Natural domain design: Enhanced thermal stability of a zinc-lacking ferredoxin isoform shows that a hydrophobic core efficiently replaces the structural metal site

Biochemistry

Volumn 45, Issue 34, 2006, Pages 10376-10384

  Rocha, Rita ^a   Leal, Sónia S ^a   Teixeira, Vitor H ^a   Regalla, Manuela ^a   Huber, Harald ^b   Baptista, António M ^a   Soares, Cláudio M ^a   Gomes, Cláudio M ^a  

^a INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

^b UNIVERSITY OF REGENSBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION; FLUORESCENCE; HYDROPHOBICITY; PH; QUENCHING; STRUCTURAL METALS;

FERREDOXIN ISOFORMS; FERREDOXINS (FD); FLUORESCENCE EMISSION; METAL CHELATORS;

PROTEINS;

BACTERIAL PROTEIN; CHELATING AGENT; DEFEROXAMINE; EDETIC ACID; FERREDOXIN; IRON; ZINC;

ARTICLE; BINDING SITE; ESCHERICHIA COLI; HYDROPHOBICITY; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; SULFOLOBUS; THERMODYNAMICS; THERMOPHILIC BACTERIUM; THERMOSTABILITY;

ARCHAEAL PROTEINS; BINDING SITES; ETHYLENEDIAMINES; FERREDOXINS; HEAT; HYDROGEN-ION CONCENTRATION; HYDROPHOBICITY; PROTEIN FOLDING; PROTEIN ISOFORMS; PROTEIN STRUCTURE, TERTIARY; SULFOLOBUS; THERMODYNAMICS; ZINC;

SULFOLOBUS METALLICUS;

EID: 33748694511     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0610698     Document Type: Article

References (37)

