The role of protein-solvent interactions in protein unfolding

Current Opinion in Biotechnology

Volumn 7, Issue 4, 1996, Pages 428-432

  Schiffer, Celia A ^a   Dötsch, Volker ^b  

^a GENENTECH INC   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; SOLVENT; WATER;

MODEL; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING; REVIEW;

EID: 0030220170     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(96)80119-4     Document Type: Article

References (58)

1. Collins KD, Washabaugh MW. The Hofmeister effect and the behaviour of water at interfaces. O Rev Biophys. 18:1985;323-422.
2. Schellman JA. The thermodynamic stability of proteins. Annu Rev Biophys Biophys Chem. 16:1987;115-137.
3. Ptitsyn OB. The molten globule state. Creighton T. Protein Folding. 1992;243-300 WH Freeman and Co, New York.
4. Timasheff SN. Water as ligand: preferential binding and exclusion of denaturants in protein unfolding. Biochemistry. 31:1992;9857-9864.
5. Timasheff SN. The control of protein stability and association by weak interactions with water: how do solvents affect these processes? Annu Rev Biophys Biomol Struct. 22:1993;67-97.
6. Fersht AR. Protein folding and stability: the pathway of folding of barnase. FEBS Lett. 325:1993;5-16.
7. Makhatadze GI, Privalov PL. Hydration effects in protein unfolding. Biophys Chem. 51:1994;291-309.
8. Ooi T. Thermodynamics of protein folding: effects of hydration and electrostatic interactions. Adv Biophys. 30:1994;105-154.
9. Caflisch A, Karplus M. Molecular dynamics studies of protein and peptide folding and unfolding. Merz K Jr, Le Grand S. The Protein Folding Problem and Tertiary Structure Prediction. 1994;Birkhäuser, Boston.
10. Dill K, Stigter D. Modeling protein stability as heteropolymer collapse. Adv Protein Chem. 46:1995;59-104.
11. Dill K, Bromberg S, Yue K, Fiebig K, Yee D, Thomas P, Chan H. Principles of protein folding - a perspective from simple exact models. Protein Sci. 4:1995;561-602.
12. Shortle D. The denatured state (the other half of the folding equation) and its role in protein stability. FASEB J. 10:1995;27-34.
13. Shortle D. Staphylococcal nuclease: a showcase of m-value effects. Adv Protein Chem. 46:1995;217-247.
14. Van Gunsteren WF, Hünenberger PH, Kovacs H, Mark AE, Schiffer CA. Investigations of protein unfolding and stability by computer simulation. Philos Trans R Soc Lond Biol Sci. 348:1995;49-59.
15. Daggett V, Levitt M. Protein folding ↔ unfolding dynamics. Curr Opin Struct Biol. 4:1994;291-295.
16. Karplus M, Šali A. Theoretical studies of protein folding and unfolding. of special interest Curr Opin Struct Biol. 5:1995;58-73 A review of recent advances in computational protein unfolding and folding.
17. Hünenberger PH, Mark AE, Van Gunsteren WF. Computational approaches to study protein unfolding: hen egg white lysozyme as a case study. Proteins. 21:1995;196-213.
18. Caflisch A, Karplus M. Molecular dynamics simulation of protein denaturation: solvation of hydrophobic cores and secondary structure of barnase. Proc Natl Acad Sci USA. 91:1994;1746-1750.
19. Pugliese L, Prevost M, Wodak SJ. Unfolding simulations of the 95-102 β-hairpin of barnase. of special interest J Mol Biol. 251:1995;432-447 A detailed analysis of the role of water in unfolding a β hairpin.
20. Mark AE, Van Gunsteren WF. Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state. Biochemistry. 31:1992;7745-7749.
21. Tirado-Rives J, Jorgensen WL. Molecular dynamics simulations of the unfolding of an α-helical analogue of ribonuclease A S-peptide in water. Biochemistry. 30:1991;3864-3871.
22. Tirado-Rives J, Jorgensen WL. Molecular dynamics simulations of the unfolding of apomyoglobin in water. Biochemistry. 32:1993;4175-4184.
23. Daggett V, Levitt M. Molecular dynamics simulations of helix denaturation. J Mol Biol. 223:1992;1121-1138.
24. Daggett V, Levitt M. Protein unfolding pathways explored through molecular dynamics simulations. J Mol Biol. 232:1993;600-619.
25. Vijayakumar S, Vishveshwara S, Ravishanker G, Beveridge DL. Differential stability of β-sheets and α-helices in β-lactamase: a high temperature molecular dynamics study of unfolding intermediates. Biophys J. 65:1993;2304-2312.
26. Alonso DOV, Daggett V. Molecular dynamics simulations of protein unfolding and limited refolding: characterization of partially unfolded states of ubiquitin in 60% methanol and in water. of special interest J Mol Biol. 247:1995;501-520 In simulations, a partially thermally unfolded protein remains unfolded in a mixed aqueous methanol solvent.
27. Soman KV, Karimi A, Case DA. Unfolding of an α-helix in water. Biopolymers. 31:1991;1351-1361.
28. Kovacs H, Mark AE, Johansson J, Van Gunsteren WF. The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfactant protein C in chloroform, methanol and water. J Mol Biol. 247:1995;808-822.
29. Kirshenbaum K, Daggett V. pH-dependent conformations of the amyloid β(1-28) peptide fragment explored using molecular dynamics. of special interest Biochemistry. 34:1995;7629-7639 The computational unfolding of a peptide by pH shows the insertion of a water molecule and the stabilization of a partially unfolded intermediate.
