Orientational disorder and entropy of water in protein cavities

Journal of Physical Chemistry B

Volumn 101, Issue 45, 1997, Pages 9380-9389

  Denisov, Vladimir P ^a   Venu, Kandadai ^a,c   Peters, Jörg ^b   Hörlein, Hans Dietrich ^b   Halle, Bertil ^a  

^a LUND UNIVERSITY   (Sweden)

^b BAYER AG   (Germany)

^c UNIVERSITY OF HYDERABAD   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ANISOTROPY; ENTROPY; HYDROGEN BONDS; MATHEMATICAL MODELS; MOLECULAR ORIENTATION; PROTEINS; SOLUTIONS;

BOVINE PANCREATIC TRYPSIN INHIBITOR; HARMONIC LIBRATION MODEL; NUCLEAR MAGNETIC RELAXATION DISPERSION;

MOLECULAR DYNAMICS;

EID: 0031556719     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp9712213     Document Type: Article

References (74)

1. Connolly, M. L. Int. J. Pept. Protein Res. 1985, 28, 360-363.
2. Rashin, A. A.; Iofin, M.; Honig, B. Biochemistry 1986, 25, 3619-3625.
3. Williams, M. A.; Goodfellow, J. M.; Thornton, J. M. Protein Sci. 1994, 3, 1224-1235.
4. Hubbard, S. J.; Gross, K.-H.; Argos, P. Protein Eng. 1994, 7, 613-626. Hubbard, S. J.; Argos, P. Protein Eng. 1995, 8, 1011-1015.
5. Hubbard, S. J.; Gross, K.-H.; Argos, P. Protein Eng. 1994, 7, 613-626. Hubbard, S. J.; Argos, P. Protein Eng. 1995, 8, 1011-1015.
6. Baker, E. N. In Protein-Solvent Interactions; Gregory, R. B., Ed.; M. Dekker: New York, 1995; Chapter 2.
7. Schoenborn, B. P.; Garcia, A.; Knott, R. Prog. Biophys. Mol. Biol. 1995, 64, 105-119.
8. McDowell, R. S.; Kossiakoff, A. A. J. Mol. Biol. 1995, 250, 553-570.
9. Elber, R.; Karplus, M. J. Am. Chem. Soc. 1990, 112, 9161-9175.
10. Carlson, M. L.; Regan, R. M.; Gibson, Q. H. Biochemistry 1996, 35, 1125-1136.
11. Gerstein, M.; Lesk, A. M.; Chothia, C. Biochemistry 1994, 33, 6739-6749.
12. Hubbard, S. J.; Argos, P. J. Mol. Biol. 1996, 261, 289-300.
13. Meyer, E. Protein Sci. 1992, 1, 1543-1562.
14. Ladbury, J. E. Chem. Biol. 1996, 3, 973-980.
15. Raymer, M. L.; Sanschagrin, P. C.; Punch, W. F.; Venkataraman, S.; Goodman, E. D.; Kuhn, L. A. J. Mol. Biol. 1997, 265, 445-464.
16. Otting, G.; Wüthrich, K. J. Am. Chem. Soc. 1989, 111, 1871-1875.
17. Otting, G.; Liepinsh, E.; Wüthrich, K. Science 1991, 254, 974-980.
18. Otting, G.; Liepinsh, E. Acc. Chem. Res. 1995, 28, 171-177.
19. Denisov, V. P.; Halle, B. J. Mol. Biol. 1995, 245, 682-697.
20. Denisov, V. P.; Halle, B.; Peters, J.; Hörlein, H. D. Biochemistry 1995, 34, 9046-9051.
21. Denisov, V. P.; Halle, B. Faraday Discussions 1996, 103, 227-244.
22. Otting, G.; Liepinsh, E.; Halle, B.; Frey, U. Nature Struct. Biol. 1997, 4, 396-404.
23. Denisov, V. P.; Peters, J.; Hörlein, H. D.; Halle, B. Nature Struct. Biol. 1996, 3, 505-509.
24. Wade, R. C.; Mazor, M. H.; McCammon, J. A.; Quiocho, F. A. Biopolymers 1991, 31, 919-931.
25. Zhang, L.; Hermans, J. Proteins: Struct. Funct. Gen. 1996, 24, 433-438.
26. Wolfenden, R.; Radzicka, A. Science 1994, 265, 936-937.
27. Buckle, A. M.; Cramer, P.; Fersht, A. R. Biochemistry 1996, 35, 4298-4305.
28. Ernst, J. A.; Clubb, R. T.; Zhou, H.-X.; Gronenborn, A. M.; Clore, G. M. Science 1995, 267, 1813-1817.
29. Berne, B. J.; Pechukas, P.; Harp, G. D. J. Chem. Phys. 1968, 49, 3125-3129.
30. Zannoni, C. In The Molecular Dynamics of Liquid Crystals; Luckhurst, G. R., Veracini, C. A., Eds.; Kluwer: Dordrecht, 1994; Chapter 2.
31. Akke, M.; Brüschweiler, R.; Palmer, A. G. J. Am. Chem. Soc. 1993, 115, 9832-9833.
32. Yang, D.; Kay, L. E. J. Mol. Biol. 1996, 263, 369-382.
