The early steps in the unfolding of azurin

Biochemistry

Volumn 43, Issue 49, 2004, Pages 15604-15609

  Rizzuti, Bruno ^a   Daggett, Valerie ^b   Guzzi, Rita ^a   Sportelli, Luigi ^a  

^a UNIVERSITY OF CALABRIA   (Italy)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; COPPER; HIGH TEMPERATURE EFFECTS; HYDROPHOBICITY; MOLECULAR DYNAMICS;

AZURIN; BLUE COPPER PROTEINS; HIGH-TEMPERATURE MOLECULAR DYNAMICS SIMULATION; PROTEIN SCAFFOLDS;

PROTEINS;

AZURIN; COPPER ION; COPPER PROTEIN;

ALPHA HELIX; ARTICLE; CONTROLLED STUDY; HIGH TEMPERATURE; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE;

AZURIN; BINDING SITES; COMPUTER SIMULATION; COPPER; HYDROPHOBICITY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PSEUDOMONAS AERUGINOSA; TEMPERATURE; THERMODYNAMICS;

EID: 10644247693     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi048685t     Document Type: Article

References (41)

1. Creighton, T. E. (1992) Protein folding, W. H. Freeman, New York.
2. Brockwell, D. J., Smith, D. A., and Radford, S. E. (2000) Protein folding mechanisms: new methods and emerging ideas, Curr. Opin. Struct. Biol. 10, 16-25.
3. Ferguson, N., and Fersht, A. R. (2003) Early events in protein folding, Curr. Opin. Struct. Biol. 13, 75-81.
4. Daggett, V. (2000) Long timescale simulations, Curr. Opin. Struct. Biol. 10, 160-164.
5. Daggett, V. (2002) Molecular dynamics simulations of the protein unfolding/folding reaction, Acc. Chem. Res. 35, 422-429.
6. Mayor, U., Johnson, C. M., Daggett, V., and Fersht, A. R. (2000) Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation, Proc. Natl. Acad. Sci. U.S.A. 97, 13518-13522.
7. Mayor, U., Guydosh, N. R., Johnson, C. M., Grossman, J. G., Sato, S., Jas, G. S., Freund, S. M. V., Alonso, D. O. V., Daggett, V., and Fersht, A. R. (2003) The complete folding pathway of a protein from nanoseconds to microseconds, Nature 421, 863-867.
8. Ferguson, N., Pires, J. R., Toepert, F., Johnson, C. J., Pan, Y. P., Volkmer-Engert, R., Schneider-Mergener, J., Daggett, V., Oschkinat, H., and Fersht, A. R. (2001) Using flexible loop mimetics to extend Φ-value analysis to secondary structure interactions, Proc. Natl. Acad. Sci. U.S.A. 98, 13008-13013.
9. Day, R., Bennion, B. J., Ham, S., and Daggett, V. (2002) Increasing temperature accelerates protein unfolding without changing the pathway of unfolding, J. Mol. Biol. 322, 189-203.
10. Adman, E. T. (1991) Copper protein structures, Adv. Protein Chem. 42, 145-197.
11. La Rosa, C., Milardi, D., Grasso, D., Guzzi, R., and Sportelli, L. (1995) Thermodynamics of the thermal unfolding of azurin, J. Phys. Chem. 99, 14864-14870.
12. Arcangeli, C., Bizzarri, A. R., and Cannistraro, S. (1999) Long-term dynamics simulation of copper azurin: structure, dynamics and functionality, Biophys. Chem. 78, 247-257.
13. Luise, A., Falconi, M., and Desideri, A. (2000) Molecular dynamics simulation of solvated azurin: correlation between surface solvent accessibility and water residence times, Proteins 39, 56-67.
14. Rizzuti, B., Sportelli, L., and Guzzi, R. (2001) Evidence of reduced flexibility in disulfide bridge-depleted azurin: a molecular dynamics simulation study, Biophys. Chem. 94, 107-120.
15. Rizzuti, B., Swart, M., Sportelli, L., and Guzzi, R. (2004) Active site modeling in copper azurin molecular dynamics simulations, J. Mol. Model. 10, 25-31.
16. Nar, H., Messerschmidt, A., Huber, R., van de Kamp, M., and Canters, G. W. (1991) Crystal structure analysis of oxidized Pseudomonas aeruginosa azurin at pH 5.5 and pH 9.0. A pH-induced conformational transition involves a peptide bond flip, J. Mol. Biol. 221, 765-772.
17. 15N nuclear magnetic resonance assignment and solution secondary structure of the blue copper protein azurin from Pseudomonas aeruginosa, Biochemistry 31, 10194-10207.
18. 15N nuclear magnetic resonance assignment, secondary structure in solution, and solvent exchange properties of azurin from Alcaligenes denitrificans, Biochemistry 33, 3560-3571.
