The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations

Journal of Computational Chemistry

Volumn 27, Issue 12, 2006, Pages 1398-1414

  Rulíšek, Lubomír ^a   Jensen, Kasper P ^b   Lundgren, Kristoffer ^b   Ryde, Ulf ^b  

^a INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY   (Czech Republic)

^b LUND UNIVERSITY   (Sweden)

Author keywords

Iron; Manganese; Reaction mechanisms; Superoxide dismutase

Indexed keywords

DISSOCIATION; IRON COMPOUNDS; MANGANESE COMPOUNDS; OXIDATION; PROBABILITY DENSITY FUNCTION; REACTION KINETICS; REDUCTION;

ASSOCIATIVE MECHANISMS; PROTONATION; SOLVATION; SUPEROXIDE DISMUTASE;

ORGANOMETALLICS;

SUPEROXIDE DISMUTASE;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METABOLISM; PROTEIN CONFORMATION;

BINDING SITES; COMPUTER SIMULATION; MODELS, MOLECULAR; PROTEIN CONFORMATION; SUPEROXIDE DISMUTASE;

EID: 33747201345     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20450     Document Type: Article

References (87)

1. Fridovich, I. Annu Rev Biochem 1995, 64, 97.
2. Sallings, W. C.; Pattridge, K. A.; Strong, R. K.; Ludwig, M. L. J Biol Chem 1984, 259, 10695.
3. Miller, A.-F. In Handbook of Metalloproteins; Messerschmidt, A.; Huber, R.; Wieghardt, K.; Poulos, T., Eds.; John Wiley & Sons: Chichester, 2001, p. 668.
4. Stroupe, M. E.; DiDonato, M.; Tainer, J. A. In Handbook of Metalloproteins; Messerschmidt, A.; Huber, R.; Wieghardt, K.; Poulos, T., Eds.; John Wiley & Sons: Chichester, 2001, p. 941.
5. Bordo, D.; Pesce, A.; Bolognesi, M.; Stroppolo, M. E.; Falconi, M.; Desideri, A. In Handbook of Metalloproteins; Messerschmidt, A.; Huber, R.; Wieghardt, K.; Poulos, T., Eds.; John Wiley & Sons: Chichester, 2001, p. 1284.
6. Lee, J.-W.; Roe, J.-H.; Kang, S.-O. Methods Enzymol 2002, 349, 90.
7. Wuerges, J.; Lee, J.-W.; Yim, Y.-I.; Yim, H.-S.; Kang, S.-O.; Carugo, K. D. Proc Natl Acad Sci USA 2004, 101, 8569.
8. Barondeau, D. P.; Kassmann, C. J.; Bruns, C. K.; Tainer, J. A.; Getzoff, E. D. Biochemistry 2004, 43, 8038.
9. Ullah Khan, A.; Kasha, M. Proc Natl Acad Sci USA 1994, 91, 12365.
10. Miller, A.-F.; Sorkin, D. L. Mol Cell Biophys 1997, 9, 1.
11. Getzoff, E. D.; Tainer, J. A.; Stempien, M. M.; Bell, G. I.; Hallewell, R. A. Proteins Struct Funct Genet 1989, 5, 322.
12. Hassan, H. M.; Fridovich, I. Eur J Rheumatol Infiamm 1981, 4, 160.
13. Steinman, H. M.; Weinstein, L.; Brenowitz, M. J Biol Chem 1994, 269, 28629.
14. Chance, B.; Sies, H.; Boveris, A. Physiol Rev 1979, 59, 527.
15. Hopkin, K. A.; Papazian, M. A.; Steinman, H. M. J Biol Chem 1992, 267, 24253.
16. Bull, C.; Niederhoffer, E. C.; Yoshida, T.; Fee, J. A. J Am Chem Soc 1991, 113, 4069.
17. Riley, D. P. Chem Rev 1999, 99, 2573.
18. Sayre, L. M.; Perry, G.; Smith, M. A. Curr Opin Chem Biol 1999, 3, 220.
