.; Angell, C. A. Science 2001, 294, 2335.
19. Angell, C. A. Chem. Rev. 2002, 102, 2627.
20. Green, J. L.; Fan, J.; Angell, C. A. J. Phys. Chem. 1994, 98, 13780.
21. Tanaka, H. Nature 1996, 380, 328.
22. Iben, I. E. T.; Braunstein, D.; Doster, W.; Frauenfelder, H.; Hong, M. K.; Johnson, J. B.; Luck, S.; Ormos, P.; Schulte, A.; Steinbach, P. J.; Xie, A. H.; Young, R. D. Phys. Rev. Lett. 1989, 62, 1916.
23. Tarek, M.; Tobias, D. J. Phys. Rev. Lett. 2002, 88, 138101.
24. Vitkup, D.; Ringe, D.; Petsko, G. A.; Karplus, M. Nat. Struct. Biol. 2000, 7, 34.
25. Réat, V.; Dunn, R.; Ferrand, M.; Finney, J. L.; Daniel, R. M.; Smith, J. C. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 9961.
26. Fitter, J. Biophys. J. 1999, 76, 1034.
27. Doster, W.; Bachleitner, A.; Dunau, R.; Hiebl, M.; Lüscher, E. Biophys. J. 1986, 50, 213.
28. Elber, R.; et al. Comput. Phys. Commun. 1995, 91, 159. The version used for this study was obtained from http://www.tc.cornell.edu/reports/ NIH/resource/CompBiologyTools/moil.
29. Levitt, M.; Sander, C.; Stern, P. S. J. Mol Biol. 1985, 181, 423.
30. See, e.g., Guggenheim, E. A. Thermodynamics; North-Holland: Amsterdam, 1967.
31. Elber, R.; Karplus, M. Science 1987, 235, 318.
32. Frauenfelder, H.; Sligar, S. G.; Wolynes, P. G. Science 1991, 254, 1598.
33. Stillinger, F. H.; Weber, T. A. J. Phys. Chem. 1983, 87, 2833.
34. Bryngelson, J. D.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 7524.
35. Onuchic, J. N.; Luthey-Schulten, Z.; Wolynes, P. G. Annu. Rev. Phys. Chem. 1997, 48, 545.
36. Speedy, R. J. J. Phys. Chem. B 1999, 103, 4060.
37. Heuer, A.; Büchner, S. J. Phys.: Condens. Matter 2000, 12, 6535.
38. Sastry, S. Nature 2001, 409, 164.
39. Starr, F. W.; Sastry, S.; La Nave, E.; Scala, A.; Stanley, H. E.; Sciortino, F. Phys. Rev. E 2000, 64, 041201.
40. Dorsey, N. E. Properties of Ordinary Water Substance; Reinhold Publ. Corp.: New York, 1940.
41. νφ.
42. Hayward, J. A.; Smith, J. C. Biophys. J. 2002, 82, 1216.
43. Fischer, S.; Verma, C. S. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9613.
44. Leitner, D. M.; Levine, B.; Quenneville, J.; Martinez, T. J.; Wolynes, P. G. J. Phys. Chem. A, in press.
45. Yu, X.; Leitner, D. M. J. Phys. Chem. B 2003, 107, 1698.