33. Li, Z.; Raychaudhuri, S.; Wand, A. J. Protein Sci. 1996, 5, 2647-2650.
34. Denisov, V. P.; Halle, B. J. Am. Chem. Soc. 1995, 117, 8456-8465.
35. Venu, K.; Denisov, V. P.; Halle, B. J. Am. Chem. Soc. 1997, 119, 3122-3134.
36. Denisov, V. P.; Halle, B. J. Mol. Biol. 1995, 245, 698-709.
37. Wlodawer, A.; Walter, J.; Huber, R.; Sjölin, L. J. Mol. Biol. 1984, 180, 301-329.
38. Berndt, K. D.; Beunink, J.; Schröder, W.; Wüthrich, K. Biochemistry 1993, 32, 4564-4570.
39. Housset, D.; Kim, K.-S.; Fuchs, J.; Woodward, C; Wlodawer, A. J. Mol. Biol. 1991, 220, 757-770.
40. Lumry, R.; Rajender, S. Biopolymers 1970, 9, 1125-1227.
41. Dunitz, J. D. Chem. Biol. 1995, 2, 709-712.
42. Berndt, K. D.; Güntert, P.; Orbons, L. P. M.; Wüthrich, K. J. Mol. Biol. 1992, 227, 757-775.
43. Kim, K.-S.; Fuchs, J. A.; Woodward, C. K. Biochemistry 1993, 32, 9600-9608.
44. Abragam, A. The Principles of Nuclear Magnetism: Clarendon Press: Oxford, 1961.
45. Halle, B.; Wennerström, H. J. Magn. Reson. 1981, 44, 89-100.
46. Halle, B.; Wennerström, H. J. Chem. Phys. 1981, 75, 1928-1943.
47. Spiess, H. W.; Garrett, B. B.; Sheline, R. K.; Rabideau, S. W. J. Chem. Phys. 1969, 51, 1201-1205. Edmonds, D. T.; Zussman, A. Phys. Lett. 1972, 41A, 167-169.
48. Spiess, H. W.; Garrett, B. B.; Sheline, R. K.; Rabideau, S. W. J. Chem. Phys. 1969, 51, 1201-1205. Edmonds, D. T.; Zussman, A. Phys. Lett. 1972, 41A, 167-169.
49. Edmonds, D. T.; Mackay, A. L. J. Magn. Reson. 1975, 20, 515-519.
50. Whalley, E. Mol. Phys. 1974, 28, 1105-1108.
51. Sceats, M. G.; Rice, S. A. J. Chem. Phys. 1980, 72, 3236-3247.
52. Berglund, B.; Lindgren, J.; Tegenfeldt, J. J. Mol. Struct. 1978, 43, 179-191.
53. Poplett, I. J. F. J. Magn. Reson. 1982, 50, 397-408.
54. Kuhs, W. F.; Lehmann, M. S. Water Sci. Rev. 1986, 2, 1-65.
55. labile, compared with the values in the fourth column of Table 4.
56. Larsson, K.; Tegenfeldt, J.; Hermansson, K. J. Chem. Soc., Faraday Trans. 1991, 87, 1193-1200.
57. Hill, T. L. An Introduction to Statistical Thermodynamics; Dover: New York, 1986.
58. Landau, L. D.; Lifshitz, E. M. Statistical Physics, 3rd ed.; Pergamon: Oxford, 1980; Part 1.
59. 2O should have 10-15% larger libration amplitudes. Since this difference is comparable to or smaller than the propagated uncertainties in Table 4, we ignore the isotope effect.
60. 2 flip interconverts two indistinguishable states, there is no associated configurational entropy.
61. Eisenberg, D.; Kauzmann, W. The Structure and Properties of Water; Clarendon: Oxford, 1969.
62. 59
63. Dunitz, J. D. Science 1994, 264, 670.
64. 71
65. For relatively large libration amplitudes, this is actually no restriction, since the classical limit of eq 6 depends only on the geometric average of the three libration amplitudes.
66. Finkelstein, A. V.; Janin, J. Protein Eng. 1989, 3, 1-3.
67. Searle, M. S.; Williams, D. H. J. Am. Chem. Soc. 1992, 114, 10690-10697.
68. Gilli, P.; Ferretti, V.; Gilli, G.; Borea, P. A. J. Phys. Chem. 1994, 98, 1515-1518.
69. Chervenak, M. C.; Toone, E. J. J. Am. Chem. Soc. 1994, 116, 10533-10539.
70. Ringe, D. Curr. Opin. Struct. Biol. 1995, 5, 825-829.
71. Tame, J. R. H.; Sleigh, S. H.; Wilkinson, A. J.; Ladbury, J. E. Nature Struct. Biol. 1996, 3, 998-1001.
72. Brink, D. M.; Satchler, G. R. Angular Momentum, 2nd ed.; Clarendon: Oxford, 1968.
73. Ringe, D.; Petsko, G. A. Prog. Biophys. Mol. Biol. 1985, 45, 197-235.
74. Beeser, S. A.; Goldenberg, D. P.; Oas, T. G. J. Mol. Biol. 1997, 269, 154-164.