Computational investigation of irreversible inactivation of the zinc-dependent protease carboxypeptidase A

Journal of Physical Chemistry B

Volumn 109, Issue 10, 2005, Pages 4761-4769

  Cross, Jason B ^a,d   Vreven, Thom ^b   Meroueh, Samy O ^c   Mobashery, Shahriar ^c   Schlegel, H Bernhard ^a  

^a WAYNE STATE UNIVERSITY   (United States)

^b GAUSSIAN INC   (United States)

^c UNIVERSITY OF NOTRE DAME   (United States)

^d Affinium Pharmaceuticals   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL INVESTIGATION; INACTIVATION; X-RAY STRUCTURE; ZINC PROTEASES;

ACTIVATION ANALYSIS; COMPUTATIONAL METHODS; HYDROLYSIS; MOLECULAR DYNAMICS; OPTIMIZATION; POLARIZATION; SUBSTRATES; ZINC;

ENZYMES;

CARBOXYPEPTIDASE A; DYES, REAGENTS, INDICATORS, MARKERS AND BUFFERS; PROTEINASE INHIBITOR; ZINC;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; DRUG ANTAGONISM; X RAY CRYSTALLOGRAPHY;

CARBOXYPEPTIDASES A; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; INDICATORS AND REAGENTS; MODELS, MOLECULAR; PROTEASE INHIBITORS; ZINC;

EID: 15944409154     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0455172     Document Type: Article

References (72)

