Possible mechanism of proton transfer through peptide groups in the H-pathway of the bovine cytochrome c oxidase

Journal of the American Chemical Society

Volumn 129, Issue 31, 2007, Pages 9663-9673

  Kamiya, Katsumasa ^a,b   Boero, Mauro ^a,b   Tateno, Masaru ^a,b   Shiraishi, Kenji ^a,b   Oshiyama, Atsushi ^a,b  

^a UNIVERSITY OF TSUKUBA   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; ENZYMES; HYDROGEN BONDS; MOLECULAR DYNAMICS; PEPTIDES;

CONFORMATIONAL CHANGES; MOLECULAR DYNAMICS SIMULATIONS; PROTON-TRANSFER PATHWAY;

PROTON TRANSFER;

AMIDE; ASPARTIC ACID; CARBONYL DERIVATIVE; CARBOXYL GROUP; CYTOCHROME C OXIDASE; IMIDE; PEPTIDE; SERINE; TYROSINE;

ARTICLE; CONFORMATIONAL TRANSITION; COW; CRYSTAL STRUCTURE; DENSITY FUNCTIONAL THEORY; ENZYME MECHANISM; HYDROGEN BOND; ISOMERIZATION; MOLECULAR DYNAMICS; NONHUMAN; PROTON TRANSPORT; SIMULATION;

AMINO ACIDS; ANIMALS; CATTLE; COMPUTER SIMULATION; ELECTRON TRANSPORT COMPLEX IV; ELECTRONS; ISOMERISM; MODELS, MOLECULAR; MUTATION; PEPTIDES; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; PROTONS;

EID: 34547794301     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja070464y     Document Type: Article

References (41)

