Computer simulations of enzyme catalysis: Finding out what has been optimized by evolution

Proceedings of the National Academy of Sciences of the United States of America

Volumn 95, Issue 11, 1998, Pages 5950-5955

  Warshel, Arieh ^a   Florián, Jan ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CATALYSIS; COMPUTER SIMULATION; ENERGY METABOLISM; ENZYME ACTIVITY; EVOLUTION; HYPOTHESIS; PRIORITY JOURNAL;

ANIMALS; COMPUTER SIMULATION; ENZYMES; EVOLUTION, MOLECULAR; HUMANS; MODELS, CHEMICAL; SUBSTRATE SPECIFICITY;

FELIS CATUS;

EID: 0032568612     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.95.11.5950     Document Type: Article

References (59)

1. Jencks, W. P. (1987) Catalysis in Chemistry and Biology (Dover, New York).
2. Fersht, A. R. (1985) Enzyme Structure and Mechanism (Freeman, New York).
3. Haldane, J. B. S. (1930) Enzymes (Longman, New York), p. 182.
4. Pauling, L. (1946) Chem. Eng. News 24, 1375.
5. Warshel, A. (1991) Computer Modeling of Chemical Reactions in Enzymes and Solutions (Wiley, New York).
6. Fuxreiter, M. & Warshel, A. (1998) J. Am. Chem. Soc., 120, 183-194.
7. Florián, J. & Warshel, A. (1997) J. Am. Chem. Soc. 119, 5473-5474.
8. Florián, J. & Warshel, A. (1998) J. Phys. Chem. B 102, 719-734.
9. Radzicka, A. & Wolfenden, R. (1996) J. Am. Chem. Soc. 118, 6105-6109.
10. Radzicka, A. & Wolfenden, R. (1995) Science 267, 90-93.
11. Phillips, D. C. (1966) Sci. Am. 215, 78-90.
12. Page, M. I. (1977) Angew. Chem. Int. Ed. Engl. 16, 449-459.
13. Cohen, S. G., Vaidya, V. M. & Schultz, R. M. (1970) Proc. Natl. Acad. Sci. USA 66, 249-256.
14. Crosby, J., Stone, R. & Lienhard, G. E. (1970) J. Am. Chem. Soc. 92, 2891-2900.
15. Menger, F. M. (1985) Acc. Chem. Res. 18, 128-134.
16. Storm, D. R. & Koshland, D. E. (1970) Proc. Natl. Acad. Sci. USA 66, 445-452.
17. Careri, G., Fasella, P. & Gratton, E. (1979) Annu. Rev. Biophys. Bioeng. 8, 69-97.
18. Gavish, B. & Werber, M. M. (1979) Biochemistry 18, 1269-1275.
19. McCammon, J. A., Wolynes, P. G. & Karplus, M. (1979) Biochemistry 18, 927-942.
20. Frey, P. A., Whitt, S. A. & Tobin, J. B. (1994) Science 264, 1927-1930.
21. Cleland, W. W. & Kreevoy, M. M. (1994) Science 264, 1887-1890.
22. Warshel, A. (1978) Proc. Natl. Acad. Sci. USA 75, 5250-5254.
23. Cha, Y., Murray, C. J. & Klinman, J. P. (1989) Science 243, 1325-1330.
24. Yagi, T., Tsuda, M., Mori, Y. & Inokuchi, H. (1969) J. Am. Chem. Soc. 91, 2801-2807.
25. Jencks, W. P. (1975) in Advances in Enzymology and Related Areas of Molecular Biology, ed. Meister, A. (Wiley, New York), Vol. 43, pp. 219-410.
26. Dewar, M. J. S. & Storch, D. M. (1985) Proc. Natl. Acad. Sci. USA 82, 2225-2229.
27. Dewar, M. J. S. & Dieter, K. M. (1988) Biochemistry 27, 3302-3308.
28. Lee, J. K. & Houk, K. N. (1997) Science 276, 942-945.
29. Lightstone, F. C., Zheng, Y. J., Maulitz, A. H. & Bruice, T. C. (1997) Proc. Natl. Acad. Sci. USA 94, 8417-8420.
30. Warshel, A., Åqvist, J. & Creighton, S. (1989) Proc. Natl. Acad. Sci. USA 86, 5820-5824.