1. Kim, D. H.; Mobashery, S. Mechanism-Based Inhibition of Metalloproteinases. Frontiers Med. Chem. 2004, 8, 959-965.
2. Ghosh, S. S.; Wu, Y.-Q.; Mobashery, S. J. Biol. Chem. 1991, 266, 8759-8764. Wu, Y. Q.; Mobashery, S. J. Med. Chem. 1991, 34, 1914-1916.
3. Ghosh, S. S.; Wu, Y.-Q.; Mobashery, S. J. Biol. Chem. 1991, 266, 8759-8764. Wu, Y. Q.; Mobashery, S. J. Med. Chem. 1991, 34, 1914-1916.
4. Tanaka, Y.; Grapsas, I.; Dakoji, S.; Cho, Y. J.; Mobashery, S. J. Am. Chem. Soc. 1994, 116, 7475-7480.
5. Massova, I.; Martin, P.; Mel, S. D.; Tanaka, Y.; Edwards, B.; Mobashery, S. J. Am. Chem. Soc. 1996, 118, 12479-12480.
6. Bloch, K. E. J. Protein Chem. 1986, 5, 69.
7. Liang, J.-Y.; Lipscomb, W. N. Biochemistry 1987, 26, 5293-5301.
8. Jacob, O.; Cardenas, R.; Tapia, O. J. Am. Chem. Soc. 1990, 112, 8692-8705.
9. Solà, M.; Lledós, A.; Bertrán J. Inorg. Chem. 1991, 30, 2523-2527.
10. Jacob, O.; Tapia, O. Int. J. Quantum Chem. 1992, 42, 1271-1289.
11. Merz, K. M., Jr.; Hoffman, R.; Dewar, M. J. S. J. Am. Chem. Soc. 1989, 111, 5636-5649.
12. Alex, A.; Clark, T. J. Comput. Chem. 1992, 13, 704-717.
13. Onciul, A. R. v.; Clark, T. J. Comput. Chem. 1993, 14, 392-400.
14. Torrent, M.; Vreven, T.; Musaev, D. G.; Morokuma, K.; Farkas, O.; Schlegel, H. B. J. Am. Chem. Soc. 2002, 124, 192-193.
15. Pelmenschikov, V.; Blomberg, M. R. A.; Siegbahn, P. E. M. J. Biol. Inorg. Chem. 2002, 7, 284-298.
16. Morihara, K.; Tsuzuky, H. Eur. J. Biochem. 1970, 15, 374.
17. Gao, J. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 1996; Vol. 7. pp 119-185.
18. Froese, R. D. J.; Morokuma, K. In Encyclopedia of Computational Chemistry, Schleyer, P. v. R.; Allinger, N. L.; Kollman, P. A.; Clark, T.; Schaefer, H. F., III; Gasteiger, J., Schreiner, P. R., Eds.; Wiley: Chichester, 1998; Vol. 2, pp 1244-1257.
19. Tomasi, J.; Pomeli, C. S. In Encyclopedia of Computational Chemistry, Schleyer, P. v. R., Allinger, N. L., Kollman, P. A., Clark, T., Schaefer, H. F., III, Gasteiger, J., Schreiner, P. R., Eds.; Wiley: Chichester, UK, 1998; Vol. 4, pp 2343-2350.
20. Ruiz-López, M. F.; Rivail, J. L. In Encyclopedia of Computational Chemistry; Schleyer, P. v. R., Allinger, N. L., Kollman, P. A., Clark, T., Schaefer, H. F., III, Gasteiger, J., Schreiner, P. R., Eds.; Wiley: Chichester, UK, 1998; Vol. 1, pp 437-448.
21. Monard, G.; Merz, K. M. Acc. Chem. Res. 1999, 32, 904-911.
22. Dinner, A. R.; Blackburn, G. M.; Karplus, M. Nature 2001, 413, 752-755.
23. Zhang, Y.; Kua, J.; McCammon, J. A. J. Am. Chem. Soc. 2002, 124, 10572-10577.
24. Castillo, R.; Silla, E.; Tunon, I. J. Am. Chem. Soc. 2002, 124, 1809-1816.
25. Thomas, A.; Field, M. J. J. Am. Chem. Soc. 2002, 124, 12432-12438.
26. Li, J.; Cross, J. B.; Vreven, T.; Meroueh, S. O.; Mobashery, S.; Schlegel, H. B. Submitted for publicaiton.
27. Warshel, A. J. Biol. Chem. 1998, 273, 27035-27038.
28. Villà, J.; Štrajbl, M.; Glennon, T. M.; Sham, Y. Y.; Chu, Z. T.; Warshel, A. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 11899-11904.
29. Andrés, J. L.; Lledós, A.; Duran, M.; Bertrán, J. Chem. Phys. Lett. 1988, 153, 82-86.
30. Carbonell, E.; Duran, M.; Lledós, A.; Bertrán, J. J. Phys. Chem. 1991, 95, 179-183.
31. Maseras, F.; Morokuma, K. J. Comput. Chem. 1995, 16, 1170-1179.
32. Dapprich, S.; Komaromi, I.; Byun, K. S.; Morokuma, K.; Frisch, M. J. J. Mol. Struct. THEOCHEM 1999, 462, 1-21.
33. Vreven, T.; Morokuma, K. Theor. Chem. Acc. 2003, 109, 125-132.
34. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo. C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. GAUSSIAN 03, Revision A.1; Gaussian, Inc.: Pittsburgh, PA, 2003.
35. Roothaan, C. C. J. Rev. Mod. Phys. 1951, 23, 69-89. Hall, G. G. Proc. R. Soc. (London) 1951, A205, 541-552.