1. Petsko, G., and Ringe, D. (2004) Protein Structure and Function, New Science Press, London, U.K.
2. Hogg, P. J. (2003) Disulfide bonds as switches for protein function, Trends Biochem. Sci. 28, 210-214.
3. Auld, D. S. (2001) Zinc coordination sphere in biochemical zinc sites, Biometals 14, 271-313.
4. Lee, M. S., Gippert, G. P., Soman, K. V., Case, D. A., and Wright, P. E. (1989) Three-dimensional solution structure of a single zinc finger DNA-binding domain, Science 245, 635-637.
5. Lee, M. S., Gottesfeld, J. M., and Wright, P. E. (1991) Zinc is required for folding and binding of a single zinc finger to DNA, FEBS Lett. 279, 289-294.
6. Perrier, V., Surewicz, W. K., Glaser, P., Martineau, L., Craescu, C. T., Fabian, H., Mantsch, H. H., Barzu, O., and Gilles, A. M. (1994) Zinc chelation and structural stability of adenylate kinase from Bacillus subtilis, Biochemistry 33, 9960-9967.
7. Perrier, V., Burlacu-Miron, S., Bourgeois, S., Surewicz, W. K., and Gilles, A. M. (1998) Genetically engineered zinc-chelating adenylate kinase from Escherichia coli with enhanced thermal stability, J. Biol. Chem. 273, 19097-19101.
8. Green, S. M., Ginsburg, A., Lewis, M. S., and Hensley, P. (1991) Roles of metal ions in the maintenance of the tertiary and quaternary structure of arginase from Saccharomyces cerevisiae, J. Biol. Chem. 266, 21474-21481.
9. Olry, A., Boschi-Muller, S., Yu, H., Burnel, D., and Branlant, G. (2005) Insights into the role of the metal binding site in methionine-R-sulfoxide reductases B, Protein Sci. 14, 2828-2837.
10. Gomes, C. M., Frazao, C., Xavier, A. V., Legall, J., and Teixeira, M. (2002) Functional control of the binuclear metal site in the metallo-beta-lactamase-like fold by subtle amino acid replacements, Protein Sci. 11, 707-712.
11. Fujii, T., Hata, Y., Oozeki, M., Moriyama, H., Wakagi, T., Tanaka, N., and Oshima, T. (1997) The crystal structure of zinc-containing ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7, Biochemistry 36, 1505-1513.
12. Gomes, C., Faria, A., Carita, J., Mendes, J., Regalla, M., Chicau, P., Huber, H., Sletter, K., and M. T. (1998) Di-cluster, seven-iron ferredoxins from hyperthermophilic Sulfolobales, J. Biol. Inorg. Chem. 3, 499-507.
13. Kojoh, K., Matsuzawa, H., and Wakagi, T. (1999) Zinc and an N-terminal extra stretch of the ferredoxin from a thermoacidophilic archaeon stabilize the molecule at high temperature, Eur. J. Biochem. 264, 85-91.
14. Kojoh, K., Fukuda, E., Matsuzawa, H., and Wakagi, T. (2002) Zinc-coordination of aspartic acid-76 in Sulfolobus ferredoxin is not required for thermal stability of the molecule, J. Inorg. Biochem. 89, 69-73.
15. Leal, S. S., and Gomes, C. M. (2005) Linear three-iron centres are unlikely cluster degradation intermediates during unfolding of iron-sulfur proteins, Biol. Chem. Hoppe-Seyler 386, 1295-1300.
16. Leal, S. S., Teixeira, M., and Gomes, C. M. (2004) Studies on the degradation pathway of iron-sulfur centers during unfolding of a hyperstable ferredoxin: cluster dissociation, iron release and protein stability, J. Biol. Inorg. Chem. 9, 987-996.
17. Moczygemba, C., Guidry, J., Jones, K. L., Gomes, C. M., Teixeira, M., and Wittung-Stafshede, P. (2001 ) High stability of a ferredoxin from the hyperthermophilic archaeon A. ambivalens: involvement of electrostatic interactions and cofactors, Protein Sci. 10, 1539-1548.
18. Stone, K. L., Williams, K. R. (1993) A Pratical Guide to Protein and Peptide Purification for Microsequencing, Academic Press, New York.
19. Sali, A., and Blundell, T. L. (1993) Comparative protein modelling by satisfaction of spacial restraints, J. Mol. Biol. 234, 779-815.
20. Laskowski, A., MacArthur, M., Moss, D., and Thorton, J. (1993) PROCHECK: a program to check the stereochemical quality of protein structures, J. Appl. Crystallogr. 26, 283-291.
21. Lindahl, E., Hess, B., and van der Spoel, D. (2001) GROMACS 3.0: A package for molecular simulation and trajectory analysis, J. Mol. Model. 7, 306-317.
22. Scott, W. R. P., Hünenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Krüger, P., and van Gunsteren, W. F. (1999) The GROMOS biomolecular simulation program package, J. Phys. Chem. A 103, 3596-3607.
23. van Gunsteren, W. F., Billeter, S. R., Eising, A. A., Hunenberger, P. H., Kruger, P., Mark, A. E., Scott, W. R. P., and Tironi, I. G. (1996) Biomolecular Simulation: The GROMOS96 Manual and User Guide, BIOMOS b.v., Zurich, Groninger.
24. Teixeira, V. H., Baptista, A. M., Soares, C. M. (2006) Pathways of H2 towards the active site of [NiFe]-hydrogenase, Biophys. J. in press.
25. Baptista, A. M., and Soares, C. M. (2001) Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins, J. Phys. Chem. B 105, 293-309.
26. Teixeira, V. H., Soares, C. M., and Baptista, A. M. (2002) Studies of the reduction and protonation behavior of the tetraheme cytochromes using atomic detail, J. Biol. Inorg. Chem. 7, 200-216.
27. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., and Haak, J. R. (1984) Molecular dynamics with coupling to an external bath, J. Chem. Phys. 81, 3684-3690.
28. Hess, B., Bekker, H., Berendsen, H. J. C., and Fraaije, J. G. E. M. (1997) LINCS: A linear constraint solver for molecular dynamics, J. Comput. Chem. 18, 1463-1472.
29. Mitou, G., Higgins, C., Wittung-Stafshede, P., Conover, R. C., Smith, A. D., Johnson, M. K., Gaillard, J., Stubna, A., Munck, E., and Meyer, J. (2003) An Isc-type extremely thermostable [2Fe2S] ferredoxin from Aquifex aeolicus. Biochemical, spectroscopic, and unfolding studies, Biochemistry 42, 1354-1364.
30. Hermans, J., Berendsen, H. J. C., van Gunsteren, W. P., and Postma, J. P. M. (1984) A consistent empirical potential for water-protein interactions, Biopolymers 23, 1513-1518.
31. Lakowicz, J. R. (1999) Principles of Fluorescence Spectroscopy, 2nd ed., Kluwer Academic/Plenum Publishers, New York.
32. Chattopadhyay, K., and Frieden, C. (2006) Steady-state and time-resolved fluorescence studies of the intestinal fatty acid binding protein, Proteins 63, 327-335.
33. Frazão, C., Silva, G., Gomes, C. M., Matias, P., Coelho, R., Sieker, L., Macedo, S., Liu, M. Y., Oliveira, S., Teixeira, M., Xavier, A. V., Rodrigues-Pousada, C., Carrondo, M. A., and Le Gall, J. (2000) Structure of a dioxygen reduction enzyme from Desulfovibrio gigas, Nat. Struct. Biol. 7, 1041-1045.
34. Wittung-Stafshede, P., Gomes, C. M., and Teixeira, M. (2000) Stability and folding of the ferredoxin from the hyperthermophilic archaeon Acidianus ambivalens, J. Inorg. Biochem. 78, 35-41.
35. Dahiyat, B. I., Sarisky, C. A., and Mayo, S. L. (1997) De novo protein design: towards fully automated sequence selection, J. Mol. Biol. 273, 789-796.
36. Dahiyat, B. I., and Mayo, S. L. (1997) De novo protein design: fully automated sequence selection, Science 278, 82-87.
37. DeLano, W. L. (2002) The PyMOL User's Manual, DeLano Scientific, San Carlos, CA.