The reaction mechanisms of heme catalases: An atomistic view by ab initio molecular dynamics

Archives of Biochemistry and Biophysics

Volumn 525, Issue 2, 2012, Pages 121-130

  Alfonso Prieto, Mercedes ^a   Vidossich, Pietro ^b   Rovira, Carme ^c,d  

^a Temple University   (United States)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^c UNIVERSITY OF BARCELONA   (Spain)

^d INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

Ab initio molecular dynamics; Catalases; Density Functional Theory; Enzyme catalysis; Hydroperoxidases; Peroxidases

Indexed keywords

CATALASE; CYTOCHROME P450; HEME; HYDROGEN; HYDROGEN PEROXIDE; NITRIC OXIDE SYNTHASE; OXYGEN;

AB INITIO CALCULATION; CHEMICAL REACTION; DENSITY FUNCTIONAL THEORY; ENZYME ACTIVITY; HELICOBACTER PYLORI; MICROCOCCUS LUTEUS; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTON TRANSPORT; REVIEW; ULTRAVIOLET SPECTROSCOPY; X RAY CRYSTALLOGRAPHY;

CATALASE; CATALYSIS; ELECTRONS; ENZYMES; HELICOBACTER PYLORI; HEME; HISTIDINE; HYDROGEN PEROXIDE; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; OXIDATION-REDUCTION; OXIDATIVE STRESS; OXYGEN; PEROXIDASE; PROTONS; SINGLET OXYGEN;

EID: 84864609214     PISSN: 00039861     EISSN: 10960384     Source Type: Journal    
DOI: 10.1016/j.abb.2012.04.004     Document Type: Review

References (81)

