The denatured state (the other half of the folding equation) and its role in protein stability

FASEB Journal

Volumn 10, Issue 1, 1996, Pages 27-34

  Shortle, David ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

denaturants; folding intermediates; protein folding

Indexed keywords

BACTERIAL PROTEIN;

AMINO ACID SEQUENCE; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STABILITY; REVIEW; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

BACTERIA (MICROORGANISMS);

EID: 0030032461     PISSN: 08926638     EISSN: None     Source Type: Journal    
DOI: 10.1096/fasebj.10.1.8566543     Document Type: Review

References (39)

1. Schellman, J. A. (1987) The thermodynamic stability of proteins. Annu. Rev. Biophys. Biophys. Chem. 16, 115-137
2. Lumry, R., Biltonen, R., and Brandts, J. F. (1966) Validity of the "two-state" hypothesis for conformational transitions of proteins. Biopolymers 4, 917-944
3. Tanford, C. (1980) the Hydrophobic Effect: Formation of Micelles and Biological Membranes, John Wiley & Sons, New York
4. Schellman, J. A. (1978) Solvent denaturation. Biopolymers 17, 1305-1322
5. Timasheff, S. N. (1992) Water as ligand: preferential binding and exclusion of dénaturants in protein unfolding. Biochemisty 31, 9857-9864
6. Shortle, D., and Meeker, A. K. (1986) Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation. Proteins Struct. Funct. Genet. 1, 81-89
7. Shortle, D., Meeker, A. K., and Freire, E. (1988) Stability mutants of staphylococcal nuclease: Large compensating enthalpy-entropy changes for the reversible denaturation reaction. Biochemistry 27, 4761-4768
8. Shortle, D., Stites, W. E., and Meeker, A. M. (1990) Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry 29, 8033-8041
9. Green, S. M., Meeker, A. K., and Shortle, D. (1992) Contributions of the polar, uncharged amino acids to the stability of staphylococcal nuclease: Evidence for mutational effects on the free energy of the denatured state. Biochemistry 31, 5717-5728
10. Matthews, B. W. (1993) Structural and genetic analysis of protein stability. Annu. Rev. Biochem. 62, 139-160
11. Tanford, C. (1968) Protein denaturation. Adv. Protein Chem. 23, 121-282
12. Tanford, C. (1970) Protein denaturation. Part C. Theoretical models for the mechanism of denaturation. Adv. Protein Chem. 24, 1-95
13. Miller, W. G., and Goebel, C. V. (1968) Dimensions of protein random coils. Biochemistry 7, 3925-3935
14. Dill, K. A., and Shortle, D. (1991) Denatured states of proteins. Annu. Rev. Biochem. 60, 795-825
15. Sosniek, T. R., and Trewhella, J. (1992) Denatured states of ribonuclease A have compact dimensions and residual secondary structure. Biochemistry 31, 8329-8335
16. Flanagan, J. A., Kataoka, M., Fujisawa, T., and Engelman, D. M. (1993) Mutations can cause large changes in the conformation of a denatured state. Biochemistry 32, 10359-10370
17. Kataoka, M. Hagihara, Y., Mihara, K., and Goto, Y. (1993) Molten globule of cytochrome c studied by small angle X-ray scattering. J. Mol. Biol. 229, 591-596
18. Neri, D., Billeter, M., Wider, G., and Wuthrich, K. (1992) NMR determination of residual structure in a urea-denatured protein, the 434 repressor. Science 257, 1559-1563
19. Logan, T. M., Theriault, Y., and Fesik, S. W. (1994) Structural characterization of the FK506 binding protein unfolded in urea and guanidine hydrochloride. J. Mol. Biol. 236, 637-648
