Dissecting contributions to the denaturant sensitivities of proteins

Biochemistry

Volumn 44, Issue 2, 2005, Pages 775-781

  Dempsey, Christopher E ^a   Piggot, Thomas J ^a   Mason, Philip E ^b  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CONFORMATIONS; ELECTROSTATICS; HYDROGEN BONDS; SENSITIVITY ANALYSIS; UREA;

HELICAL PEPTIDES; PROTEIN DENATURATION; RING INTERACTIONS; SIDE CHAIN;

PROTEINS;

ALANINE; ALANYLALANYLGLUTAMINYLALANYLALANYLALANYLGLUTAMYLGLUTAMINYLALANYLALANYLALANYLALANYLGLUTAMINYLALANYLALANYLTYROSINAMIDE; GUANIDINE; INDOLE; LYSYLTRYPTOPHANYLTHREONYLTRYPTOPHANYLLYSINAMIDE; PEPTIDE; POTASSIUM CHLORIDE; SERYLTRYPTOPHANYLTHREONYLTRYPTOPHANYLGLUTAMYLASPARAGINYLGLYCYLLYSYLTRYPTOPHANYLTHREONYLTRYPTOPHANLYSINAMIDE; SERYLTRYPTOPHANYLTHREONYLTRYPTOPHANYLGLUTAMYLGLYCYLASPARAGINYLLYSYLTRYPTOPHANYLTHREONYLTRYPTOPHANYLLYSINAMIDE; SODIUM CHLORIDE; TRYPTOPHAN; UNCLASSIFIED DRUG; UREA;

ARTICLE; COMPARATIVE STUDY; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN STABILITY; REACTION ANALYSIS; TEMPERATURE DEPENDENCE;

AMINO ACID SEQUENCE; CIRCULAR DICHROISM; GUANIDINE; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SOLUTIONS; THERMODYNAMICS; TRYPTOPHAN; UREA;

EID: 12144259012     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi048389g     Document Type: Article

References (41)

