QM/MM study on the mechanism of peptide hydrolysis by carboxypeptidase A

Journal of Molecular Structure: THEOCHEM

Volumn 898, Issue 1-3, 2009, Pages 106-114

  Szeto, Michelle W Y ^a   Mujika, Jon I ^a   Zurek, Jolanta ^a   Mulholland, Adrian J ^a   Harvey, Jeremy N ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

Density functional theory; Enzyme reaction mechanisms; QM MM calculations; Reaction paths

Indexed keywords

EID: 60749124902     PISSN: 01661280     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.theochem.2008.06.033     Document Type: Article

References (61)

1. Christianson D.W., and Lipscomb W.N. Acc. Chem. Res. 22 (1989) 62
2. Quiocho F.A., and Lipscomb W.N. Adv. Protein Chem. 25 (1971) 1
3. Vallee B.L., Galdes A., Auld D.S., and Riordan J.F. In: Spiro T.G. (Ed). Zinc Enzymes (1983), Wiley-Interscience, New York 26-75
4. Alvarez-Santos S., Gonzalez-Lafont A., Lluch J.M., Oliva B., and Aviles F.X. New J. Chem. 22 (1998) 319
5. Kilshtain-Vardi A., Shoham G., and Goldblum A. Int. J. Quantum Chem. 88 (2002) 87
6. Mulholland A.J., Grant G.H., and Richards W.G. Prot. Eng. 6 (1993) 133
7. Suh J.H., Park T.H., and Hwang B.K. J. Am. Chem. Soc. 114 (1992) 5141
8. Warshel A., and Levitt M. J. Mol. Biol. 103 (1976) 227
9. Field M.J., Bash P.A., and Karplus M. J. Comput. Chem. 11 (1990) 700
10. Vallee B.L., and Auld D.S. Faraday Discuss. (1992) 47
11. Vallee B.L., and Auld D.S. Biochemistry 29 (1990) 5647
12. Nakagawa S., and Umeyama H. J. Am. Chem. Soc. 100 (1978) 7716
13. Alex A., and Clark T. J. Comput. Chem. 13 (1992) 704
14. Alvarez-Santos S., Gonzalez-Lafont A., Lluch J.M., Oliva B., and Aviles F.X. Can. J. Chem. 72 (1994) 2077
15. Pelmenschikov V., Blomberg M.R.A., and Siegbahn P.E.M. J. Biol. Inorg. Chem. 7 (2002) 284
16. Matthews B.W. Acc. Chem. Res. 21 (1988) 333
17. Mulholland A.J. Drug Discov. Today 10 (2005) 1393
18. Claeyssens F., Harvey J.N., Manby F.R., Mata R.A., Mulholland A.J., Ranaghan K.E., Schutz M., Thiel S., Thiel W., and Werner H.J. Angew. Chem. Int. Ed. 45 (2006) 6856
19. Claeyssens F., Ranaghan K.E., Manby F.R., Harvey J.N., and Mulholland A.J. Chem. Commun. (2005) 5068
20. Hu H., and Yang W. Ann. Rev. Phys. Chem. 59 (2008) 573
21. Henkelman G., and Jonsson H. J. Chem. Phys. 113 (2000) 9978
22. Lippard S.J., and Berg J.M. Principles of Bioinorganic Chemistry (1994), University Science Books, Mill Valley pp. 259-262
23. Phoon L., and Burton N.A. J. Mol. Graph. Model. 24 (2005) 94
24. Cross J.B., Vreven T., Meroueh S.O., Mobashery S., and Schlegel H.B. J. Phys. Chem. B 109 (2005) 4761
25. Blumberger J., Lamoureux G., and Klein M.L. J. Chem. Theory Computat. 3 (2007) 1837
26. Kim H.D., and Lipscomb W.N. Biochemistry 30 (1991) 8171
27. Maestro, version 5.0. Schrodinger, LLC, New York, 2003.
28. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. J. Comput. Chem. 4 (1983) 187
29. Ponder J.W. Tinker: Software Tools for Molecular design (2003), St. Louis, MO
30. 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., Wiórkiewicz-Kuczera J., Yin D., and Karplus M. J. Phys. Chem. B 102 (1998) 3586
31. Harvey J.N. Faraday Discuss. 127 (2004) 165
32. Jaguar, 6.0 ed., Schrodinger, Inc., New York, 2005.
33. Hay P.J., and Wadt W.R. J. Chem. Phys. 82 (1985) 299
34. 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. J. Phys. Chem. B 102 (1998) 3586
35. MacKerell A.D., Banavali N., and Foloppe N. Biopolymers 56 (2000) 257
36. Reuter N., Dejaegere A., Maigret B., and Karplus M. J. Phys. Chem. A 104 (2000) 1720
37. J.N. Harvey, A.J. Mulholland, F.R. Manby, S. Kittusamy, J. Zurek, in press.
38. Greenblatt H.M., Feinberg H., Tucker P.A., and Shoham G. Acta Crystallogr. D Biol. Crystallogr. 54 (1998) 289
39. Massova I., Martin P., deMel S., Tanaka Y., Edwards B., and Mobashery S. J. Am. Chem. Soc. 118 (1996) 12479
40. Mangani S., Carloni P., and Orioli P. J. Mol. Biol. 223 (1992) 573
41. van Aalten D.M.F., Chong C.R., and Joshua-Tor L. Biochemistry 39 (2000) 10082
42. Cho J.H., Kim D.H., Chung S.J., Ha N.C., Oh B.H., and Choi K.Y. Biorg. Med. Chem. 10 (2002) 2015
43. Park J.D., Kim D.H., Kim S.J., Woo J.R., and Ryu S.E. J. Med. Chem. 45 (2002) 5295
44. Teplyakov A., Wilson K.S., Orioli P., and Mangani S. Acta Crystallogr. D Biol. Crystallogr. 49 (1993) 534
45. Christianson D.W., and Lipscomb W.N. Proc. Natl. Acad. Sci. USA 83 (1986) 7568
46. Kim H., and Lipscomb W.N. Biochemistry 29 (1990) 5546
47. Dudev T., and Lim C. Chem. Rev. 103 (2003) 773
48. Hall T.M., Porter J.A., Beachy P.A., and Leahy D.J. Nature 378 (1995) 212
49. Ryde U. Biophys. J. 77 (1999) 2777
50. Fersht A. Enzyme Structure and Mechanism (1985), Freeman
51. Phillips M.A., Fletterick R., and Rutter W.J. J. Biol. Chem. 265 (1990) 20692
52. Harvey J.N. Annu. Rep. C Phys. Chem. 102 (2006) 203
53. Hermann J.C., Hensen C., Ridder L., Mulholland A.J., and Höltje H.D. J. Am. Chem. Soc. 127 (2005) 4454
54. Hermann J.C., Ridder L., Höltje H.D., and Mulholland A.J. Org. Biomol. Chem. 4 (2006) 206
55. Henkelman G., Uberuaga B.P., and Jonsson H. J. Chem. Phys. 113 (2000) 9901
56. van der Kamp M.W., Perruccio F., and Mulholland A.J. Prot. Struct. Funct. Bioinform. 69 (2007) 521
57. Christianson D.W. Adv. Prot. Chem. 42 (1991) 281
58. Rees D.C., Lewis M., Honzatko R.B., Lipscomb W.N., and Hardman K.D. Proc. Natl. Acad. Sci. USA-Biol. Sci. 78 (1981) 3408
59. Christianson D.W., David P.R., and Lipscomb W.N. Proc. Natl. Acad. Sci. USA 84 (1987) 1512
60. Christianson D.W., and Lipscomb W.N. Proc. Natl. Acad. Sci. USA 82 (1985) 6840
61. Pelmenschikov V., and Siegbahn P.E.M. Inorg. Chem. 41 (2002) 5659