Do enzymes change the nature of transition states? Mapping the transition state for general acid-base catalysis of a serine protease

Biochemistry

Volumn 42, Issue 36, 2003, Pages 10545-10553

  Bott, Richard R ^a   Chan, Gina ^a   Domingo, Blanca ^a   Ganshaw, Grant ^a   Hsia, Constance Y ^a,b   Knapp, Mark ^a,c   Murray, Christopher J ^a  

^a GENENCOR INTERNATIONAL INC   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

^c ROCHE BIOSCIENCE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CATALYST ACTIVITY; ELECTROSTATICS; HYDROLYSIS; RATE CONSTANTS;

ACID-BASE CATALYSIS;

ENZYMES;

ACID; AMIDE; AMINE; ANILIDE; BASE; HISTIDINE; IMIDAZOLE DERIVATIVE; SERINE PROTEINASE; SOLVENT; TETRAPEPTIDE;

ACYLATION; ARTICLE; EGGERTHELLA LENTA; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STRUCTURE; HYDROGEN BOND; HYDROLYSIS; IONIC STRENGTH; MOLECULAR INTERACTION; MOLECULAR STABILITY; MUTATION; PKA; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; ANILIDES; BACILLUS; BINDING SITES; CATALYSIS; ENZYME INHIBITORS; HISTIDINE; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; HYDROLYSIS; KINETICS; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; OLIGOPEPTIDES; SERINE ENDOPEPTIDASES; SUBTILISINS; VISCOSITY;

BACILLUS LENTUS; EGGERTHELLA LENTA;

EID: 0041317494     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi034773m     Document Type: Article

References (50)

