The charge density distribution in a model compound of the catalytic triad in serine proteases

Chemistry - A European Journal

Volumn 7, Issue 17, 2001, Pages 3756-3767

  Overgaard, Jacob ^a   Schiøtt, Birgit ^a   Larsen, Finn K ^a   Iversen, Bo B ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

Charge density analysis; Density functional calculations; Enzyme catalysis; Hydrogen bonds

Indexed keywords

CATALYST ACTIVITY; CRYSTALLINE MATERIALS; ELECTRIC CHARGE; HYDROGEN BONDS; NEUTRON DIFFRACTION; X RAY DIFFRACTION ANALYSIS;

CATALYTIC TRIAD; CHARGE DENSITY DISTRIBUTION; PIRIC ACID; SERINE PROTEASES;

ENZYMES;

BETAINE; IMIDAZOLE DERIVATIVE; PICRIC ACID; SERINE PROTEINASE;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COLD; COMPARATIVE STUDY; COVALENT BOND; CRYSTAL STRUCTURE; ELECTRON; ENZYME ACTIVE SITE; ENZYME MECHANISM; HYDROGEN BOND; LOW TEMPERATURE PROCEDURES; MOLECULAR MODEL; NEUTRON; NEUTRON SCATTERING; RADIATION SCATTERING; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

BINDING SITES; CATALYTIC DOMAIN; COLD; CRYSTALLOGRAPHY, X-RAY; ELECTRONS; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NEUTRONS; SCATTERING, RADIATION; SERINE ENDOPEPTIDASES;

EID: 20644441004     PISSN: 09476539     EISSN: None     Source Type: Journal    
DOI: 10.1002/1521-3765(20010903)7:17<3756::AID-CHEM3756>3.0.CO;2-Q     Document Type: Article

References (90)