19. Kalverda, A. P., Ubbink, M., Gilardi, G., Wijmenga, S. S., Crawford, A., Jeuken, L. J. C., and Canters, G. W. (1999) Backbone dynamics of azurin in solution: slow conformational change associated with deprotonation of histidine 35, Biochemistry 38, 12690-12697.
20. Levitt, M. (1990) ENCAD-Energy Calculations and Dynamics, Yeda, Rehovat, Israel.
21. Levitt. M., Hirshberg, M., Sharon, R., and Daggett, V. (1995) Potential energy function and parameters for simulations of the molecular-dynamics of proteins and nucleic-acids in solution, Comput. Phys. Commun. 91, 215-231.
22. Levitt, M., Hirshberg, M., Sharon, R., Laidig, K. E., and Daggett, V. (1997) Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution, J. Phys. Chem. B 101, 5051-5061.
23. Sandberg, A., Leckner, J., Shi, Y., Schwarz, F. P., and Karlsson, B. G. (2002) Effects of metal ligation and oxygen on the reversibility of the thermal denaturation of Pseudomonas aeruginosa azurin, Biochemistry 41, 1060-1069.
24. De Beer, S., Wittung-Stafshede, P., Leckner, J., Karlsson, B. G., Winkler, J. R., Gray, H. B., Malmström, B. G., Solomon, E. I., Hedman, B., and Hodgson, K. O. (2000) X-ray absorption spectroscopy of folded and unfolded copper(I) azurin, Inorg. Chim. Acta 297, 278-282.
25. Pozdnyakova, I., Guidry, J., and Wittung-Stafshede, P. (2001) Probing copper ligands in denatured Pseudomonas aeruginosa azurin: unfolding His117Gly and His46Gly mutants, J. Biol Inorg. Chem. 6, 182-188.
26. Marks, J., Pozdnyakova, I., Guidry, J., and Wittung-Stafshede, P. (2004) Methionine-121 coordination determines metal specificity in unfolded Pseudomonas aeruginosa azurin, J. Biol. Inorg. Chem. 9, 281-288.
27. Holm, R. H., Kennepohl, P., and Solomon, E. I. (1999) Structural and functional aspects of metal sites in biology, Chem. Rev. 96, 2239-2314.
28. Kell, G. S. (1967) Precise representation of volume properties of water at one atmosphere, J. Chem. Eng. Data 12, 66-69.
29. Haar, L., Gallagher, J. S., and Kell, G. S. (1984) NBS/NRC steam tables: thermodynamics and transport properties and computer programs for vapor and liquid states of water in SI units, Hemisphere Pub. Corp, Washington, DC.
30. Guzzi, R., Sportelli, L., La Rosa, C., Milardi, D., and Grasso, D. (1996) Experimental model for the thermal denaturation of azurin, Biophys. Chem. 60, 29-38.
31. Guzzi, R., Sportelli, L., La Rosa, C., Milardi, D., Grasso, D., Verbeet, M. P., and Canters, G. W. (1999) A spectroscopic and calorimetric investigation on the thermal stability of the Cys3Ala/Cys26Ala azurin mutant, Biophys. J. 77, 1052-1063.
32. Pozdnyakova, I., Guidry, J., and Wittung-Stafshede, P. (2000) Copper triggered β-hairpin formation. Initiation site for azurin folding?, J. Am. Chem. Soc. 122, 6337-6338.
33. Bonander, N., Leckner, J., Guo, H., Karlsson, B. G., and Sjölin, L. (2000) Crystal structure of the disulfide bond-deficient azurin mutant C3A/C26A. How important is the S-S bond for folding and stability?, Eur. J. Biochem. 267, 4511-4519.
34. Bond, C. J., Wong, K., Clarke, J., Fersht, A. R., and Daggett, V. (1997) Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway, Proc. Natl. Acad. Sci. U.S.A. 94, 13409-13413.
35. Guzzi, R., Sportelli, L., La Rosa, C., Milardi, D., and Grasso, D. (1998) Solvent isotope effect on azurin thermal unfolding, J. Phys. Chem. B 102, 1021-1028.
36. Bartucci, R., Guzzi, R., and Sportelli, L. (2001) Electron para-magnetic resonance investigation of biological systems, Recent Res. Dev. Biophys. Chem. 2, 85-101.
37. Johnson, W. C. (1999) Analyzing protein circular dichroism spectra for accurate secondary structure, Proteins 35, 307-312.
38. Greenfield, N. J. (1999) Applications of circular dichroism in protein and peptide analysis, Trends Anal. Chem. 18, 236-244.
39. Greenfield, N. J., and Fasman, G. D. (1969) Computed circular dichroism spectra for the evaluation of protein conformation, Biochemistry 8, 4108-4116.
40. Rodger, A., and Norden, B. (1997) Circular dichroism and linear dichroism, Oxford University Press, Oxford.
41. Koradi, R., Billeter, M., and Wuthrich, K. (1996) J. Mol. Graphics 14, 51-55.