Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins

Journal of Synchrotron Radiation

Volumn 17, Issue 1, 2010, Pages 41-52

  Giachini, Lisa ^a   Veronesi, Giulia ^b,c   Francia, Francesco ^b   Venturoli, Giovanni ^b   Boscherini, Federico ^b,c  

^a AUSTRALIAN SYNCHROTRON   (Australia)

^b UNIVERSITY OF BOLOGNA   (Italy)

^c OGG   (France)

Author keywords

Binding motifs; Cytochrome c oxidase; Metalloproteins; Superoxide dismutase; Thermolysin; XAFS; Zinc binding sites

Indexed keywords

BINDING MOTIF; CYTOCHROME C OXIDASE; METALLO-PROTEINS; SUPER OXIDE DISMUTASE; THERMOLYSIN; XAFS; ZINC-BINDING SITES;

AMINO ACIDS; BINDING ENERGY; BIOCHEMISTRY; CRYSTALLOGRAPHY; DATA HANDLING; DENSITY FUNCTIONAL THEORY; MEMBRANE STRUCTURES; METAL ANALYSIS; ORGANIC ACIDS; OXYGEN; PROTEINS; TIN; TITANIUM COMPOUNDS; X RAY SPECTROSCOPY; ZINC;

BINDING SITES;

BIOPOLYMER; METAL; METALLOPROTEIN; ZINC;

ALGORITHM; ARTICLE; BINDING SITE; CHEMISTRY; METHODOLOGY; PROTEIN BINDING; PROTEIN MOTIF; STATISTICAL ANALYSIS; X RAY ABSORPTION SPECTROSCOPY;

ALGORITHMS; AMINO ACID MOTIFS; BINDING SITES; BIOPOLYMERS; DATA INTERPRETATION, STATISTICAL; METALLOPROTEINS; METALS; PROTEIN BINDING; X-RAY ABSORPTION SPECTROSCOPY; ZINC;

EID: 73449121405     PISSN: 09090495     EISSN: 16005775     Source Type: Journal    
DOI: 10.1107/S090904950904919X     Document Type: Article

References (49)