1. D. M. Blow, J. J. Birktoft, B. S. Hartley, Nature 1969, 221, 337-340.
2. a) J. A. Gerlt, P. G. Gassman, Biochemistry 1993, 32, 11943-11952;
3. b) P. A. Frey, S. A. Whitt, J. B. Tobin, Science 1994, 264, 1927-1930;
4. c) J. B. Tobin, S. A. Whitt, C. S. Cassidy, P. A. Frey, Biochemistry 1995, 34, 6919-6924;
5. d) W. W. Cleland, P. A. Frey, J. A. Gerlt, J. Biol. Chem. 1998, 273, 25529-25532;
6. e) J. A. Gerlt, M. M. Kreevoy, W. W. Cleland, P. A. Frey, Chem. Biol. 1997, 4, 259-267;
7. f) C. S. Cassidy, J. Lin, P. A. Frey, Biochemistry 1997, 36, 4576-4584;
8. g) A. Kahyaoglu, K. Haghjoo, F. Guo, F. Jordan, C. Kettner, F. Felfoldi, L. Polgar, J. Biol. Chem. 1997, 272, 25547-25554;
9. h) C. S. Kraik, S. Roczniak, C. Largman, W. J. Rutter, Science 1987, 237, 909-913;
10. i) W. R. Cannon, S. R. Benkovic, J. Biol. Chem. 1998, 273, 26527-26260;
11. j) J. P. Guthrie, R. Kluger, J. Am. Chem. Soc. 1993, 115, 11569-11572;
12. k) J. P. Guthrie, Chem. Biol. 1996, 3, 163-170;
13. l) C. S. Cassidy, J. Lin, P. A. Frey, Biochem. Biophys. Res. Commun. 2000, 273, 789-792.
14. F. Hibbert, J. Emsley, Adv. Phys. Org. Chem. 1990, 26, 255-379.
15. a) A. Warshel, J. Biol. Chem. 1998, 273, 27035-27038;
16. b) A. Warshel, A. Papazyan, P. A. Kollman, W. W. Cleland, M. M. Kreevoy, P. A. Frey, Science 1995, 269, 102-106;
17. c) A. Warshel, A. Papazyan, Proc. Natl. Acad. Sci. USA 1996, 93, 13665-13670.
18. C. L. Perrin, Science 1994, 266, 1665-1668.
19. a) G. K. H. Madsen, B. B. Iversen, F. K. Larsen, M. Kapon. G. M. Reisner, F. H. Herbstein, J. Am. Chem. Soc. 1998, 120, 10040-10045;
20. b) B. Schiøtt, B. B. Iversen, G. K. H. Madsen, F. K. Larsen, T. C. Bruice, Proc. Natl. Acad. Sci. USA 1998, 95, 12799-12802;
21. c) B. Schiøtt, B. B. Iversen, G. K. H. Madsen, T. C. Bruice, J. Am. Chem. Soc. 1998, 120, 12117-12124;
22. d) F. H. Herbstein, B. B. Iversen, M. Kapon, F. K. Larsen, G. K. H. Madsen, G. M. Reisner, Acta Crystallogr. Sect. B 1999, 55, 767-787.
23. a) Y. Pan, M. A. McAllister, J. Am. Chem. Soc. 1997, 119, 7561-7566;
24. b) Y. Pan, M. A. McAllister, J. Am. Chem. Soc. 1998, 120, 166-169;
25. c) Y. Pan, M. A. McAllister, J. Org. Chem. 1997, 62, 8171-8176;
26. d) C. J. Smallwood, M. A. McAllister, J. Am. Chem. Soc. 1997, 119, 11277-11281;
27. e) G. A. Kumar, M. A. McAllister, J. Am. Chem. Soc. 1998, 120, 3159-3165.
28. a) M. Garcia-Viloca, A. Gonzalez-Lafont, J. M. Lluch, J. Am. Chem. Soc. 1997, 119, 1081-1086;
29. b) M. Garcia-Viloca, A. Gonzalez-Lafont, J. M. Lluch, J. Phys. Chem. 1997, 101, 3880-3886;
30. c) J. Chen, M. A. McAllister, J. K. Lee, K. N. Houk, J. Org. Chem. 1998, 63, 4611-4619.
31. S. Shan, S. Loh, D. Herschlag, Science 1996, 272, 97-101.
32. G. A. Jeffrey, An Introduction to Hydrogen Bonding, Oxford University Press, New York, 1997.
33. a) E. Espinosa, C. Lecomte, E. Molins, Chem. Phys. Lett. 1999, 300, 745-748;
34. b) E. Espinosa, C. Lecomte, E. Molins, Chem. Phys. Lett. 1998, 285, 170-173;
35. c) E. Espinosa, M. Souhassou, H. Lachekar, C. Lecomte, Acta Crystallogr. Sect. B 1999, 55, 563-572.
36. J. J. Danneberg, R. Rios, J. Phys. Chem. 1994, 95, 6714-6718.