19. McCord, J. M. Methods Enzymol 2002, 349, 331.
20. Hsu, J. L.; Hsieh, Y.; Tu, C.; O'Connor, D.; Nick, H. S.; Silverman, A. N. J Biol Chem 1996, 271, 17687.
21. Vance, C. K.; Miller, A.-F. J Am Chem Soc 11998, 20, 461.
22. Anderson, B. F.; Edwards, R. A.; Whittaker, M. M.; Whittaker, J. W.; Baker, E. N.; Jameson, G. B., to appear.
23. Lah, M. S. Biochemistry 1995, 34, 1646.
24. Kerfeld, C. A. J Biol Inorg Chem 2003, 8, 707.
25. Stallings, W. C.; Metzger, A. L.; Pattridge, K. A.; Fee, J. A.; Ludwig, M. L. Free Radic Res Commun 1991, 12-13, 259.
26. Han, W.-G.; Lovell, T.; Noodleman, L. Inorg Chem 2002, 41, 205.
27. Hunter, T.; Ikebukuro, K.; Bannister, W. H.; Bannister, J. V.; Hunter, G. J. Biochemistry 1997, 36, 4925.
28. Jackson, T. A.; Brunold, T. C. Ace Chem Res 2004, 37, 461.
29. Hsieh, Y.; Guan, Y.; Tu, C.; Bratt, P. J.; Angerhofer, A.; Lepock, J. R.; Hickey, M. J.; Tainer, J. A.; Nick, H. S.; Silverman, D. N. Biochemistry 1998, 37, 4731.
30. Yikilmaz, E.; Xie, J.; Brunold, T. C.; Miller, A.-F. J Am Chem Soc 2002, 124, 3482.
31. Miller, A.-F.; Padmakumar, K.; Sorkin, D. L.; Karapetian, A.; Vance, C. K. J Inorg Biochem 2003, 93, 71.
32. Lah, M. S.; Dixon, M. M.; Pattridge, K. A.; Stallings, W. C.; Fee, J. A.; Ludwig, M. L. Biochemistry 1995, 34, 1646.
33. Jackson, T. A.; Yikilmaz, E.; Miller, A.-F.; Brunold, T. C. J Am Chem Soc 2003, 125, 8348.
34. Whittaker. J. W.; Whittaker. M. M. J Am Chem Soc 1991, 113, 5528.
35. Whittaker, J. W.; Solomon, E. I. J Am Chem Soc 1988, 110, 5329.
36. Vatyam, S.; Byrd, R. A.; Miller, A.-F. Magn Reson Chem 2000, 38, 536.
37. Miller, A.-F.; Sorkin, D. L.; Padmakumar, K. Biochemistry 2005, 44, 5969.
38. Whittaker, M. M.; Whittaker, J. W. Biochemistry 1996, 35, 6762.
39. Whittaker, M. M.; Whittaker, J. W. J Biol Inorg Chem 1997, 2, 667.
40. Jackson, T. A.; Karapetian, A.; Miller, A.-F.; Brunold, T. C. J Am Chem Soc 2004, 126, 12477.
41. Sines, J.; Alison, S; Wierzbicki, A.; McCammon, J. A. J Phys Chem 1990, 94, 959.
42. Whittaker, M. M.; Ekberg, C. A.; Edwards, R. A.; Baker, E. N.; Jameson, G. B.; Whittaker, J. W. J Phys Chem B 1998, 102, 4668.
43. Yikilmaz, E.; Xie, J.; Brunold, T. C.; Miller, A.-F. J Am Chem Soc 2002, 124, 3482.
44. Xie, J.; Yikilmaz, E.; Miller, A.-F.; Brunold, T. C. J Am Chem Soc 2002, 124, 3769.
45. Jackson, T. A.; Xie, J.; Yikilmaz, E.; Miller, A.-F.; Brunold, T. C. J Am Chem Soc 2002, 124, 10833.
46. Fisher, C. L.; Chen, J.-L.; Li, J.; Bashford, D.; Noodleman, L. J Phys Chem 11996, 00, 13498.
47. Li, J.; Fisher, C. L.; Konecny, R.; Bashford, D.; Noodleman, L. Inorg Chem 1999, 38, 929.
48. Treutler, O.; Ahlrichs, R. J Chem Phys 1995, 102, 346.
49. Becke, A. D. Phys Rev A 1988, 38, 3098.
50. Perdew, J. P. Phys Rev B 1986, 33, 8822.
