Improving pK(a) calculations with consideration of hydration entropy

Protein Engineering

Volumn 10, Issue 7, 1997, Pages 809-814

  Warwicker, J ^a  

^a INSTITUTE OF FOOD RESEARCH   (United Kingdom)

Author keywords

Electrostatics; Hydration shell; pK(a) calculations; Thioredoxin

Indexed keywords

ASPARTIC ACID; CYSTEINE; GLUTAMIC ACID; PROTEIN; THIOREDOXIN; AMINO ACID; WATER;

ACCURACY; ARTICLE; CALCULATION; ENTROPY; GEOMETRY; HYDRATION; MACROMOLECULE; MOLECULAR MODEL; PKA; PRIORITY JOURNAL; SIMULATION; STRUCTURE ACTIVITY RELATION; ANIMAL; CHEMISTRY; ELECTRICITY; FACTUAL DATABASE; PH; PROTEIN ENGINEERING;

AMINO ACIDS; ANIMALS; DATABASES, FACTUAL; ELECTROSTATICS; ENTROPY; HYDROGEN-ION CONCENTRATION; PROTEIN ENGINEERING; PROTEINS; THIOREDOXIN; WATER;

EID: 0030613531     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/10.7.809     Document Type: Article

References (35)

1. Antosiewicz, J., McCammon, J.A. and Gilson, M.K. (1994) J. Mol. Biol., 238, 415-436.
2. Bashford, D. and Karplus, M. (1990) Biochemistry, 29, 10219-10225.
3. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Jr, Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) J. Mol. Biol., 112, 535-542.
4. Born, M. (1920) Z. Phys., 1, 45-48.
5. Brown, L.R., Marco, A.D., Wagner, G. and Wuthrich, K. (1976) Eur. J. Biochem., 62, 103-107.
6. Brown, L.R., Marco, A.D., Richarz, R., Wagner, G. and Wuthrich, K. (1978) Eur. J. Biochem., 88, 87-95.
7. Buckle, A.M., Henrick, K. and Fersht, A.R. (1993) J. Mol. Biol., 234, 847-860.
8. Gane, P.J., Freedman, R.B. and Warwicker, J. (1995) J. Mol. Biol., 249, 376-387.
9. Gilson, M.K. and Honig, B.H. (1987) Nature, 330, 84-86.
10. Honig, B. and Nicholls, A. (1995) Science, 268, 1144-1149.
11. Howlin, B., Moss, D.S. and Harris, G.W. (1989) Acta Crystallogr., A45, 851-861.
12. Kallis, G.-B. and Holmgren, A. (1980) J. Biol. Chem., 255, 10261-10265.
13. Katti, S.K., LeMaster, D.M. and Eklund, H. (1990) J. Mol. Biol., 212, 167-184.
14. Kuramitsu, S. and Hamaguchi, K. (1980) J. Biochem., 87, 1215-1219.
15. Langsetmo, K., Fuchs, J.A., Woodward, C. and Sharp, K.A. (1991) Biochemistry, 30, 7609-7614.
16. Lee, B.K. and Richards, F.M. (1971) J. Mol. Biol., 55, 379-100.
17. Marcus, Y. (1985) In Ion Solvation. John Wiley and Sons Ltd, Chichester, UK.
18. Martin, J.L., Bardwell, J.C.A. and Kuriyan, J. (1993) Nature, 365, 464-468.
19. Nelson, J.W. and Creighton, T.E. (1994) Biochemistry, 33, 5974-5983.
20. Oliveberg, M., Arcus, V.L. and Fersht, A.R. (1995) Biochemistry, 34, 9424-9433.
21. Rashin, A.A. and Honig, B. (1985) J. Phys. Chem., 89, 5588-5593.
22. Rashin, A.A. and Bukatin, M.A. (1993) J. Phys. Chem., 97, 1974-1979.
23. Richarz, R. and Wuthrich, K. (1978) Biochemistry, 17, 2263-2269.
24. Rico, M., Santoro, J., González, C., Bruix, M. and Neira, J.L. (1991) In Cuchillo, C.M., de Llorens, R., Nogués, M.V. and Parés, X. (eds), Structure, Mechanism and Function of Ribonucleases. Proceedings of the 2nd International Meeting. Universitat Autònoma de Barcelona, Barcelona, pp. 9-14.
25. Sharp, K. (1991) J. Comp. Chem., 12, 454-468.
26. Sharp. K.A. and Honig, B. (1990) Annu. Rev. Biophys. Chem., 19, 301-332.
27. Simonson, T. and Perahia, D. (1995) Proc. Natl Acad. Sci. USA, 92, 1082-1086.
28. Sternberg, M.J.E., Hayes, F.R.F., Russell, A.J., Thomas, P.G. and Fersht, A.R. (1987) Nature, 330, 86-88.
29. Takahashi, N. and Creighton, T.E. (1996) Biochemistry, 35, 8342-8353.
30. van Gunsteren, W.F. and Berendsen, H.J.C. (1987) GROMOS Manual, BIOMOS Biomolecular Software, Laboratory of Physical Chemistry, University of Groningen.
31. Warwicker, J. (1986) J. Theor. Biol., 121, 199-210.
32. Warwicker, J. (1994) J. Mol. Biol., 236, 887-907.
33. Warwicker, J. and Watson, H.C. (1982) J. Mol. Biol., 157, 671-679.
34. Wlodawer, A., Walter, J., Huber, R. and Sjolin, L. (1984) J. Mol. Biol., 180, 301-329.
35. You, T.J. and Bashford, D. (1995) Biophys, J., 69, 1721-1733.