37. V. Barone, C. Adamo, J. Chem. Phys. 1996, 105, 11007-11019.
38. T. Steiner, J. Phys. Chem. A 1998, 102, 7041-7052.
39. P. Roversi, M. Barzaghi, F. Merati, R. Destro, Can. J. Chem. 1996, 74, 1145-1161.
40. a) J. Overgaard, B. Schiøtt, F. K. Larsen, A. J. Schultz, J. C. MacDonald, B. B. Iversen, Angew. Chem. 1999, 111, 1321-1324;
41. Angew. Chem. Int. Ed. 1999, 38, 1239-1242;
42. b) G. K. H. Madsen, C. Wilson, T. M. Nymand, G. J. McIntyre, F. K. Larsen, J. Phys. Chem. 1999, 103, 8684-8690.
43. c) P. Macchi, B. B. Iversen, A. Sironi, B. C. Chakoumakos, F. K. Larsen, Angew. Chem. 2000, 112, 2831-2834;
44. Angew. Chem. Int. Ed. 2000, 39, 2719-2722.
45. a) D. Madsen, C. Flensburg, S. Larsen, J. Phys. Chem. A 1998, 102, 2177-2188;
46. b) C. Flensburg, S. Larsen, R. F. Stewart, J. Phys. Chem. 1995, 99, 10130-10141.
47. For N-H⋯O interactions, Gilli and co-workers have recently presented comprehensive structural correlations for resonance-assisted hydrogen bonds: P. Gilli, V. Bertolasi, V. Ferretti, G. Gilli, J. Am. Chem. Soc. 2000, 122, 10405-10417.
48. C. Gatti, R. F. W. Bader, Chem. Phys. Lett. 1998, 287, 233-238.
49. T. Steiner, W. Saenger, Acta Crystallogr. Sect. B 1994, 50, 348-357.
50. M. Würtele, M. Hahn, K. Hilpert, W. Höhne, Acta Crystallogr. Sect. D 2000, 56, 520-523.
51. P. Kuhn, M. Knapp, S. M. Soltis, G. Ganshaw, M. Thoene, R. Bott, Biochemistry 1998, 37, 13446-13452.
52. D. Neidhart, Y. Wei, C. Cassidy, J. Lin, W. W. Cleland, P. A. Frey, Biochemistry 2001, 40, 2439-2447.
53. R. F. W. Bader, Atoms in Molecules: A Quantum Theory, Oxford University Press, Oxford, 1990.
54. Y. Abramov, Acta Crystallogr. Sect. A 1997, 53, 264-272.
55. F. W. Biegler-König, R. F. W. Bader, T. -H. Tang, J. Comput. Chem. 1982, 3, 317-328.
56. a) M. Souhassou, C. Lecomte, R. H. Blessing, A. Aubry, M. M. Rohmer, R. Wiest, M. Benard, M. Marraud, Acta Crystallogr. Sect. B 1991, 47, 253-266;
57. b) M. Souhassou, C. Lecomte, N. E. Ghermani, M. M. Rohmer, R. Wiest, M. Benard, R. H. Blessing, J. Am. Chem. Soc. 1992, 114, 2371-2382;
58. c) V. Pishon-Pesme, C. Lecomte, H. Lachekar, J. Phys. Chem. 1995, 99, 6242-6250.
59. a) G. S. Chandler, B. N. Figgis, P. A. Reynolds, S. K. Wolff, Chem. Phys. Lett. 1994, 225, 421-426.
60. b) B. B. Iversen, F. K. Larsen, B. Figgis, P. A. Reynolds, Trans. Am. Crystallogr. Assoc. 1995, 31, 1-10.
61. C. Gatti, personal communication.
62. For more comprehensive NMR tables and structural correlations consult for example:a) P. Gilli, V. Bertolasi, V. Ferretti, G. Gilli, J. Am. Chem. Soc. 2000, 122, 10405-10417.
63. b) W. D. Arnold, E. Oldfield, J. Am. Chem. Soc. 2000, 122, 12835-12841.
64. NMR measurements thanks to Dr. J. Skibsted, Instrument Center for Solid-State NMR Spectroscopy, Department of Chemistry, University of Aarhus, Denmark.
65. In transition metal bonding it is well known that coordination bonds may have very different covalent contributions, but this is not an indication of the bond strength. See for example: a) G. Frenking, U. Pidum, J. Chem. Soc. Dalton. Trans. 1997, 1653-1662.
