Factors Governing the Protonation State of Zn-Bound Histidine in Proteins: A DFT/CDM Study

Journal of the American Chemical Society

Volumn 126, Issue 8, 2004, Pages 2602-2612

  Lin, Yen Lin ^a   Lim, Carmay ^a,b  

^a INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

^b NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; COMPLEXATION; DIELECTRIC MATERIALS; OXYGEN; POSITIVE IONS; PROTONS; QUANTUM THEORY; SOLVENTS; ZINC;

DEPROTONATION; PROTONATION;

PROTEINS;

ASPARTIC ACID; CARBONYL DERIVATIVE; CARBOXYLIC ACID; GLUTAMIC ACID; HISTIDINE; LIGAND; SOLVENT; ZINC; ZINC COMPLEX;

ARTICLE; BINDING SITE; CATALYSIS; DENSITY FUNCTIONAL THEORY; DIELECTRIC CONSTANT; ENERGY; METAL BINDING; MOLECULAR STABILITY; PROTEIN ANALYSIS; PROTON TRANSPORT; QUANTUM MECHANICS;

BINDING SITES; HISTIDINE; LIGANDS; METALLOPROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTONS; SOLUTIONS; THERMODYNAMICS; ZINC;

EID: 1542306884     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja038827r     Document Type: Article

References (79)