1. Ankudinov, A. L., Ravel, B., Rehr, J. J. & Conradson, S. D. (1998). Phys. Rev. B, 58, 7565-7576.
2. Aoyama, H., Muramoto, K., Shinzawa-Itoh, K., Hirata, K., Yamashita, E., Tsukihara, T., Ogura, T. & Yoshikawa, S. (2009). Proc. Natl. Acad. Sci. USA, 106, 2165-2169.
3. Banci, L., Bertini, I. & Mangani, S. (2005). J. Synchrotron Rad. 12, 94-97.
4. Berry, E. A., Zhang, Z., Bellamy, H. D. & Huang, L. (2000). Biochim. Biophys. Acta, 1459, 440-448.
5. Binsted, N., Strange, R. W. & Hasnain, S. S. (1992). Biochemistry, 31, 12117-12125.
6. Castagnetto, J. M., Hennessy, S. W., Roberts, V. A., Getzoff, E. D., Tainer, J. A. & Pique, M. E. (2002). Nucl. Acids Res. 30, 379-382.
7. Cheung, K.-C., Strange, R. W. & Hasnain, S. S. (2000). Acta Cryst. D56, 697-704.
8. Ciatto, G., d'Acapito, F., Boscherini, F. & Mobilio, S. (2004). J. Synchrotron Rad. 11, 278-283.
9. Clark-Baldwin, K., Tierney, D. L., Govindaswamy, N., Gruff, E. S., Kim, C., Berg, J., Koch, S. A. & Penner-Hahn, J. E. (1998). J. Am. Chem. Soc. 120, 8401-8409.
10. Co, M. S., Scott, R. A. & Hodgson, K. O. (1981). J. Am. Chem. Soc. 103, 986-988.
11. Dau, H., Liebisch, P. & Haumann, M. (2005). Phys. Scr. T115, 844-846.
12. Dimakis, N. & Bunker, G. (2004). Phys. Rev. B, 70, 195114.
13. Dimakis, N. & Bunker, G. (2006). Biophys. J. 91, L87-L89.
14. Engh, R. A. & Huber, R. (1991). Acta Cryst. A47, 392-400.
15. Errede, B., Kamen, M. O. & Hatefi, Y. (1978). Methods Enzymol. 53, 40-47.
16. Feiters, M. C., Eijkelenboom, A. P. A. M., Nolting, H.-F., Krebs, B., van den Ent, F. M. I., Plasterk, R. H. A., Kaptein, R. & Boelens, R. (2003). J. Synchrotron Rad. 10, 86-95.
17. Francia, F., Giachini, L., Boscherini, F., Venturoli, G., Capitanio, G., Martino, P. L. & Papa, S. (2007). FEBS Lett. 581, 611-616.
18. Giachini, L., Francia, F., Boscherini, F., Pacelli, C., Cocco, T., Papa, S. & Venturoli, G. (2007). FEBS Lett. 581, 5645-5648.
19. Giachini, L., Francia, F., Mallardi, A., Palazzo, G., Carpene, E., Boscherini, F. & Venturoli, G. (2005). Biophys. J. 88, 2038-2046.
20. Giachini, L., Francia, F., Veronesi, G., Lee, D. W., Daldal, F., Huang, L. S., Berry, E. A., Cocco, T., Papa, S., Boscherini, F. & Venturoli, G. (2007). Biophys. J. 93, 2934-2935.
21. Harding, M. M. (1999). Acta Cryst. D55, 1432-1443.
22. Harding, M. M. (2000). Acta Cryst. D56, 857-867.
23. Harding, M. M. (2002). Acta Cryst. D58, 872-874.
24. Harding, M. M. (2004). Acta Cryst. D60, 849-859.
25. Harding, M. M. (2006). Acta Cryst. D62, 678-682.
26. Hasnain, S. S. (2004). J. Synchrotron Rad. 11, 7-11.
27. Hasnain, S. S. & Hodgson, K. O. (1999). J. Synchrotron Rad. 6, 852-864.
28. Hasnain, S. S. & Strange, R. W. (2003). J. Synchrotron Rad. 10, 9-15.
29. Hough, M. A. & Hasnain, S. S. (1999). J. Mol Biol. 287, 579-692.
30. Hsin, K., Sheng, Y., Harding, M. M., Taylor, P. & Walkinshaw, M. D. (2008). J. Appl. Cryst. 41, 963-968.
31. Joly, Y. (2001). Phys. Rev. B, 63, 125120.
32. Joly, Y. (2003). J. Synchrotron Rad. 10, 58-63.
33. Kelly, S. D., Kenner, K. M., Fryxell, G. E., Liu, J., Mattigod, S. V. & Ferris, K. F. (2001). J. Phys. Chem. B, 105, 6337-6346.
34. Levina, A., Armstrong, R. S. & Lay, P. A. (2005). Coord. Chem. Rev. 249, 141-160.
35. Matsubara, H. (1970). Methods Enzymol. 19, 642-651.
36. Matthews, B. W., Jansonius, J. N., Colman, P. M., Titani, K., Walsh, K. A. & Neurath, H. (1972). Nat. New Biol. 238, 37-41.
37. Mijovilovich, A. &Meyer-Klaucke,W. (2003). J. Synchrotron Rad. 10, 64-68.
38. Muramoto, K., Hirata, K., Shinzawa-Itoh, K., Yoko-o, S., Yamashita, E., Aoyama, H., Tsukihara, T. & Yoshikawa, S. (2007). Proc. Natl. Acad. Sci. USA, 104, 7881-7886.
39. Newville, M., Ravel, B., Haskel, D., Rehr, J. J., Stern, E. A. & Yacoby, Y. (1995). Physica B, 208-209, 154-155.
40. Pascarelli, S., Boscherini, F., D'Acapito, F., Hrdy, J., Meneghini, C. & Mobilio, S. (1996). J. Synchrotron Rad. 3, 147-155.
41. Peariso, K., Huffman, D. L., Penner-Hahn, J. E. & O'Halloran, T. V. (2003). J. Am. Chem. Soc. 125, 342-343.
42. Ravel, B. & Newville, M. (2005). J. Synchrotron Rad. 12, 537-541.
43. Shinzawa-Itoh, K., Aoyama, H., Muramoto, K., Terada, H., Kurauchi, T., Tadehara, Y., Yamasaki, A., Sugimura, T., Kurono, S., Tsujimoto, K., Mizushima, T., Yamashita, E., Tsukihara, T. & Yoshikawa, S. (2007). EMBO J. 26, 1713-1725.
44. Stern, E. A., Newville, M., Ravel, B., Yacoby, Y. & Haskel, D. (1995). Physica B, 208-209, 117-120.
45. Strange, R.W., Blackburn, N. J., Knowles, P. F. & Hasnain, S. S. (1987). J. Am. Chem. Soc. 109, 7157-7162.
46. Strange, R. W., Ellis, M. & Hasnain, S. S. (2005). Coord. Chem. Rev. 249, 197-208.
47. Trainer, J. A., Getzoff, E. D., Richardson, J. S. & Richardson, D. C. (1983). Nature (London), 306, 284-287.
48. Ugliengo, P., Viterbo, D. & Chiari, G. (1993). Z. Kristallogr. 207, 9-23.
49. Veronesi, G., Whitehead, S. J., Francia, F., Giachini, L., Cotton, N. P., Boscherini, F. Venturoli, G. & Jackson, J. B. (2010). Biochim. Biophys. Acta. Submitted.