1. D. S. Goodsell, RCSB Protein Databank (2004-09-01).
2. P. Chelikani, I. Fita, and P.C. Loewen Cell. Mol. Life Sci. 61 2004 192 208
3. A. Díaz, P.C. Loewen, I. Fita, and X. Carpena Arch. Biochem. Biophys. 525 2012 102 110
4. M. Alfonso-Prieto, A. Borovik, X. Carpena, G. Murshudov, W. Melik-Adamyan, I. Fita, C. Rovira, and P.C. Loewen J. Am. Chem. Soc. 129 2007 4193 4205
5. M. Alfonso-Prieto, X. Biarnes, P. Vidossich, and C. Rovira J. Am. Chem. Soc. 131 2009 11751 11761
6. M. Alfonso-Prieto, H. Oberhofer, M.L. Klein, C. Rovira, and J. Blumberger J. Am. Chem. Soc. 133 2011 4285 4298
7. J.T. Groves, R.C. Haushalter, M. Nakamura, T.E. Nemo, and B.J. Evans J. Am. Chem. Soc. 103 1981 2884 2886
8. J.H. Dawson Science 240 1988 433 439
9. A. Messerschmidt, R. Huber, K. Wieghardt, and T. Poulos Handbook of Metalloproteins 2001 Wiley Chichester
10. S.P. de Visser, S. Shaik, P.K. Sharma, D. Kumar, and W. Thiel J. Am. Chem. Soc. 125 2003 15779 15788
11. G.R. Schonbaum, and B. Chance Catalase 1976 Academic Press New York
12. P. Jones, and H.B. Dunford J. Inorg. Biochem. 99 2005 2292 2298
13. R.C. Jarnagin, and J.H. Wang J. Am. Chem. Soc. 80 1958 786 787
14. J. Vlasits, C. Jakopitsch, M. Schwanninger, P. Holubar, and C. Obinger FEBS Lett. 581 2007 320 324
15. T. Matsui, S. Ozaki, E. Liong, G.N. Phillips Jr. , and Y. Watanabe J. Biol. Chem. 274 1999 2838 2844
16. I. F. P. Nichols, P. C. Loewen, in: G. M. A. G. Sykes (Ed.), Advances in Inorganic Chemistry, Academic Press, 2001, pp. 51-106.
17. A. Ivancich, H.M. Jouve, and J. Gaillard J. Am. Chem. Soc. 118 1996 12852 12853
18. T. Spolitak, J.H. Dawson, and D.P. Ballou J. Biol. Inorg. Chem. 13 2008 599 611
19. A.T. Smith, W.A. Doyle, P. Dorlet, and A. Ivancich Proc. Natl. Acad. Sci. U. S. A. 106 2009 16084 16089
20. R. Car, and M. Parrinello Phys. Rev. Lett. 55 1985 2471 2474
21. A. Laio, J. VandeVondele, and U. Rothlisberger J. Chem. Phys. 116 2002 6941 6947
22. A. Laio, and M. Parrinello Proc. Natl. Acad. Sci. USA 99 2002 12562 12566
23. M. Iannuzzi, A. Laio, and M. Parrinello Phys. Rev. Lett. 90 2003 238302
24. P. Vidossich, M. Alfonso-Prieto, X. Carpena, P.C. Loewen, I. Fita, and C. Rovira J. Am. Chem. Soc. 129 2007 13436 13446
25. P. Vidossich, X. Carpena, P.C. Loewen, I. Fita, and C. Rovira J. Phys. Chem. Lett. 2 2011 196 200
26. A. Ivancich, H.M. Jouve, B. Sartor, and J. Gaillard Biochemistry 36 1997 9356 9364
27. M.J. Benecky, J.E. Frew, N. Scowen, P. Jones, and B.M. Hoffman Biochemistry 32 1993 1933 11929 11933
28. M.T. Green J. Am. Chem. Soc. 123 2001 9218 9219
29. P. Rydberg, E. Sigfridsson, and U. Ryde J. Biol. Inorg. Chem. 9 2004 203 223
30. S.P. de Visser Inorg. Chem. 45 2006 9551 9557
31. R.K. Behan, L.M. Hoffart, K.L. Stone, C. Krebs, and M.T. Green J. Am. Chem. Soc. 128 2006 11471 11474
32. E. Derat, S. Cohen, S. Shaik, A. Altun, and W. Thiel J. Am. Chem. Soc. 127 2005 13611 13621
33. S. Shaik, S. Cohen, Y. Wang, H. Chen, D. Kumar, and W. Thiel Chem. Rev. 110 2010 949 1017
34. C.A. Bonagura, B. Bhaskar, H. Shimizu, H. Li, M. Sundaramoorthy, D.E. McRee, D.B. Goodin, and T.L. Poulos Biochemistry 42 2003 5600 5608
35. A. Ivancich, C. Jakopitsch, M. Auer, S. Un, and C. Obinger J. Am. Chem. Soc. 125 2003 14093 14102
36. C. Rovira Chemphyschem 6 2005 1820 1826
37. O. Horner, J.L. Oddou, J.M. Mouesca, and H.M. Jouve J. Inorg. Chem. 100 2006 477 479
38. M.T. Green, J.H. Dawson, and H.B. Gray Science 304 2004 1653 1656
39. H.P. Hersleth, U. Ryde, P. Rydberg, C.H. Gorbitz, and K.K. Andersson J. Inorg. Biochem. 100 2006 460 476
40. G.I. Berglund, G.H. Carlsson, A.T. Smith, H. Szoke, A. Henriksen, and J. Hajdu Nature 417 2002 463 468
41. A. Gumiero, C.L. Metcalfe, A.R. Pearson, E.L. Raven, and P.C. Moody J. Biol. Chem. 286 2011 1260 1268