31. Warshel, A. and Russell, S. T. (1984) Q. Rev. Biol. 17, 283-422.
32. Warshel, A. (1981) Biochemistry 20, 3167-3177.
33. Arjunan, P., Umland, T., Dyda, F., Swaminathan, S., Furey, W., Sax, M., Farrenkopf, B., Gao, Y., Zhang, D. & Jordan, F. (1996) J. Mol. Biol. 256, 590-600.
34. Metzler, D. F. (1977) Biochemistry (Academic, New York).
35. Verschueren, K. H. G., Franken, S. M., Rozenboom, H. J., Kalk, K. H. & Dijkstra, B. W. (1993) J. Mol. Biol. 1993, 856-872.
36. Verschueren, K. H. G., Seljee, F., Rozenboom, H. J., Kalk, K. H. & Dijkstra, B. W. (1993) Nature (London) 363, 693-698.
37. Maulitz, A. H., Lightstone, F. C., Zheng, Y.-J. & Bruice, T. C. (1997) Proc. Natl. Acad. Sci. USA 94, 6591-6595.
38. Sharp, K. A. & Honig, B. (1990) Annu. Rev. Biophys. Biophys. Chem. 19, 301-332.
39. Levitt, M. (1974) in Peptides, Polypeptides and Proteins, eds. Blout, E. R., Bovey, F. A., Goodman, M. & Lotan, N. (Wiley, New York), pp. 99-113.
40. Warshel, A. & Levitt, M. (1976) J. Mol. Biol. 103, 227-249.
41. Bruice, T. C., Brown, A. & Harris, D. O. (1971) Proc. Natl. Acad. Sci. USA 68, 658-661.
42. Warshel, A. & Papazyan, A. (1996) Proc. Natl. Acad. Sci. 93, 13665-13670.
43. Warshel, A., Sussman, F. & Hwang, J.-K. (1988) J. Mol. Biol. 201, 139-159.
44. Lightstone, F. C. & Bruice, T. C. (1996) J. Am. Chem. Soc. 118, 2595-2605.
45. Wilks, H. M., Hart, K. W., Feeney, R., Dunn, C. R., Muirhead, H., Chia, W. N., Barstow, D. A., Atkinson, T., Clarke, A. R. & Holbrook, J. J. (1988) Science 242, 1541-1544.
46. Leatherbarrow, R. J., Fersht, A. R. & Winter, G. (1985) Proc. Natl. Acad. Sci. USA 82, 7840-7844.
47. Carter, P. & Wells, J. A. (1990) Proteins 7, 335-342.
48. Waszkowycz, B., Hillier, I. H., Gensmantel, N. & Payling, D. W. (1990) J. Chem. Soc. Perkin Trans. 2, 1259-1264.
49. Bash, P. A., Field, M. J., Davenport, R. C., Petsko, G. A., Ringe, D. & Karplus, M. (1991) Biochemistry 30, 5826-5832.
50. Mulholland, A. J., Grant, G. H. & Richards, W. G. (1993) Protein Eng. 6, 133-147.
51. Bentzien, J., Muller, R. P., Florian, J. & Warshel, A. (1998) J. Phys. Chem. B, 102, 2293-2301.
52. Warshel, A. & Weiss, R. M. (1980) J. Am. Chem. Soc. 102, 6218-6226.
53. Åqvist, J. & Warshel, A. (1993) Chem. Rev. (Washington, D.C.) 93, 2523-2544.
54. Åqvist, J. & Fothergill, M. (1996) J. Biol. Chem. 271, 10010-10016.
55. Fothergill, M., Goodman, M. F., Petruska, J. & Warshel, A. (1995) J. Am. Chem. Soc. 117, 11619-11627.
56. Hwang, J. K. & Warshel, A. (1996) J. Am. Chem. Soc. 118, 11745-11751.
57. Dunn, B. M. & Bruice, T. C. (1973) Adv. Enzymol. Relat. Areas Mol. Biol. 37, 1-60.
58. Fife, T. H., Jaffe, S. H. & Natarajan, R. (1991) J. Am. Chem. Soc. 113, 7646-7653.
59. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Gill, P. M. W., Johnson, B. G., Robb, M. A., Cheeseman, J. R., Keith, T., Petersson, G. A., Montgomery, J. A., et al. (1995) Gaussian 94, Revision C.2 (Gaussian, Pittsburgh).