66. b) P. E. M. Siegbahn, J. Phys. Chem. 1993, 97, 9096-9102.
67. c) P. Macchi, A. J. Schultz, F. K. Larsen, B. B. Iversen, J. Phys. Chem. 2001, in press.
68. 1H NMR spectrum of 1 shows a broad maximum at δ = 14.8, which consists of the signals for all three short N-H⋯O HB's. Thus the environment around H3A in 1 is different from the corresponding hydrogen in the catalytic triad in its activated state. a) T. -C. Liang, R. H. Abeles, Biochemistry 1987, 26, 7603-7608;
69. b) G. Robillard, R. G. Shulman, J. Mol. Biol. 1972, 72, 507-511.
70. A. J. Schultz, K. Srinivasan, R. G. Teller, J. M. Williams, C. M. Lukehart, J. Am. Chem. Soc. 1984, 106, 999-1003.
71. a) A. J. Schultz, P. C. W. Leung, J. Phys Colloq. 1986, 5, 137-142;
72. b) A. J. Schultz, Trans. Am. Crystallogr. Assoc. 1987, 23, 61-69.
73. M. Lehmann, F. K. Larsen, Acta Crystallogr. Sect. A 1974, 30, 580-584.
74. V. F. Sears, Neutron News 1992, 3, 26-37.
75. J. A. K. Howard, O. Johnson, A. J. Schultz, A. M. Stringer, J. Appl. Crystallogr. 1987, 20, 120-122.
76. A. Darovsky, R. Bolotovsky, P. Coppens, J. Appl. Crystallogr. 1994, 27, 1039-1040.
77. Z. Otwinowski, Oscillation Data Reduction Program, in Data Collection and Processing, Proceedings of the CCP4 Study Weekend, Jan 29-30, 1993.
78. R. Bolotovsky, M. White, A. Darovsky, P. Coppens, J. Appl. Crystallogr. 1995, 28, 86-95.
79. J. Zalelski, G. Wu, P. Coppens, J. Appl. Crystallogr. 1998, 31, 302-304.
80. R. H. Blessing, J. Appl. Crystallogr. 1989, 22, 396-397.
81. P. Coppens, Program DATAP, Chemistry Department, state University of New York at Buffalo, Buffalo, New York 14260-3000, (USA).
82. M. J. Frisch, G. W. Trucks, H. B. Schlegel, P. M. W. Gill, B. G. Johnson, M. A. Robb, J. R. Cheeseman, T. A Keith, G. A. Peterson, J. A. Montgomery, K. Raghavachari, M. A. Al-Laham, V. G. Zakrzewski, J. V. Ortiz, J. B. Foresman, J. Cioslowski, B. B. Stefanov, A. Nanayakkara, M. Challacombe, C. Y. Peng, P. Y. Ayala, W. Chen, M. W. Wong, J. L. Andres, E. S. Repogle, R. Gomperts, R. L. Martin, D. J. Fox, J. S. Binkley, D. J. Defrees, J. Baker, J. J. P. Stewart, M. Head-Gordon, C. Gonzalez, J. A. Pople, Gaussian 94, Revision B.2 Gaussian, Pittsburg, PA, 1995.
83. J. C. MacDonald, unpublished results.
84. B. B. Iversen, F. K. Larsen, A. A. Pinkerton, A. Martin, A. Darovsky, P. A. Reynolds, Acta Crystallogr. Sect. B 1999, 55, 363-374.
85. N. K. Hansen, P. Coppens, Acta Crystallogr. Sect. A 1978, 34, 909-921.
86. T. Koritszansky, S. T. Howard, P. R. Mallinson, Z. Su, T. Richter, N. K. Hansen, XD, a Computer Program Package for Multipole Refinement and Analysis of Charge Densities from X-ray Diffraction Data, Freie Universität Berlin, 1999.
87. A. El Haouzi, N. K. Hansen, C. Le Hénaff, J. Protas, Acta Crystallogr. Sect. A 1996, 52, 291-301.
88. B. B. Iversen, F. K. Larsen, B. N. Figgis, P. A. Reynolds, A. J. Schultz, Acta Crystallogr. Sect. A 1996, 52, 923-931.
89. a) B. N. Figgis, B. B. Iversen, F. K. Larsen, P. A. Reynolds, Acta Crystallogr. Sect B 1993, 49, 794-806;
90. b) B. B. Iversen, F. K. Larsen, B. N. Figgis, P. A. Reynolds, J. Chem. Soc. Dalton Trans. 1997, 2227-2240.