Dissecting the vibrational entropy change on protein/ligand binding: Burial of a water molecule in bovine pancreatic trypsin inhibitor

Journal of Physical Chemistry B

Volumn 105, Issue 33, 2001, Pages 8050-8055

  Fischer, Stefan ^a   Smith, Jeremy C ^a   Verma, Chandra S ^b  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b UNIVERSITY OF YORK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

VIBRATIONAL ENTROPY;

CHEMICAL BONDS; COMPLEXATION; CRYSTALLOGRAPHY; DEGREES OF FREEDOM (MECHANICS); ENTROPY; ENZYME INHIBITION; MOLECULAR VIBRATIONS; WATER;

PROTEINS;

EID: 0035940247     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0120920     Document Type: Article

References (29)

1. Brooks, C.L.; Karplus, M. J. Mol. Biol. 1989, 208, 159-181.
2. Levitt, M.; Park, B.H. Structure 1993, 1, 223-226.
3. Daggett, V.; Levitt, M. Realistic Simulations of Native Protein Dynamics in Solution and Beyond. Annu. Rev. Biophys. Biomol. Struct. 1993, 22, 353-380.
4. Zhang, L.; Herman, J. Proteins: Struct., Funct., Genet. 1996, 24, 433-438.
5. Roux, B.; Nina, M.; Pomes, R.; Smith, J.C. Biophys. J. 1996, 71, 670-681.
6. Denisov, P.; Halle, B. Faraday Discuss. 1996, 103, 227-244.
7. Pettitt, B.M.; Makarov, V.A.; Andrews, B.K. Curr. Opin. Struct. Biol. 1998, 8, 218-221.
8. Prevost, M. Folding Design 1998, 3, 345-351.
9. Helms, V.; Wade, R.C. Proteins: Stuct., Funct., Genet. 1998, 32, 381-396.
10. Garcia, A.E.; Hummer, G. Proteins: Stuct., Funct., Genet. 2000, 38, 261-272.
11. Likic, V.A.; Juranic, N.; Macura, S.; Pendergast, F.G. Protein Sci. 2000, 9, 497-504.
12. Wlodaver, A.; Walter, J.; Huber, R.; Sjolin, L. J. Mol. Biol. 1984, 180, 301-329.
13. Otting, G.; Wuthrich, K. J. Am. Chem. Soc. 1989, 111, 1871-1875.
14. Denisov, V.P.; Peters, J.; Horlein, H.D.; Halle, B. Nat. Struct. Biol. 1996, 3, 505-509.
15. Woenckhaus, J.; Hudgins, P.R.; Jarrold, M.F. J. Am. Chem. Soc. 1997, 119, 9586-9587.
16. Fischer, S.; Verma, C.S.; Hubbard, R.E. J. Phys. Chem. B 1998, 102, 1797-1805.
17. Fischer, S., Verma, C.S. Proc. Nat. Acad. Sci. U.S.A. 1999, 96, 9613-9615.
18. Mao, Y.; Rather, M.A.; Jarrold, M.F. J. Am. Chem. Soc. 2000, 122, 2950-2951.
19. McQuarrie, D.A. Statistical Mechanics; Harper Row: New York 1976.
20. Tidor, B.; Karplus, M. J. Mol. Biol. 1994, 238, 405-414.
21. Denisov, V.P.; Venu, K.; Peters, J.; Horlein, H.D.; Halle, B. J. Phys. Chem. B 1997, 101, 9380-9389.
22. Brooks, B.R.; Bruccoleri, R.E.; Olafson, B.D.; States, D.J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
23. Neria, E.; Fischer, S.; Karplus, M. J. Chem. Phys. 1996, 105, 1902-1921.
24. Wilson, E.B., Jr.; Decius, J.C.; Cross, P.C. Molecular Vibrations; Dover: New York, 1980.
25. Brooks, B.R.; Janezic, D.; Karplus, M. J. Comput. Chem. 1995, 16, 1522-1542.
26. Karplus, M.; Janin, J. Protein Eng. 1999, 12, 185-186.
27. Eisenberg, D.; Kauzmann, W. The Structure and Properties of Water; Oxford University Press: Oxford, 1969.
28. Dunitz, J. Science 1994, 264, 670.
29. Schwarzl, S.M.; Tschopp, T.; Smith, J.C.; Fischer, S. J. Med. Chem., submitted.