Structure, protonation state and dynamics of catalase compound II

ChemPhysChem

Volumn 6, Issue 9, 2005, Pages 1820-1826

  Rovira, Carme ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

Catalase; Density functional calculations; Molecular dynamics; Proteins; Protonation

Indexed keywords

CRYSTAL STRUCTURE; DENSITY FUNCTIONAL THEORY; MOLECULAR DYNAMICS; PROTEINS; PROTONATION; REACTION INTERMEDIATES; REACTION KINETICS;

ACTIVE CENTER; BINDING POCKETS; CATALASE; CATALYTIC RESIDUE; HIGH RESOLUTION CRYSTAL STRUCTURE; MOLECULAR DYNAMICS SIMULATIONS; PROTONATION STATE; REACTION CYCLES;

IRON COMPOUNDS;

EID: 24944559223     PISSN: 14394235     EISSN: None     Source Type: Journal    
DOI: 10.1002/cphc.200400633     Document Type: Article

References (37)

1. P. Chelikani, I. Fita, P. C. Loewen, Cell. Mol. Life Sci. 2004, 61, 192-208.
2. I. Fita, M. G. Rossmann, J. Mol. Biol. 1985, 185, 21-37.
3. P. Nichols, I. Fita, P. C. Loewen, Adv. Inorg. Chem. 2001, 51, 51-106.
4. M. J. Maté, G. Murshudov, J. Bravo, W. Melik-Adamyan, P. C. Loewen, I. Fita in The Handbook of Metalloproteins (Eds.: A. Messerschmidt, R. Huber, T. Poulos), John Wiley & Sons, Chichester, 2001, pp. 486-502.
5. A. Ivancich, H. M. Jouve, J. Gaillard, Biochemistry 1997, 36, 9356-9364.
6. G. N. Murshudov, J. A. Grebenko, J. A. Branningan, A. A. Antson, V. V. Barynin, G. G. Dodson, Z. Dauter, K. Wilson, W. R. Melik-Adamyan, Acta Crystallogr. D, 2002, 58, 1972-1982.
7. G. N. Murshudov, W. R. Melik-Adamyan, Al Grebenko, V. V. Barynin, A. A. Vagin, B. K. Vainshtein, Z. Dauter, K. S. Wilson, unpublished results.
8. C. Rovira, I. Fita, J. Phys. Chem. B 2003, 107, 5300-5305.
9. P. Rydberg, E. Sigfridsson, U. Ryde, J. Biol. Inorg. Chem. 2004, 9, 203-223.
10. H.-P. Hersleth, B. Dalhus, C. H. Görbitz, K. K. Andersson, J. Biol. Inorg. Chem. 2002, 7, 299-304.
11. K. Nilsson, H.-P. Hersleth, T. H. Rod, K. K. Andersson, U. Ryde, Biophys. J. 2004, 87, 3437-3447.
12. M. T. Green, J. H. Dawson, H. Gray, Science 2004, 304, 1653-1656.
13. G. I. Berglund, G. H. Carlsson, A. T. Smith, H. Szöke, A. Henriksen, J. Hajdu, Nature 2002, 417, 463-468.
14. a) Y. Hayashi, I. Yamazaki, Arch. Biochem. Biophys. 1978, 190, 446-453;
15. b) Y. Hayashi, I. Yamazaki, J. Biol. Chem. 1979, 254, 9101-9106;
16. c) H. B. Dunford, Heme Peroxidases, Wiley-VCH, New York, 1999, p. 82;
17. d) A. J. Sitter, C. M. Reczek, J. Terner, J. Biol. Chem. 1985, 260, 7515-7522.
18. C. Rovira, unpublished results.
19. R. Car, M. Parrinello, Phys. Rev. Lett. 1985, 55, 2471-2474.
20. CPMD program, Copyright IBM Corp. 1990-2003, Copyright MPI für Festkörperforschung, Stuttgart 1997-2001; http://www.cpmd.org.
21. D. Marx, J. Hutter in Modern Methods and Algorithms of Quantum Chemistry (Ed.: J. Grotendorst), John von Neumann Institute for Computing, Jülich, Germany, 2000, pp. 301-409.
22. C. Rovira, K. Kunc, J. Hutter, P. Ballone, M. Parrinello, J. Phys. Chem. A 1997, 101, 8914-8925.
23. C. Rovira, J. Hutter, K. Kunc, M. Parrinello, Inorg. Chem. 2001, 40, 11-17.
24. M. Troullier, J. L. Martins, Phys. Rev. B 1991, 43, 1993-2006.
25. S. G. Louie, S. Froyen, M. L. Cohen, Phys. Rev. B 1982, 26, 1738-1742.
26. a) A. D. Becke, J. Chem. Phys. 1986, 84, 4524-4529;
27. b) J. P. Perdew, Phys. Rev. B 1986, 33, 8822-8824.
28. a) B. Delley, Physica B 1991, 172, 185;
29. b) N. Matsuzawa, M. Ata, D. A. Dixon, J. Phys. Chem. 1995, 99, 7698.
30. M.-S. Liao, S. Scheiner, J. Chem. Phys. 2002, 116, 3635-3645.
31. D. A. Scherlis, D. A. Estrin, Int. J. Quant. Chem. 2002, 87, 158-166.
32. W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graphics 1996, 14, 33-38.
33. W.-J. Chuang, J. Heldt, H. E. Van Wart, J. Biol. Chem. 1989, 264, 14 209-14 215.
34. P. E. Blöchl, Phys. Rev. B 1994, 50, 17 953-17 979.
35. P. Tangney, S. Scandolo, J. Chem. Phys. 2002, 116, 14-24.
36. FeO calculated using an electronic mass of 700 au. in the CP simulation should be rescaled by a factor of 1.13.
37. E. Baciocchi, O. Lanzalunga, S. Malandrucco, M. loele, S. Steeken, J. Am. Chem. Soc. 1996, 118, 8973-8974.