1. Voet, D.; Voet J. G. Biochemistry, 3rd ed.; John Wiley and Sons: Hoboken, NJ, 2004.
2. Decoursey, T. E. Physiol. Rev. 2003, 83, 476-579.
3. (a) Tsukihara, T.; Shimokata, K.; Katayama, Y.; Shimada, H.; Muramoto, K.; Aoyama, H.; Mochizuki, M.; Shinzawa-Itoh, K.; Yamashita, E.; Yao, M.; Ishimura, Y.; Yoshikawa, S. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 15304-15309.
4. (b) Brookhaven Protein Data Bank, entry number 1V54.
5. Ostermeir, C.; Harrenga, A.; Ermler, U.; Michel, H. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 10547-10553.
6. Svensson-Ek, M.; Abramson, J.; Larsson, G.; Törnroth, S.; Brzezinski, P.; Iwata, S. J. Mol. Biol. 2002, 321, 329-339.
7. Brzezinski, P.; Larsson, G. Biochim. Biophys. Acta 2003, 1605, 1-13.
8. Yoshikawa, S. Adv. Protein Chem. 2002, 60, 341-395.
9. Pomés, R.; Roux, B. J. Phys. Chem. 1996, 100, 2519-2527.
10. Agmon, N. Chem. Phys. Lett. 1995, 244, 456-462.
11. Yoshikawa, S.; Muramoto, K.; Shinzawa-Itoh, K.; Aoyama, H.; Tsukihara, T.; Ogura, T.; Shimokata, K.; Katayama, Y.; Shimada, H. Biochim. Biophys. Acta 2006, 1757, 395-400.
12. Yoshikawa, S.; Muramoto, K.; Shinzawa-Itoh, K.; Aoyama, H.; Tsukihara, T.; Shimokata, K.; Katayama, Y.; Shimada, H. Biochim. Biophys. Acta 2006, 1757, 1110-1116.
13. Shimokata, K.; Katayama, Y.; Murayama, H.; Muramoto, K.; Suematsu, M.; Tsukihara, T.; Muramoto, K.; Aoyama, H.; Yoshikawa, S.; Shimada. H. Proc. Nat. Acad. Sci. U.S.A. 2007, 104, 4200-4205.
14. Hohenberg, P.; Kohn, W. Phys. Rev. 1964, 136, B864-B871.
15. Kohn, W.; Sham, L. J. Phys. Rev. 1965, 140, A1133-A1138.
16. Barone, V.; Adamo, C. J. Chem. Phys. 1996, 105, 11007-11019.
17. Sadhukhan, S.; Muñoz, D.; Adamo, C.; Scuseria, G. E. Chem. Phys. Lett. 1999, 306, 83-87.
18. Aplincourt, P.; Bureau, C.; Anthoine, J-L.; Chong, D. P. J. Phys. Chem. A 2001, 105, 7364-7370.
19. Boero, M.; Terakura, K.; Tateno, M. J. Am. Chem. Soc. 2002, 124, 8949-8957.
20. Boero, M.; Ikeshoji, T.; Liew, C. C.; Terakura, K.; Parrinello, M. J. Am. Chem. Soc. 2004, 126, 6280-6286.
21. Boero, M.; Tateno, M.; Terakura, K.; Oshiyama, A. J. Chem. Theory Comput. 2005, 1, 925-934.
22. Iannuzzi, M.; Laio, A.; Parrinello, M. Phys. Rev. Lett. 2003, 90, 238302.
23. Laio, A.; Rodriguez-Fortea, A.; Gervasio, F. L.; Ceccarelli, M.; Parrinello, M. J. Phys. Chem. B 2005, 109, 6714-6721.
24. Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471-2474.
25. Gervasio, F. L.; Boero, M.; Parrinello, M. Angew. Chem., Int. Ed. 2006, 45, 5606-5609.
26. Boero, M.; Ikeda, T.; Ito, E.; Terakura, K. J. Am. Chem. Soc. 2006, 128, 16798-16807.
27. Perrin, C. L.; Lollo, C. P.; Johnston. E. R. J. Am. Chem. Soc. 1984, 106, 2749-2753.
28. Kamiya, K.; Boero, M.; Shiraishi, K.; Oshiyama, A. J. Phys. Chem. B 2006, 110, 4443-4450.
29. Miteva, M. A.; Tufféry, P.; Villoutreix, B. O. Nucleic Acid Res. 2005, 33, W372-W375 (http://bioserv.rpbs.jussieu.fr/PCE). Since a maximum of 50 residues can be treated, we had to extract a subsystem from the whole CcO not exceeding this limit.
30. Makov, G. and Payne, M. C. Phys. Rev. B 1995, 51, 4014-4022.
31. CPMD, Copyright IBM Corp., 1990-2006; Copyright MPI für Festkörperforschung Stuttgart, 1997-2001.
32. Hamprecht, F. A.; Cohen, A. J.; Tozer, D. J.; Handy, N. C. J. Chem. Phys. 1998, 109, 6264-6271.
33. Troullier, N.; Martins, J. L. Phys. Rev. B 1991, 43, 1993-2006.
34. Grossman, J. C.; Schwegeler, E.; Draeger, E. W.; Gygi, F.; Galli, G. J. Chem. Phys. 2004, 120, 300-311.
35. Schwegeler, E.; Grossman, J. C.; Gygi, F.; Galli, G. J. Chem. Phys. 2004, 121, 5400-5409.
36. Boero, M.; Ikeshoji, T.; Terakura, K. ChemPhysChem 2005, 6, 1775-1779.
37. Schemer, S. J. Am. Chem. Soc. 1981, 103, 315-320.
38. Kollman, P. Chem. Rev. 1993, 93, 2395-2417.
39. Takano, Y.; Nakamura, H. Chem. Phys. Lett. 2006, 430, 149-155.
40. Marx, D.; Tuckerman, M. E.; Hutter, J.; Parrinello, M. Nature 1999, 397, 601-604.
41. Abramson, J.; Svensson-Ek, M.; Byrne, B.; Iwata, S. Biochim. Biophys. Acta 2001, 1544, 1-9.