1. Pace, C. N. (1986) Determination and analysis of urea and guanidinium hydrochloride denaturation curves, Methods Enzymol. 131, 266-280.
2. Myers, J. K., Pace, C. N., and Scholtz, J. M. (1995) Denaturant m-values and heat-capacity changes: Relation to changes in accessible surface-areas of protein unfolding, Protein Sci. 4, 2138-2148.
3. Zou, Q., Habermann-Rottingaus, S. M., and Murphy, K. P. (1998) Urea effects on protein stability: Hydrogen bonding and the hydrophobic effect, Proteins 31, 107-115.
4. Kita, Y., Arakawa, T., Lin, T.-Y., and Timasheff, S. N. (1994) Contribution of the surface free-energy perturbation to protein solvent interactions. Biochemistry 33, 15178-15189.
5. Makhatadze, G. I., and Privalov, P. L. (1992) Protein interactions with urea and guanidinium chloride: A calorimetric study, J. Mol. Biol. 226, 491-505.
6. Scholtz, J. M., Barrick, D., York, E. J., Stewart, J. M., and Baldwin, R. L. (1995) Urea unfolding of peptide helices as a model for interpreting protein unfolding. Proc. Natl. Acad. Sci. U.S.A. 92, 185-190.
7. Vanzi, F., Madan, B., and Sharp, K. (1998) Effect of the protein denaturants urea and guanidinium on water structure: A structural and thermodynamic study, J. Am. Chem. Soc. 120, 10748-10752.
8. Omta, A. W., Kropman, M. F., Woutersen, S., and Bakker, H. J. (2003) Negligible effect of ions on the hydrogen-bond structure in liquid water, Science 301, 347-349.
9. Batchelor, J. D., Olteanu, A., Tripathy, A., and Pielak, G. J. (2004) Impact of protein denaturants and stabilizers on water structure, J. Am. Chem. Soc. 126, 1958-1961.
10. Scholtz, J. M., Qian, H., Robbins, V. H., and Baldwin, R. L. (1993) The energetics of ion-pair and hydrogen-bonding interactions in a helical peptide, Biochemistry 32, 9668-9676.
11. Celinski, S. A., and Scholtz, J. M. (2002) Osmolyte effects on helix formation in peptides and the stability of coiled-coils, Protein Sci. 11, 2048-2051.
12. Cochran, A. G., Skelton, N. J., and Starovasnik, M. A. (2001) Tryptophan zippers: Stable, monomeric β-hairpins, Proc. Natl. Acad. Sci. U.S.A. 98, 5578-5583.
13. Nozaki, Y., and Tanford, C. (1963) Solubility of amino acids and related compounds in aqueous urea solutions, J. Biol. Chem. 238, 4074-4081.
14. Nozaki, Y., and Tanford, C. (1970) Solubility of amino acids, diglycine, and triglycine in aqueous guanidine hydrochloride solutions, J. Biol. Chem. 245, 1648-1652.
15. Nandi, P. K., and Robinson, D. R. (1984) Effects of urea and guanidine-hydrochloride on peptide and nonpolar groups, Biochemistry 23, 6661-6668.
16. Liu, Y., and Bolen, D. W. (1995) The peptide backbone plays a dominant role in protein stabilization by naturally occurring osmolytes, Biochemistry 34, 12884-12891.
17. Smith, J. S., and Scholtz, J. M. (1996) Guanidine hydrochloride unfolding of peptide helices: Separation of denaturant and salt effects, Biochemistry 35, 7292-7297.
18. Avbelj, F., Luo, P. Z., and Baldwin, R. L. (2000) Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities, Proc. Natl. Acad. Sci. U.S.A. 97, 10786-10791.
19. Yang, W. Y., Pitera, J. W., Swope, W. C., and Gruebele, M. (2004) Heterogeneous folding of the trpzip hairpin: Full atom simulation and experiment, J. Mol. Biol. 336, 241-251.
20. Milnes, J. T., Dempsey, C. E., Ridley, J. M., Crociani, O., Arcangeli, A., Hancox, J. C., and Witchel, H. J. (2003) Preferential closed channel blockade of HERG potassium currents by a chemically synthesised BeKm-1 scorpion toxin, FEBS Lett. 547, 20-26.
21. Dempsey, C. E., Ueno, S., and Avison, M. B. (2003) Enhanced membrane permeabilization and antibacterial activity of a disulfide-dimerized magainin analogue, Biochemistry 42, 402-409.
22. Luo, P. Z., and Baldwin, R. L. (1997) Mechanism of helix induction by trifluoroethanol: A framework for extrapolating the helix-forming properties of peptides from trifluoroethanol/water mixtures back to water, Biochemistry 36, 8413-8421.
23. Zimm, B. H., and Bragg, J. K. (1959) Theory of the phase transition between helix and random coil in polypeptide chains, J. Chem. Phys. 31, 526-535.
24. Pace, C. N., and Vanderburg, K. E. (1979) Determining globular protein stability: Guanidine hydrochloride denaturation of myoglobin, Biochemistry 18, 288-292.
25. Santoro, M. M., and Bolen, D. W. (1988) Unfolding free-energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl α-chymotrypsin using different denaturants, Biochemistry 27, 8063-8068.
26. Scholtz, J. M., York, E. J., Stewart, J. M., and Baldwin, R. L. (1991) A neutral, water-soluble, α-helical peptide: The effect of ionic-strength on the helix coil equilibrium, J. Am. Chem. Soc. 113, 5102-5104.
27. Lacroix, E., Viguera, A. R., and Serrano, L. (1998) Elucidating the folding problem of α-helices: Local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters, J. Mol. Biol. 284, 173-191.
28. Baldwin, R. L. (2003) In search of the energetic role of peptide hydrogen bonds, J. Biol. Chem. 278, 17581-17588.
29. Mason, P. E., Neilson, G. W., Dempsey, C. E., Barnes, A. C., and Cruickshank, J. M. (2003) The hydration structure of guanidinium and thiocyanate ions: Implications for protein stability in aqueous solution, Proc. Natl. Acad. Sci. U.S.A. 100, 4557-4561.
30. Kameda, Y., Naganuma, H., Mochiduki, K., Imano, M., Usuki, T., and Uemura, O. (2002) Hydration structure of the urea molecule in highly concentrated aqueous solutions, Bull. Chem. Soc. Jpn. 75, 2579-2585.
31. Courtenay, E. S., Capp, M. W., and Record, M. T. (2001) Thermodynamics of interactions of urea and guanidinium salts with protein surface: Relationship between solute effects on protein processes and changes in water-accessible surface area, Protein Sci. 10, 2485-2497.
32. Searle, M. S. (2004) Insights into stabilizing weak interactions in designed peptide β-hairpins, Pept. Sci. 76, 185-195.
33. Colley, C. S., Griffiths-Jones, S. R., George, M. W., and Searle, M. S. (2000) Do interstrand hydrogen bonds contribute to β-hairpin peptide stability in solution? IR analysis of peptide folding in water, Chem. Commun., 593-594.
34. Mason, P. E., Neilson, G. W., Enderby, J. E., Saboungi, M.-L., Dempsey, C. E., MacKerell, A. D., Jr., and Brady, J. W. (2004) The Structure of Aqueous Guanidinium Chloride Solutions, J. Am. Chem. Soc. 126, 11462-11470.
35. Kuharski, R. A., and Rossky, P. J. (1984) Molecular-dynamics study of solvation in urea water solution, J. Am. Chem. Soc. 106, 5794-5800.
36. Muller, N. (1990) A model for the partial reversal of hydrophobic hydration by addition of a urea-like cosolvent, J. Phys. Chem. 94, 3856-3859.
37. Flocco, M. M., and Mowbray, S. L. (1994) Planar stacking interactions of arginine and aromatic side chains in proteins, J. Mol. Biol. 235, 109-117.
38. Ma, J. C., and Dougherty, D. A. (1997) The cation-π interaction, Chem. Rev. 97, 1304-1324.
39. Hu, J. X., Barbour, L. J., and Gokel, G. W. (2002) Probing alkali metal-π interactions with the side chain residue of tryptophan, Proc. Natl. Acad. Sci. U.S.A. 99, 5121-5126.
40. Espinosa, J. F., Munoz, V., and Gellman, S. H. (2001) Interplay between hydrophobic cluster and loop propensity in β-hairpin formation, J. Mol. Biol. 306, 397-402.
41. Dyer, R. B., Maness, S. J., Peterson, E. S., Franzen, S., Fesinmeyer, R. M., and Andersen, N. H. (2004) The mechanism of β-hairpin formation, Biochemistry 43, 11560-11566.