36. Roothaan, C. C. J. Rev. Mod. Phys. 1951, 23, 69-89. Hall, G. G. Proc. R. Soc. (London) 1951, A205, 541-552.
37. Ditchfield, R.; Hehre, W. J.; Pople, J. A. J. Chem. Phys. 1971, 54, 724-728.
38. Hariharan, P. C.; Pople, J. A. Theor. Chim. Acta 1973, 28, 213-222.
39. Chandrasekhar, J.; Smith, S. F.; Jorgensen, W. L. J. Am. Chem. Soc. 1985, 107, 154-163.
40. Wachters, A. J. H. J. Chem. Phys. 1970, 52, 1033-1036.
41. Hay, P. J. J. Chem. Phys. 1977, 66, 4377-4384.
42. Raghavachari, K.; Trucks, G. W. J. Chem. Phys. 1989, 91, 1062-1065.
43. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F. J. Am. Chem. Soc. 1985, 107, 3902-3909.
44. Vreven, T.; Morokuma, K.; Farkas, O.; Schlegel, H. B.; Frisch, M. J. J. Comput. Chem. 2003, 24, 760-769.
45. Kollman, P. A.; Dixon, R.; Cornell, W. D.; Fox, T.; Chipot, C.; Pohorille, A. In Computer Simulations of Biomolecular Systems; Wilkinson, A., Weiner, P., van Gunsteren, W., Eds.; Elsevier: New York, 1997; Vol. 3, pp 83-96.
46. SYBYL 6.7; Tripos Inc.: 1699 South Hanley Rd., St. Louis, MO, 63144.
47. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III; Ross, W. S.; Simmerling, C. L.; Darden, T. A.; Merz, K. M.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Tsui, V.; Radmer, R. J.; Duan, Y.; Pitera, J.; Massova, I.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. AMBER 6; University of California: San Francisco, CA, 1999.
48. Wang, J.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074.
49. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Chem. Phys. 1993, 97, 10269-10280.
50. Yang, P. F.; Yang, G. K. J. Am. Chem. Soc. 1992, 114, 6937-6938.
51. Gomes-Carneiro, T. M.; Jackson, R. D.; Downing, J. H.; Orpen, A. G.; Pringle, P. G. J. Chem. Soc., Chem. Commun. 1991, 317.
52. Kulawiec, R. J.; Faller, J. W.; Crabtree, R. H. Organometallics 1990, 9, 745-755.
53. Colsman, M. R.; Newbound, T. D.; Marshall, L. J.; Noirot, M. D.; Miller, M. M.; Wulfsberg, G. P.; Frye, J. S.; Andersen, O. P.; Strauss, S. H. J. Am. Chem. Soc. 1990, 112, 2349-2362.
54. Brown, M.; Waters, J. M. J. Am. Chem. Soc. 1990, 112, 2442-2443.
55. Winter, C. H.; Veal, W. R.; Gamer, C. M.; Arif, A. M.; Gladysz, J. A. J. Am. Chem. Soc. 1989, 111, 4766-4776.
56. Kulawiec, R. J.; Crabtree, R. H. Coord. Chem. Rev. 1990, 99, 89-115.
57. Mitchell, D. J.; Schlegel, H. B.; Shaik, S. S.; Wolfe, S. Can. J. Chem. 1985, 63, 1642-1648.
58. Luke, B. T.; Loew, G. H.; McLean, A. D. Int. J. Quantum Chem. 1986, 29, 883-896.
59. Tucker, S. C.; Truhlar, D. G. J. Phys. Chem. 1989, 93, 8138-8142.
60. Mann, D. J.; Hase, W. L. J. Phys. Chem. A 1998, 102, 6208-6214.
61. Li, G.; Hase, W. L. J. Am. Chem. Soc. 1999, 121, 7124-7129.
62. Shaik, S. S.; Press, A. J. Am. Chem. Soc. 1982, 104, 2708-2719.
63. Mulliken, R. S. J. Chem. Phys. 1955, 23, 1833-1840.
64. Singh, U. C.; Kollman, P. A. J. Comput. Chem. 1984, 5, 129-145.
65. Besler, B. H.; Merz, K. M., Jr.; Kollman, P. A. J. Comput. Chem. 1990, 11, 431-439.
66. Reed, A. E.; Curtiss, L. A.; Weinhold, F. Chem. Rev. 1988, 88, 899-926.
67. This includes the following residues: Asp-65, Leu-66, Gly-67, Ile-68, His-69, Ser-70, Arg-71, Glu-72, Arg-127, Asp-142, Ala-143, the peptide backbone of Asn-144, the side chain of Arg-145, Ser-194, Ile-195, His-196, Ser-197, Ser-199, Thr-268, the peptide backbone of Phe-269, Glu-270, Leu-271, and the side chain of Phe-279.
68. Christianson, D. W.; Lipscomb, W. N. Proc. Natl. Acad Sci. U.S.A. 1986, 83, 7568-7572.
69. Christianson, D. W.; Lipscomb, W. N. Acc. Chem. Res. 1989, 22, 62-69.
70. Makinen, M. W.; Kuo, L.; Dymowski, J. J.; Jaffer, S. J. Biol. Chem. 1979, 254, 356-366.
71. Makinen, M. W.; Wells, G. B.; Kang, S. O. Adv. Inorg. Biochem. 1984, 6, 1-69.
72. Suh, J. Bioorg. Chem. 1990, 18, 345-360.