Insights into enzyme catalysis from QM/MM modelling: Transition state stabilization in chorismate mutase

Molecular Physics

Volumn 101, Issue 17, 2003, Pages 2695-2714

  Ranaghan, Kara E ^a   Ridder, Lars ^a,b   Szefczyk, Borys ^a,c   Sokalski, W Andrzej ^c   Hermann, Johannes C ^a,d   Mulholland, Adrian J ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b NV ORGANON   (Netherlands)

^c WROCLAW UNIVERSITY OF TECHNOLOGY   (Poland)

^d HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CHEMICAL BONDS; ELECTROSTATICS; ENZYME KINETICS; MOLECULAR DYNAMICS; PHASE TRANSITIONS; POTENTIAL ENERGY; QUANTUM THEORY; SUBSTRATES;

CHORISMATE MUTASE; CLAISEN REARRANGEMENT; TRANSITION STATE STABILIZATION;

MOLECULAR PHYSICS;

EID: 0346940853     PISSN: 00268976     EISSN: None     Source Type: Journal    
DOI: 10.1080/00268970310001593286     Document Type: Article

References (72)

1. Mulholland, A. J., Grant, G. H., and Richards, W. G., 1993, Protein Engng., 6, (2), 133.
2. Warshel, A., 1991, Computer Modeling of Chemical Reactions in Enzymes and Solutions. (New York: Wiley).
3. Mulholland, A. J., and Karplus, M., 1996, Biochem. Soc. Trans., 24, 247.
4. Mulholland, A. J., 2001, Theoretical Biochemistry - Processes and Properties of Biological Systems, edited by L. A. Eriksson, Amsterdam: Elsevier, pp. 597-653.
5. Gao, J. L., and Truhlar, D. G., 2002, Annu. Rev. phys. Chem., 53, 467.
6. Field, M. J., 2002, J. comput. Chem., 23, 48.
7. Ridder, L., Harvey, J., Rietjens, I., Vervoort, J., and Mulholland, A. J., 2003, J. phys. Chem. B, 107, 2118.
8. Bash, P. A., Field, M. J., Davenport, R. C., Petsko, G. A., Ringe, D., and Karplus, M., 1991, Biochemistry, 30, 5826.
9. Warshel, A., and Levitt, M., 1976, J. Molec Biol., 103, 227.
10. Field, M. J., Bash, P. A., and Karplus, M., 1990, J. comput. Chem., 11, 700.
11. Lyne, P. D., Hodoscek, M., and Karplus, M., 1999, J. phys. Chem. A, 103, 3462.
12. Mulholland, A. J., Lyne, P. D., and Karplus, M. J., 2000, J. Am. chem. Soc., 122, 534.
13. Stanton, R., Hartsough, D., and Merz, K., 1995, J. comput. Chem., 16, 113.
14. Guildford, W. J., and Knowles, J. R., 1987, J. Am. chem. Soc., 109, 5103.
15. Chook, Y., Ke, H., and Lipscomb, W., 1993, Proc. Natl. Acad. Sci. USA, 90, 8600.
16. Chook, Y., Gray, J., Ke, H., and Lipscomb, W., 1994, J. molec Biol., 240, 476.
17. Kast, P., Asif-Ullah, M., and Hilvert, D., 1996, Tetrahedron Lett., 37, 2691.
18. Lyne, P., Mulholland, A. J., and Richards, W. G., 1995, J. Am. chem. Soc., 117, 11345.
19. Martí, S., Andrés, J., Moliner, V., Silla, E., Tuñón, I., and Bertrán, J., 2001, Theo. chem. Acc., 105, 207.
20. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M., 1983, J. comput. Chem., 4, 187.
21. Turner, A. J., Moliner, V., and Williams, I. H., 1999, Phys. Chem. chem. Phys., 1, 1323.
22. Hall, R. J., Hindle, S. A., Burton, N. A., and Hillier, I. H., 2000, J. comput. Chem., 21, 1433.
23. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Zakrzewski, V. G., Montgomery, J. A., Stratmann, R. E., Burant, J. C., Dapprich, S., Millam, J. M., Daniels, A. D., Kudin, K. N., Strain, M. C., Farkas, O., Tomasi, J., Barone, V., Cossi, M., Cammi, R., Mennucci, B., Pomelli, C., Adamo, C., Clifford, S., Ochterski, J., Petersson, G. A., Ayala, P. Y., Cui, Q., Morokuma, K., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Cioslowski, J., Ortiz, J. V., Baboul, A. G., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Gomperts, R., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Gonzalez, C., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Andres, J. L., Gonzalez, C., Head-Gordon, M., Replogle, E. S., and Pople, J. A., 1994, Gaussian 94 (Pittsburgh, PA: Gaussian, Inc.).
24. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M. Jr., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J.W.M. and Kollman, P.A., 1995, J. Am. chem. Soc., 117, 5179.
25. Worthington, S. E., Roitberg, A. E., and Krauss, M., 2001, J. phys. Chem. B, 105, 7087.
26. Stevens, W. J., Basch, H., and Krauss, M., 1984, J. chem. Phys., 81, 6026.
27. Wiest, O., and Houk, K. N., 1995, J. Am. chem. Soc., 117, 11 628.
28. Davidson, M., Gould, I. R., and Hillier, I. H., 1996, J. Chem. Soc., Perkin Trans. 2, 525.
29. Martí, S., Andrés, J., Moliner, V., Silla, E., Tuñon, I., and Bertrán, J., 2000, J. phys. Chem. B, 104, 11 308.
30. Carlson, H. A., and Jorgensen, W. L., 1996, J. Am. chem. Soc., 118, 8475.
31. Davidson, M., Guest, J., Craw, J., and Hillier, I., 1997, J. chem. Soc., Perkin Trans. 2, 1395.
32. Kast, P., Tewari, Y., Wiest, O., Hilvert, D., Houk, K. N., and Goldberg, R. N., 1997, J. phys. Chem. B, 101, 10 976.
33. Guo, H., Cui, Q., Lipscomb, W. N., and Karplus, M., 2001, Proc. Natl. Acad. Sci., USA, 98, 9032.
34. Elstner, M., Porezag, D., Jungnickel, G., Elstner, J., Haugk, M., Frauenheim, T., Suhai, S., and Seifert, G., 1998, Phys. Rev. B, 58, 7260.
35. Cui, Q., Elstner, M., Kaxiras, E., Frauenheim, T., and Karplus, M., 2001, J. phys. Chem. B, 105, 569.
36. Strater, N., Schnappuaf, G., Braus, G., and Lipscomb, W. N., 1997, Structure (London), 5, 1437.
37. Hur, S., and Bruice, T. C., 2003, J. Am. chem. Soc., 125, 1472.
38. Shurki, A., Štrajbl, M., Villa, J., and Warshel, A., 2002, J. Am. chem. Soc., 124, 4097.
39. Kienhöfer, A., Kast, P., and Hilvert, D., 2003, J. Am. chem. Soc., 125, 3206.
40. Kast, P., Grisostomi, C., Chen, I. A., Li, S., Krengel, U., Xue, Y., and Hilvert, D., 2000, J. Biol. Chem., 275, 36832
41. Cload, S. T., Liu, D. R., Pastor, R. M., and Schultz, P. G., 1996, J. Am. chem. Soc., 118, 1787.
42. Martí, S., Andrés, J., Moliner, V., Silla, E., Tuñón, I., and Bertrán, J., 2003, Chem. Eur. J., 9, 984.
43. Martí, S., Andrés, J., Moliner, V., Silla, E., Tuñón, I., Bertrán, J., and Field, M., 2001, J. Am. chem. Soc., 123, 1709.
44. Torre, G. M., and Valleau, J. P., 1977, J. comput. Phys., 23, 187.
45. Field, M. J., Albe, M., Bret, C., Proust-De Martin, F., and Thomas, A., 2000, J. comput. Chem., 21, 1088.
46. MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M., 1998, J. phys. Chem. B, 102, 3586.
47. Billeter, S. R., Hanser, C. F. W., Mordasini, T. Z., Scholten, M., Thiel, W., and van Gunsteren, W. F., 2001, Phys. Chem. Chem. Phys., 3, 688-695.