30. Kirshenbaum K, Daggett V. Sequence effects on the conformational properties of amyloid β(1-28) peptide: testing a proposed mechanism for α→β transition. Biochemistry. 34:1995;7640-7647.
31. Caflisch A, Karplus M. Acid and thermal denaturation of barnase investigated by molecular dynamics simulations. of outstanding interest J Mol Biol. 252:1995;672-708 A detailed analysis of the role of water molecules in the unfolding of barnase compared with thermal unfolding.
32. Sticht H, Willbold D, Rösch P. Molecular dynamics simulation of equine infectious anemia virus Tat protein in water and in 40% trifluroethanol. J Biomol Struct Dyn. 12:1994;19-36.
33. Pace CN, Laurents DV, Erickson RE. Urea denaturation of barnase: pH dependence and characterization of the unfolded state. Biochemistry. 31:1992;2728-2734.
34. Pace CN, Laurents DV, Thomson JA. pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1. Biochemistry. 29:1990;2564-2572.
35. Arcus VL, Vuilleumier S, Freund SMV, Bycroft M, Fersht AR. A comparison of the pH, urea, and temperature-denatured states of barnase by heteronuclear NMR: implications for the initiation of protein folding. J Mol Biol. 254:1995;305-321.
36. Agashe VR, Udgaonkar JB. Thermodynamics of denaturation of barstar: evidence for cold denaturation and evaluation of the interaction with guanidine hydrochloride. of special interest Biochemistry. 34:1995;3286-3299 A careful study of temperature denaturation at varying concentrations of GdnHCl.
37. Johnson CM, Fersht AR. Protein stability as a function of denaturant concentration: the thermal stability of barnase in the presence of urea. Biochemistry. 34:1995;6795-6804.
38. Plaza del Pino IM, Pace CN, Freire E. Temperature and guanidine hydrochloride dependence of the structural stability of ribonuclease T1. Biochemistry. 31:1992;11196-11202.
39. Dötsch V, Wider G, Siegal G, Wüthrich K. Interaction of urea with an unfolded protein the DNA-binding domain of the 434-repressor. FEBS Lett. 366:1995;6-10.
40. Liepinsh E, Otting G. Specificity of urea binding of proteins. J Am Chem Soc. 116:1994;9670-9674.
41. Dötsch V. Characterization of protein - solvent interactions with NMR-spectroscopy: the role of urea in the unfolding of proteins. Pharm Acta Helv. 1996;. in press.
42. Khurgin Y, Maksareva E. Urea-generated free rotating water molecules are active in the protein unfolding process. FEBS Lett. 315:1993;149-152.
43. Dötsch V, Wider G, Siegal G, Wüthrich K. Salt-stabilized globular protein structure in 7 M aqueous solution. of outstanding interest FEBS Lett. 372:1995;288-290 The protein refolds in the presence of 7 M urea with the addition of kosmotropes.
44. Von Hippel PH, Wong K-Y. Neutral salts: the generality of their effects on the stability of macromolecular conformations. Science. 145:1964;577-580.
45. Von Hippel PH, Wong K-Y. On the conformational stability of globular proteins: the effects of various electrolytes and nonelectrolytes on the thermal ribonuclease transition. J Biol Chem. 240:1965;3909-3923.
46. Paresegian VA, Rand RP, Rau DC. Macromolecules and water: probing with osmolytic stress. Methods Enzymol. 259:1995;43-94.
47. Goto Y, Fink AL. Conformational states of β-lactamase: molten-globule states at acidic and alkaline pH and high salt. Biochemistry. 28:1989;945-952.
48. Saunders AJ, Marmorino JL, Erie D, Pielak GJ. Osmolyte induced A-state formation [abstract]. Biophys J. 79:1996;439.
49. Plaza del Pino IM, Sanchez-Ruiz JM. An osmolyte effect on the heat capacity change for protein folding. Biochemistry. 34:1995;8621-8630.
50. Oliveira AC, Gaspar LP, Da Poian AT, Silva JL. Arc repressor will not denature under pressure in the absence of water. J Mol Biol. 240:1994;184-187.
51. Tanford C. Isothermal unfolding of globular proteins in aqueous urea solution. J Am Chem Soc. 86:1964;2050-2059.
52. Aue K, Tanford C. Thermodynamics of the denaturation of lysozyme by guanidine hydrochloride. II. Dependence on denaturant concentration at 25°C. Biochemistry. 8:1969;4586-4590.
53. Greene RF Jr, Pace CN. Urea and guanidine hydrochloride denaturation of ribonuclease, lysozyme, alpha-chymotrypsin and beta-lactoglobin. J Biol Chem. 249:1974;5388-5393.
54. Pace CN. Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol. 131:1986;266-280.
55. Duffy EM, Kowalczyk PJ, Jorgensen WL. Do denaturants interact with aromatic hydrocarbons in water? J Am Chem Soc. 115:1993;9271-9275.
56. Jorgensen WL, Duffy EM, Tirado-Rives J. Computational investigations of protein denaturation: apomyoglobin and chaotrope-arene interactions. Philos Trans R Soc Lond Biol Sci. 345:1993;87-96.
57. Schiffer CA, Dötsch V, Wüthrich K, Van Gunsteren WF. Exploring the role of the solvent in the denaturation of a protein: a molecular dynamics study of the DNA binding domain of the 434 repressor. of outstanding interest Biochemistry. 34:1995;15057-15067 A computational method to unfold proteins by increasing the affinity of water for proteins.
58. Neri D, Billeter M, Wider G, Wüthrich K. NMR determination of residual structure in a urea-denatured protein, the 434-repressor. Science. 257:1992;1559-1563.