Evolution of metal selectivity in templated protein interfaces

Journal of the American Chemical Society

Volumn 132, Issue 25, 2010, Pages 8610-8617

  Brodin, Jeffrey D ^a   Medina Morales, Annette ^a   Ni, Thomas ^a   Salgado, Eric N ^a   Ambroggio, Xavier I ^b   Akif Tezcan, F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Rosetta Design Group LLC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL CHANGE; DIVALENT METALS; ELECTRON TRANSFER PROTEINS; FUNCTIONAL DIVERSITY; HIGH-AFFINITY SITES; METAL BINDING PROPERTIES; METAL SELECTIVITY; METALLO-PROTEINS; PROTEIN ARCHITECTURES; PROTEIN INTERFACES; RATIONAL DESIGN; SELECTIVE BINDING; SIGNALING PROTEINS; TEMPLATED; TEMPLATING;

BINDING ENERGY; METAL IONS; PROTEINS; ZINC;

METALS;

COPPER ION; CYTOCHROME; CYTOCHROME CB562; NICKEL; UNCLASSIFIED DRUG; ZINC ION; CYTOCHROME C; METAL; ZINC;

ARTICLE; BINDING AFFINITY; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; METAL BINDING; METAL TEMPLATED INTERFACE REDESIGN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ASSEMBLY; PROTEIN STRUCTURE; STUDY DESIGN; X RAY FLUORESCENCE; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME SPECIFICITY; METABOLISM; PROTEIN MULTIMERIZATION; PROTEIN QUATERNARY STRUCTURE; THERMODYNAMICS;

CYTOCHROMES C; METALS; MODELS, MOLECULAR; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; SUBSTRATE SPECIFICITY; THERMODYNAMICS; ZINC;

EID: 77955443867     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja910844n     Document Type: Article

References (41)

1. Outten, C. E.; O'Halloran, T. V. Science 2001, 292, 2488.
2. Rosenzweig, A. C. Acc. Chem. Res. 2001, 34, 119.
3. Tottey, S.; Waldron, K. J.; Firbank, S. J.; Reale, B.; Bessant, C.; Sato, K.; Cheek, T. R.; Gray, J.; Banfleld, M. J.; Dennison, C.; Robinson, N. J. Nature 2008, 455, 1138.
4. Blundell, T. L. The evolution of metal-binding sites in proteins; Symposium. Press London: University of Sussex, 1977.
5. Liu, C. L.; Xu, H. B. J. Inorg. Biochem. 2002, 88, 77.
6. Salgado, E. N.; Ambroggio, X. I.; Brodin, J. D.; Lewis, R. A.; Kuhlman, B.; Tezcan, F. A. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 1827.
7. Salgado, E. N.; Faraone-Mennella, J.; Tezcan, F. A. J. Am. Chem. Soc. 2007, 129, 13374.
8. Salgado, E. N.; Lewis, R. A.; Faraone-Mennella, J.; Tezcan, F. A. J. Am. Chem. Soc. 2008, 130, 6082.
9. Salgado, E. N.; Lewis, R. A.; Mossin, S.; Rheingold, A. L.; Tezcan, F. A. Inorg. Chem. 2009, 48, 2726.
10. Wegner, S. V.; Boyaci, H.; Chen, H.; Jensen, M. P.; He, C. Angew. Chem., Int. Ed. 2009, 48, 2339.
11. McCaIl, K. A.; Fierke, C. A. Anal. Biochem. 2000, 284, 307.
12. 2+ were determined separately using EGTA as a competing ligand. See Experimental Section for more details.
13. Walkup, G. K.; Imperiali, B. J. Am. Chem. Soc. 1997, 119, 3443.
14. 4 scaffold.
15. Krantz, B. A.; Sosnick, T. R. Nat. Struct. Biol. 2001, 8, 1042.
16. Ghadiri, M. R.; Choi, C. J. Am. Chem. Soc. 1990, 112, 1630.
17. Frausto da Silva, J. J. R.; Williams, R. J. P. The biological chemistry of the elements; Oxford University Press: Oxford, 2001.
18. Nolan, E. M.; Ryu, J. W.; Jaworski, J.; Feazell, R. P.; Sheng, M.; Lippard, S. J. J. Am. Chem. Soc. 2006, 128, 15517.
19. Hunt, J. A.; Ahmed, M.; Fierke, C. A. Biochemistry 1999, 38, 9054.
20. Kwan, C.-Y.; Putney, J. W. J. Biol. Chem. 1990, 265, 678.
21. 4. If they are bound to the core in a fashion that would compete with Zn binding, their average dissociation constants would have to be ∼40 μM each to compensate for the free energy difference between the four-Zn-bound and two-Cu-bound. species listed in Table 1.
22. Thompson, M. C.; Busch, D. H. J. Am. Chem. Soc. 1964, 86, 3651.
23. Creaser, I.I.; Geue, R. J.; Harrowfield, J. M.; Herlt, A. J.; Sargeson, A. M.; Snow, M. R.; Springborg, J. J. Am. Chem. Soc. 1982, 104, 6016.
24. McMurry, T. J.; Raymond, K. N.; Smith, P. H. Science 1989, 244, 938.
25. Waldron, K. J.; Robinson, N. J. Nat. Rev. Microbiol. 2009, 7, 25.
26. Pande, V. S.; Grosberg, A. Y.; Tanaka, T. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 12976.
27. Saito, S.; Sasai, M.; Yomo, T. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 11324.
28. Braun, M.; Thony-Meyer, L. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 12830.
29. Schuck, P. Biophys. Chem. 2004, 108, 187.
30. Vistica, J.; Dam, J.; Balbo, A.; Yikilmaz, E.; Mariuzza, R. A.; Rouault, T. A.; Schuck, P. Anal. Biochem. 2004, 326, 234.
31. Collaborative Computational Project, Number 4. 1994. Acta Crystallogr. 1994, D50, 760-763.
32. Vagin, A.; Teplyakov, A. J. Appl. Crystallogr. 1998, 30, 1022.
33. Brünger, A. T.; Adams, P. D.; Clore, G. M.; DeLano, W. L.; Gros, P.; Grosse-Kunstleve, R. W.; Jiang, J. S.; Kuszewski, J.; Nilges, M.; Pannu, N. S.; Read, R. J.; Rice, L. M.; Simonson, T.; Warren, G. L. Acta Crystallogr. 1998, D54, 905.
34. Murshudov, G.; Vagin, A.; Dodson, E. Acta Crystallogr. 1996, D53, 240.
35. McRee, D. E. J. Mol. Graphics 1992, 10, 44.
36. Emsley, P.; Cowtan, K. Acta Ciystallogr. 2004, D60, 2126.
37. Laskowski, R. A.; Macarthur, M. W.; Moss, D. S.; Thornton, J. M. J. Appl. Crystallogr. 1993, 26, 283.
38. Klotz, I. M. Ligand-receptor energetics: a guide for the perplexed; John Wiley & Sons, Inc.: New York, 1997.
39. Grynkiewicz, G.; Poenie, M.; Tsien, R. Y. J. Biol. Chem. 1985, 260, 3440.
40. Kuzmic, P. Anal. Biochem. 1996, 237, 260.
41. Atar, D.; Backx, P. H.; Appel, M. M.; Gao, W. D.; Marban, E. J. Biol. Chem. 1995, 270, 2473.