51. Schäfer, A.; Horn, H.; Ahlrichs, R. J Chem Phys 1992, 97, 2571.
52. Schäfer, A.; Huber, C.; Ahlrichs, R. J Chem Phys 1994, 100, 5829.
53. Hehre, W. J.; Radom, L.; Schleyer, P. v. R.; Pople, J. A. In Ab Initio Molecular Orbital Theory; Wiley-Interscience: New York, 1986.
54. Eichkorn, K.; Treutier, O.; Öhm, H.; Häser, M.; Ahlrichs, R. Chem Phys Lett 1995, 240, 283.
55. Eichkorn, K.; Weigend, F.; Treutler, O.; Ahlrichs, R. Theor Chem Acc 1997, 97, 119.
56. Hertwig, R. H.; Koch, W. Chem Phys Lett 1997, 268, 345.
57. Jensen, F. Introduction to Computational Chemistry; John Wiley & Sons: New York, 1999.
58. Amzel, L. M. Proteins Struct Funct Genet 1997, 28, 144.
59. Bauschlicher, C. W. Chem Phys Lett 1995, 246, 40.
60. Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Pople, J. A. J Chem Phys 1997, 106, 1063.
61. Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Pople, J. A. J Chem Phys 2000, 112, 7374.
62. Siegbahn, P. E. M.; Blomberg, M. R. A. Annu Rev Phys Chem 1999, 50 221.
63. Siegbahn, P. E. M.; Blomberg, M. R. A. Chem Rev 2000, 100, 421.
64. Peterson, J.; Fee, J. A.; Day, E. P. Biochim Biophys Acta 1991, 113, 5528.
65. Klamt, A.; Schuurmann, G. J Chem Soc Perkin Trans 2 1993, 799.
66. Schäfer, A.; Klamt, A.; Sattel, D.; Lohrenz, J. C. W.; Eckert, F. Phys Chem Chem Phys 2000, 2, 2187.
67. Sharp, K. A. Annu Rev Biophys Biophys Chem 1990, 19, 301.
68. Honig, B. Science 1995, 268, 1144.
69. Klamt, A.; Jonas, V.; Bürger, T.; Lohrenz, J. C. W. J Phys Chem 1998, 102, 5074.
70. Reiss, H.; Heller, A. J Phys Chem 1985, 89, 4207.
71. Scheidt, W. R.; Reedk, C. A. Chem Rev 1981, 81, 543.
72. Siegbahn, P. E. M. Curr Opin Chem Biol 2002, 6, 227.
73. Sigfridsson, E.; Olsson, M. H. M.; Ryde, U. J Phys Chem B 2001, 105, 5546.
74. Olsson, M. H. M.; Ryde, U. J. Am Chem Soc 2001, 123, 7866.
75. Ryde, U.; Nilsson, K. J Am Chem Soc 2003, 125, 14232.
76. Wilmot, C. M.; Sjögren, T.; Carlsson, G. H.; Berglund, G. I.; Hajdu, J. Methods Enzymol 2002, 353, 301.
77. Rulisek, L.; Ryde, U. J Inorg Biochem, J Phys Chem B, in press.
78. Fields, B. A.; Bartsch, H. H.; Bartunik, H. D.; Cordes, F.; Guss, J. M.; Freeman, H. C. Acta Crystallogr D 1994, 50, 709.
79. Cruickshank, D. W. J. Acta Crystallogr D 1999, 55, 583.
80. Nilsson, K.; Lecerof, D.; Sigfridsson, E.; Ryde, U. Acta Crystallogr D 2003, 59, 274.
81. Nilsson, K.; Ryde, U. J Inorg Biochem 2004, 98, 1539.
82. Holm, R. H.; Kennepohl, P.; Solomon, E. I. Chem Rev 1996, 96, 2239.
83. Ryde, U. Eur J Biophys 1996, 24, 213.
84. Noodleman, L.; Lovell, T.; Han, W.-G.; Li, J.; Himo, F. Chem Rev 2004, 104, 459.
85. Pelmenschikov, V.; Siegbahn, P. E. M. Inorg Chem 2005, 44, 3311.
86. Jensen, K. P.; Ryde, U. J Biol Chem 2004, 279, 14561.
87. Danovich, D.; Shaik, S. J Am Chem Soc 1997, 119, 1773.