48. Elcock, A. H., Lyne, P. D., Mulholland, A. J., Nandra, A., and Richards, W. G., 1995, J. Am. chem. Soc., 117, 4706.
49. Harrison, M. J., Burton, N. A., and Hillier, I. H., 1997, J. Am. chem. Soc., 119, 11 285.
50. Zhang, Y. K., Liu, H. Y., and Yang, W. T., 2000, J. chem. Phys., 112, 3483.
51. Ridder, L., and Mulholland, A. J., 2003, Curr. Top. Med. Chem., 3, 1241-1256.
52. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Zakrzewski, V. G., Montgomery, J. A., Stratmann, R. E., Burant, J. C., Dapprich, S., Millam, J. M., Daniels, A. D., Kudin, K. N., Strain, M. C., Farkas, O., Tomasi, J., Barone, V., Cossi, M., Cammi, R., Mennucci, B., Pomelli, C., Adamo, C., Clifford, S., Ochterski, J., Petersson, G. A., Ayala, P. Y., Cui, Q., Morokuma, K., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Cioslowski, J., Ortiz, J. V., Baboul, A. G., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Gomperts, R., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Gonzalez, C., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Andres, J. L., Gonzalez, C., Head-Gordon, M., Replogle, E. S., and Pople, J. A., 1998, Gaussian 98 (Pittsburgh PA: Gaussian, Inc.).
53. Fischer, S., and Karplus, M., 1992, Chem. Phys. Lett., 194, 252.
54. Bartlett, P. A. and Johnson, C. R., 1985, J. Am. chem. Soc., 107, 7792.
55. Brooks, C. L., and Karplus, M., 1983, J. chem. Phys., 79, 6312.
56. Stote, R. H., and Karplus, M., 1998, Proteins: Struct., Funct. Genetics, 23, 12.
57. Hadfield, A. T., and Mulholland, A. J., 1999, Int. J. quantum Chem. (Biophys. Q.), 73, 137.
58. Eurenius, K. P., Chatfield, D. C., Brooks, B. R., and Hodoscek, M., 1996, Int. J. quantum Chem., 60, 1189.
59. Brooks, C. L. III, Karplus, M., and Pettitt, B. M., 1988, Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics (New York: Wiley).
60. Williams, I. H., and Moliner, V., 2000, Chem. Commun., 19, 1843.
61. Pauling, L., 1948, Am. Sci., 36, 51.
62. Fersht, A., 1999, Structure and Mechanism in Protein Science. A Guide to Enzyme Catalysis and Protein Folding., 2nd edn (New York: Freeman).
63. Warshel, A., 1998, J. Biol. Chem., 273, 27 035.
64. Mulholland, A. J., and Richards, W. G., 1997, Proteins: Struct., Funct. Genetics, 27, 9.
65. Ridder, L., Mulholland, A. J., Rietjens, I. M. C. M., and Vervoort, J., 1999, J. Molec Graphics Model, 17, 163.
66. Ridder, L., Mulholland, A. J., Rietjens, I. M. C. M., and Vervoort, J., 2000, J. Am. chem. Soc., 122, 8728.
67. QUANTA98, 1998, San Diego: CA: Accelrys, Inc.
68. Lee, Y. S., Worthington, S. E., Krauss, M., and Brooks, B. R., 2002, J. phys. Chem. B, 106, 12 059.
69. Schmidt, M. W., Baldridge, K. K., Boatz, J. A., Elbert, S. T., Gordon, M. S., Jensen, J. H., Koseki, S., Matsunaga, N., Nguyen, K. A., Su, S. J., Windus, T. L., Dupuis, M., and Montgomery, J. A., 1993, J. comput. Chem., 14. 1347.
70. Copley, S. D., and Knowles, J. R., 1987, J. Am. chem. Soc., 109, 5008.
71. Fersht, A., 1985, Enzyme Structure and Mechanism, 2nd edn (New York: Freeman).
72. Miertus, S., and Tomasi, J., 1982, Chem. Phys., 65, 239.