1. Fischer, E. (1894) Ber. Dtsch. Chem. Ges. 27, 2985.
2. Polgar, L., and Bender, M. L. (1969) Proc. Natl. Acad. Sci. U.S.A. 64, 1335-42.
3. Fersht, A. (1985) Enzyme Structure and Mechanism, 2nd ed., W. H. Freeman and Co., New York.
4. Schowen, K. B., Limbach, H. H., Denisov, G. S., and Schowen, R. L. (2000) Biochim. Biophys. Acta 1458, 43-62.
5. Albery, W. J., and Knowles, J. R. (1976) Biochemistry 15, 5627-31.
6. Toney, M. D., and Kirsch, J. F. (1989) Science 243, 1485-8.
7. Richard, J. P. (1998) Biochemistry 37, 4305-9.
8. Mulder, F. A., Schipper, D., Bott, R., and Boelens, R. (1999) J. Mol. Biol. 292, 111-23.
9. Graycar, T., Knapp, M., Ganshaw, G., Dauberman, J., and Bott, R. (1999) J. Mol. Biol. 292, 97-109.
10. Kuhn, P., Knapp, M., Soltis, S. M., Ganshaw, G., Thoene, M., and Bott, R. (1998) Biochemistry 37, 13446-52.
11. Alston, W. C., II, Kanska, M., and Murray, C. J. (1996) Biochemistry 35, 12873-81.
12. Alston, W. C., II, Haley, K., Kanski, R., Murray, C. J., and Pranata, J. (1996) J. Am. Chem. Soc. 118, 6562-9.
13. Kraut, D. A., Carroll, K. S., and Herschlag, D. (2003) Annu. Rev. Biochem. 72, 517-571.
14. Bronsted, J., and Pedersen, K. (1924) Z. Phys. Chem. 108, 185.
15. Bell, R. (1958) The Proton in Chemistry, Chapman and Hall, London.
16. Admiraal, S. J., Meyer, P., Schneider, B., Deville-Bonne, D., Janin, J., and Herschlag, D. (2001) Biochemistry 40, 403-13.
17. Estell, D. A., Graycar, T. P., Miller, J. V., Powers, D. B., Bumier, J. P., Ng, P. G., and Wells, J. A. (1986) Science 233, 659-63.
18. Estell, D. A. (1987) Protein Eng. 1,445-6.
19. Jencks, W. (1985) Chem. Rev. 85, 511-27.
20. Halkides, C. J., Wu, Y. Q., and Murray, C. J. (1996) Biochemistry 35, 15941-8.
21. Hsia, C. Y., Ganshaw, G., Paech, C., and Murray, C. J. (1996) Anal. Biochem. 242, 221-7.
22. Ballinger, M. D., Tom, J., and Wells, J. A. (1996) Biochemistry 35, 13579-85.
23. Russell, A. J., Thomas, P. G., and Fersht, A. R. (1987) J. Mol. Biol. 193, 803-13.
24. Leatherbarrow, R. J. (1998) Grafit version 3.0, Erithacus Software Ltd., Staines, UK.
25. Bernasconi, C. (1976) Relaxation Kinetics, Academic Press, New York.
26. Jackson, S. E., and Fersht, A. R. (1993) Biochemistry 32, 13909-16.
27. Stratton, J. R., Pelton, J. G., and Kirsch, J. F. (2001) Bochemistry 40, 10411-6.
28. Day, R. M., Thalhauser, C. J., Sudmeier, J. L., Vincent, M. P., Torchilin, E. V., Sanford, D. G., Bachovchin, C. W., and Bachovchin, W. W. (2003) Protein Sci. 12, 794-810.
29. Wells, J. A., Powers, D. B., Bott, R. R., Graycar, T. P., and Estell, D. A. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 1219-23.
30. Chothia, C. (1975) Nature 254, 304-8.
31. Philipp, M., and Bender, M. L. (1983) Mol. Cell Biochem. 51, 5-32.
32. Wells, J. A., Cunningham, B. C., Graycar, T. P., and Estell, D. A. (1986) Philos. Trans. R. Soc. London Ser. A 317, 415-23.
33. Gron, H., and Breddam, K. (1992) Biochemistry 31, 8967-71.
34. Rheinnecker, M., Baker, G., Eder, J., and Fersht, A. R. (1993) Biochemistry 32, 1199-203.
35. Loewenthal, R., Sancho, J., Reinikainen, T., and Fersht, A. R. (1993) J. Mol. Biol. 232, 574-83.
36. Siezen, R. J., de Vos, W. M., Leunissen, J. A., and Dijkstra, B. W. (1991) Protein Eng. 4, 719-37.
37. Satterthwait, A. C., and Jencks, W. P. (1974) J. Am. Chem. Soc. 96, 7018-31.
38. Hiroara, H., Bender, M. L., and Stark, R. S. (1974) Proc. Natl. Acad. Sci. U.S.A. 71, 1643-7.
39. Hegazi, M. F., Quinn, D. M., and Schowen, R. L. (1976) in Transition States of Biochemical Processes (Gandour, R. D., and Schowen, R. L., Eds.) pp 355-423, Plenum Press, New York.
40. Stewart, R., and O'Donnell, J. P. (1962) J. Am. Chem. Soc. 84, 493-4.
41. Williams, A. (1992) Adv. Phys. Org. Chem 27, 1-55.
42. Warshel, A. (1998) J. Biol. Chem. 273, 27035-8.
43. Warshel, A., and Florian, J. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 5950-5.
44. Yang, C. C., and Jencks, W. P. (1988) J. Am. Chem. Soc. 110, 2972-3.
45. Hine, J. (1959) J. Am. Chem. Soc. 81, 1126-1129.
46. Stahl, N., and Jencks, W. P. (1986) J. Am. Chem. Soc. 108, 4196-205.
47. Shan, S. O., and Herschlag, D. (1999) Methods Enzymol. 308, 246-76.
48. Coleman, C. A., and Murray, C. J. (1992) J. Org. Chem. 57, 3578-82.
49. Hine, J. (1972) J. Am. Chem. Soc. 94, 5766-71.
50. Carter, P., and Wells, J. A. (1988) Nature 332, 564-8.