42. Y.T. Meharenna, T. Doukov, H. Li, S.M. Soltis, and T.L. Poulos Biochemistry 49 2010 2984 2986
43. P. Chelikani, X. Carpena, R. Perez-Luque, L.J. Donald, H.W. Duckworth, J. Switala, I. Fita, and P.C. Loewen Biochemistry 44 2005 5597 5605
44. C. Obinger, M. Maj, P. Nicholls, and P. Loewen Arch. Biochem. Biophys. 342 1997 58 67
45. I. Fita, and M.G. Rossmann J. Mol. Biol. 185 1985 21 37
46. S. Kato, T. Ueno, S. Fukuzumi, and Y. Watanabe J. Biol. Chem. 279 2004 52376 52381
47. A.U. Khan, P. Gebauer, and L.P. Hager Proc. Natl. Acad. Sci. U. S. A. 80 1983 5195 5197
48. C. Jakopitsch, M. Auer, G. Regelsberger, W. Jantschko, P.G. Furtmuller, F. Ruker, and C. Obinger Biochemistry 42 2003 5292 5300
49. F. Lledias, P. Rangel, and W. Hansberg J. Biol. Chem. 273 1998 10630 10637
50. S. Michan, F. Lledias, J.D. Baldwin, D.O. Natvig, and W. Hansberg Free. Radic. Biol. Med. 33 2002 521 532
51. J.R. Kanofsky J. Am. Chem. Soc. 106 1984 4278 4279
52. Alia, P. Mohanty, and J. Matysik Amino Acids 21 2001 195 200
53. W. Adam, D.V. Kazakov, and V.P. Kazakov Chem. Rev. 105 2005 3371 3387
54. P. Jones, and A. Suggett Biochem. J. 110 1968 621 629
55. M. Alfonso-Prieto, P. Vidossich, A. Rodriguez-Fortea, X. Carpena, I. Fita, P.C. Loewen, and C. Rovira J. Phys. Chem. A 112 2008 12842 12848
56. W.M. Latimer The oxidation states of the elements and their potentials in aqueous solutions 1952 Prentice-Hall, Englewood Cliffs N.J.
57. J. Petlicki, T. G. van de Ven, J. Chem Soc., Faraday Trans. 94 (1998) 2763-2767.
58. H. Taube J. Gen. Physiol. 49 Suppl 1965 29 52
59. D.M. Wagnerová Z. Phys. Chem. 215 2001 133 138
60. I.F.P. Nicholls, P.C. Loewen, in: G.M.A.G. Sykes (Ed.), Advances in Inorganic Chemistry, Academic Press, 2001, pp. 51-106.
61. E. Derat, S. Shaik, C. Rovira, P. Vidossich, and M. Alfonso-Prieto J. Am. Chem. Soc. 129 2007 6346 6347
62. E. Derat, and S. Shaik J. Phys. Chem. B 110 2006 10526 10533
63. P. Vidossich, G. Fiorin, M. Alfonso-Prieto, E. Derat, S. Shaik, and C. Rovira J. Phys. Chem. B 114 2010 5161 5169
64. T.L. Poulos, and J. Kraut J. Biol. Chem. 255 1980 8199 8205
65. Y. Watanabe, H. Nakajima, and T. Ueno Acc. Chem. Res. 40 2007 554 562
66. T.L. Poulos J. Biol. Inorg. Chem. 1 1996 356 359
67. O. Horner, J.M. Mouesca, P.L. Solari, M. Orio, J.L. Oddou, P. Bonville, and H.M. Jouve J. Biol. Inorg. Chem. 12 2007 509 525
68. A.J. Fielding, R. Singh, B. Boscolo, P.C. Loewen, E.M. Ghibaudi, and A. Ivancich Biochemistry 47 2008 9781 9792
69. C.D. Putnam, A.S. Arvai, Y. Bourne, and J.A. Tainer J. Mol. Biol. 296 2000 295 309
70. T. Spolitak, J.H. Dawson, and D.P. Ballou J. Inorg. Biochem. 100 2006 2034 2044
71. H. de Groot, O. Auferkamp, T. Bramey, K. de Groot, M. Kirsch, H.G. Korth, F. Petrat, and R. Sustmann Free Radic Res 40 2006 67 74
72. H.N. Kirkman, and G.F. Gaetani Trends Biochem. Sci. 32 2007 44 50
73. A. Ivancich, T.A. Mattioli, and S. Un J. Am. Chem. Soc. 121 1999 5743 5753
74. P. Andreoletti, S. Gambarelli, G. Sainz, V. Stojanoff, C. White, G. Desfonds, J. Gagnon, J. Gaillard, and H.M. Jouve Biochemistry 40 2001 13734 13743
75. W.J. Chuang, and H.E. Vanwart J. Biol. Chem. 267 1992 13293 13301
76. A. Warshel J. Phys. Chem. 86 1982 2218
77. J. Blumberger Phys. Chem. Chem. Phys. 10 2008 5651 5667
78. V. Tipmanee, H. Oberhofer, M. Park, K.S. Kim, and J. Blumberger J. Am. Chem. Soc. 132 2010 17032 17040
79. R.A. Marcus, and N. Sutin Biochim. Biophys. Acta 811 1985 265 322
80. P. Andreoletti, G. Sainz, M. Jaquinod, J. Gagnon, and H.M. Jouve Proteins 50 2003 261 271
81. G.N. Murshudov, A.I. Grebenko, J.A. Brannigan, A.A. Antson, V.V. Barynin, G.G. Dodson, Z. Dauter, K.S. Wilson, and W.R. Melik-Adamyan Acta Crystallogr. D Biol. Crystallogr. 58 2002 1972 1982