20. Wang, Y., Alexandreseu, A.T., and Shortle, D. (1995) Initial studies of the equilibrium folding pathway of staphylococcal nuclease. Phil. Trans. R. Soc. London B. 348, 27-34
21. Wang, Y., and Shortle, D. (1995). The equilibrium folding pathway of staphylococcal nuclease: Identification of the most stable chain-chain interactions. Biochemistry 34 In press
22. Fink, A. L., Calciano, L. J., Goto, Y., Kurotsu, T., and Palleros, D. R. (1994) Classification of acid denaturation of proteins: intermediates and unfolded states. Biochemistry 33, 12504-12511
23. Hawkes, R., Grutter, M. G., and Schcllman, J. (1984) Thermodynamic stability and point mutations of bacteriophage T4 lysozyme. J. Mol. Biol. 175, 193-212
24. Kimura, S., Nakamura, H., Hashimoto, T., Oobatake, M., and Kanaya, S. (1992) Stabilization of Escherichia coli ribonuclease HI by strategic replacement of amino acid residues with those from the thermophile counterpart. J. Biol. Chem. 267, 21535-21542
25. Lim, W. A., Farringgio, D. C., and Sauer, R. T. (1992) Structural and energetic consequences of disruptive mutations in a protein core. Biochemistry 31, 4324-4333
26. Hu, C. Q., Kitamura, S., Tanaka, A., and Sturtevant, J. M. (1992) Differential scanning calorimetric study of the thermal unfolding of mutant forms of phage T4 lysozyme. Biochemistry 31, 1643-1647
27. Sturtevant, J. M. (1994) The thermodynamic effects of protein mutations. Curr. Opin. Struct. Biol. 4, 69-78
28. Tanaka, A., Flanagan, J., and Sturtevant, J. M. (1993) Thermal unfolding of staphylococeal nuclease and several mutant forms thereof studied by differ-ential scanning calorimetry. Protein Sci. 2;, 567-576
29. Shortle, D. (1992) Mutational studies of protein structures and their stabilities. Q. Rev. Biophys. 25, 205-250
30. Green, S.M., and Shortle, D. (1993). Patterns of nonadditivity between pairs of stability mutations in staphylococeal nuclease. Biochemistry 32, 10131-10139
31. Shortle, D., and Meeker, A.K. (1989) Residual structure in large fragments of staphylococcal nuclease: Effects of amino acid substitutions. Biochemistry 28, 936-944
32. Shortle, D. (1995) Staphylocoecal nuclease: A showcase of m-value effects. Adv. Protein Chem. 46, 217-247
33. Shortle, D., and Abeygunawardana, C. (1993). NMR analysis of the residual structure in the denatured state of an unusual mutant of staphylococcal nuclease. Structure 1, 121-134
34. Alexandrescu, A. T., Gittis, A. P., Abeygunawardana, C., and Shortle, D. (1995) NMR structure of a stable "OB-fold" subclomain isolated from staphylococcal nuclease. J. Mol. Biol. 250, 134-143
35. Pepys, M. B., Hawkins, P. N., Booth, D. R., Vigushin, D. M., Tennent, G. A., Soutar, A. K., Totty, N., Nguyen, O., Blake, C. C. F., Terry, C. J., Feest, T. G., Zalin, A. M., and Hsuan, J. J. (1993) Human lysozyme gene mutations cause hereditary systemic amyloidosis. Nature (London) 362, 553-557
36. Mitraki, A., and King, J. (1989) Protein folding intermediates and inclusion body formation. Bio/Technology 7, 690-697
37. Dill, K. A. (1990) Dominant forces in protein folding. Biochemistry 29, 7133-7155
38. Dill, K. A., Bromberg, S., Yue, K., Fiebig, K. M., Yee, D. P., Thomas, P. D., and Chan, H. S. (1995) Principles of protein folding- A perspective from simple exact models. Protein Sci. 4, 561-602
39. Shortle, D., Chan, H.S., and Dill, K.A. (1992) Modelling the effects of mutations on the denatured states of proteins. Protein Sci. 1, 201-215