1. Christianson, D. W. Adv. Protein Chem. 1991, 42, 281.
2. Coleman, J. E. Annu. Rev. Biochem. 1992, 61, 897.
3. Alberts, I. L.; Nadassy, K.; Wodak, S. J. Protein Sci. 1998, 7, 1700.
4. Christianson, D. W.; Alexander, R. S. J. Am. Chem. Soc. 1989, 111, 6412.
5. Cox, E. H.; Hunt, J. A.; Compher, K. M.; Fierke, C. A.; Christianson, D. W. Biochemistry 2000, 39, 13687.
6. Gockel, P.; Vahrenkamp, H. Chem. Ber. 1996, 129, 1243.
7. Gockel, P.; Vahrenkamp, H.; Zuberbuhler, A. D. Helv. Chim. Acta 1993, 76, 511.
8. Ian, L. A.; Katalin, N.; Shoshana, J. W. Protein Sci. 1998, 7, 1700.
9. Ippolito, J. A.; Baird, T. T.; McGee, S. A.; Christianson, D. W.; Fierke, C. A. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 5017.
10. Karlin, S.; Zhu, Z.-Y.; Karlin, K. D. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 14225.
11. Karlin, S.; Zhu, Z.-Y. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 14231.
12. Kiefer, L. L.; Paterno, S. A.; Fierke, C. A. J. Am. Chem. Soc. 1995, 117, 6831.
13. Laity, J. H.; Lee, B. M.; Wright, P. E. Curr. Opin. Struct. Biol. 2001, 11, 39.
14. McCall, K. A.; Huang, C.-C.; Fierke, C. A. J. Nulr. 2000, 130, 1437S.
15. Predki, P. F.; Sarkar, B. J. Biol. Chem. 1992, 267, 5842.
16. Schwabe, J. W. R.; Klug, A. Nat. Struct. Biol. 1994, 1, 345.
17. Vallee, B. L.; Auld, D. S. Biochemistry 1990, 29, 5647.
18. Abola, E. E.; Sussman, J. L.; Prilusky, J.; Manning, N. O. Protein Data Bank Archives of Three-Dimensional Macromolecular Structures; Academic Press: San Diego, 1997; Vol. 277.
19. Dudev, T.; Lin, Y. L.: Dudev, M.; Lim, C. J. Am. Chem. Soc. 2003, 125, 3168.
20. Hakansson, K.; Carlsson, M.; Svensson, L. A.; Liljas, A. J. Mol. Biol. 1992, 227, 1192.
21. Teplyakov, A.; Wilson, K. S.; Orioli, P.; Mangani, S. Acta Crystallogr.. Sect. D: Biol. Crystallogr. 1993, 49, 534.
22. Cho, H.; Ramaswamy, S.; Plapp, B. V. Biochemistry 1997, 36, 382.
23. Nakagawa, S.; Umeyama, H.; Kitaura, K.; Morokuma, K. Chem. Pharm. Bull. (Tokyo) 1981, 29, 1.
24. El Yazal, J.; Roe, R. R.; Pang, Y.-P. J. Phys. Chem. B 2000, 104, 6662.
25. Liljas, A.: Rossmann, M. G. Annu. Rev. Biochem. 1974, 3, 475.
26. Kester, W. R.; Matthews, B. W. J. Biol. Chem. 1977, 252, 7704.
27. Argos, P.; Garavito, R. M.; Eventoff, W.; Rossmann, M. G.; Branden, C. I. J. Mol. Biol. 1978, 126, 141.
28. Kiefer, L. L.; Krebs, J. F.; Paterno, S. A.; Fierke, C. A. Biochemistry 1993, 32, 9896.
29. Banci, L.; Bertini, I.; Cabelli, D. E.; Hallewell, R. A.; Tung, J. W.; Viezzoli, M. S. Eur. J. Biochem. 1991, 196, 123.
30. Marino, S. F.; Regan, L. Chem. Biol. 1999, 6, 649.
31. Christianson, D. W.; Fierke, C. A. Acc. Chem. Res. 1996, 29, 331.
32. Kiefer, L. L.; Fierke, C. A. Biochemistry 1994, 33, 15233.
33. Lesburg, C. A.; Christianson, D. W. J. Am. Chem. Soc. 1995, 117, 6838.
34. El Yazal, J.; Pang, Y.-P. J. Phys. Chem. B 1999, 103, 8773.
35. Gervasio, F. L.; Schettino, V.; Mangani, S.; Krack, M.; Carloni, P.; Parrinello, M. J. Phys. Chem. B 2003, 107, 6886.
36. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, M. C.; Strain, K. N.; 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.; 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.; Pople, J. A. Gaussian 98, revision A.5; Gaussian, Inc.: Pittsburgh, PA, 1998.
37. Foresman, J. B.; Frisch, E. Exploring Chemistry with Electronic Structure Methods, 2nd ed.; Gaussian, Inc.: Pittsburgh, PA, 1996.
38. Hohenberg, P.; Kohn, W. Phys. Rev. 1964, 136, B864.
39. Kohn, W.; Sham, L. J. Phys. Rev. 1965, 140, A1133.
40. Slater, J. C. Quantum Theory of Molecules and Solids. Vol. 4: The Self-Consistent Field for Molecules and Solids; McGraw-Hill: New York, 1974.
41. Vosko, S. H.; Wilk, L.; Nusair, M. Can. J. Phys. 1980, 58, 1200.
42. Fuentealba, P.; Preuss, H.; Stoll, H.; Szentpaly, L. V. Chem. Phys. Lett. 1989, 89, 418.
43. Szentpaly, L. V.; Fuentealba, P.; Preuss, H.; Stoll, H. Chem. Phys. Lett. 1982, 93, 555.
44. Wong, M. W. Chem. Phys. Lett. 1996, 256, 391.
45. Allen, F. H. Acta Crystallogr., Sect. B 2002, 58, 380.
46. Cohen, B.; Mastropaolo, D.; Potenza, J. A.; Schugar, H. J. Acta Crystallogr., Sect. B 1978, 34, 2859.
47. Becke, A. D. Phys. Rev. 1988, A38, 3098.
48. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. 1988, B37, 785.
49. Miehlich, B.; Savin, A.; Stoll, H.; Preuss, H. Chem. Phys. Lett. 1989, 157, 200.
50. Perdew, J. P. Phys. Rev. B 1986, 33, 8822.
51. Bytheway, I.; Wong, M. W. Chem. Phys. Lett. 1998, 282, 219.
52. Legge, F. S.; Nyberg, G. L.; Peel, J. B. J. Phys. Chem. A 2001, 105, 7905.
53. Dudev, T.; Lim, C. J. Phys. Chem. B 2001, 105, 10709.
54. Rao, C. P.; Dorfman, J. R.; Holm, R. H. Inorg. Chem. 1986, 25, 428.
55. Saebo, S.; Almlof, J. Chem. Phys. Lett. 1989, 154, 83.
56. Frisch, M. J.; Head-Gordon, M.; Pople, J. A. Chem. Phys. Lett. 1990, 166, 275.
57. Head-Gordon, M.; Pople, J. A.; J., F. M. Chem. Phys. Lett. 1988, 153, 503.
58. Head-Gordon, M.; Head-Gordon, T. Chem. Phys. Lett. 1994, 220, 122.
59. Lias, S. G.; Liebman, J. F.; Levin, D. J. Phys. Chem. Ref. Data 1984, 13.
60. Gilson, M. K.; Honig, B. Biopolymers 1986, 25, 2097.
61. Lim, C.; Bashford, D.; Karplus, M. J. Phys. Chem. 1991, 95, 5610.
62. Reed, A. E.; Curtiss, L. A.; Weinhold, F. Chem. Rev. 1988, 88, 899.
63. Wolfenden, R.; Anderson, L.; Gullis, P. M.; Southgate, C. C. B. Biochemistry 1981, 20, 849.
64. Wolfenden, R. Biochemistry 1978, 17, 201.
65. Hine, J.; Mookerjee, P. K. J. Org. Chem. 1975, 40, 287.
66. Pearson, R. G. J. Am. Chem. Soc. 1986, 108, 6109.
67. Bartmess, J. E.; McIver, R. T., Jr. Gas-Phase Ion Chemistry; Academic Press: New York, 1979; Vol. 2.
68. Handbook of Physical Properties of Organic Chemicals; Howard, P. H., Meylan, W. M., Eds.; Lewis Publishers: Boca Raton, FL, 1997.
69. Jencks, W. P.; Regenstein, J. Handbook of Biochemistry and Molecular Biology, 3rd ed.; CRC Press: Cleveland, OH, 1976; Vol. 1.
70. Burgess, M. A. Metal Ions in Solution; Ellis Horwood: Chichester, England, 1978.
71. Richens, D. T. The Chemistry of Aqua Ions; John Wiley & Sons: New York, 1997.
72. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
73. Tissandier, M. D.; Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, M. H. ; Earhart, A. D.; Coe, J. V.; Tuttle, T. R., Jr. J. Phys. Chem. A 1998, 102, 7787.
74. Chao, Y. F.; Deubel, D. V.; Lim, C., in preparation.
75. Silverman, D.; Vincent, S. H. CRC Crit. Rev. Biochem. 1983, 14, 207.
76. Silverman, D. N.; Lindskog, S. Acc. Chem. Res. 1988, 21, 30.
77. Lindskog, S. Carbonic Anhydrase In Zinc Enzymes; Wiley: New York, 1983.
78. Lipscomb, W. N.; Strater, N. Chem. Rev. 1996, 96, 2375.
79. Carver, J. A.; Bradbury, J. H. Biochemistry 1984, 23, 4890.