Electrophoretic characterization of the denatured states of staphylococcal nuclease

Journal of Molecular Biology

Volumn 242, Issue 5, 1994, Pages 670-682

  Creighton, Thomas E ^a   Shortle, David ^b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

Mutations; Protein stability; Staphylococcal nuclease; Unfolded proteins; Urea gradient electrophoresis

Indexed keywords

EID: 0028033157     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1994.1616     Document Type: Article

References (49)

1. Alexandresou, A. T., Hinck, A. P & Markley, J. L. (1990). Coupling between local structure and global stability of a protein: mutants of staphylococcal nuclease. Biochemistry, 29, 4516-4525.
2. Alexandrescu, A. T., Abeygunawardana, C. & Shortle, D. (1994). Structure and dynamics of a denatured 131-residue fragment of staphylococcal nuclease: a heteronuclear NMR study. Biochemistry, 33, 1063-1072.
3. Baker, D., Sohl, J. L. & Agard, D. A. (1992). A protein folding reaction under kinetic control. Nature (London), 356, 263-265.
4. Baldisseri, D. M., Torchia, D. A., Poole, L. B. & Gerlt, J. A. (1991). Deletion of the Ω-loop in the active site of staphylococcal nuclease. 2. Effects on protein structure and dynamics.Biochemistry, 30, 3628-3633.
5. Carra, J. H, Anderson, E. A. & Privaloy R L. (1994), Thermodynamics of staphylococcal nuclease dénaturation. 1. The acid-denatured state. Protein Sci. 3, 944-951.
6. Cotton, E. A., Hazen, E. E. & Legg, M. J. (1979). Staphylococcal nuclease: proposed mechanism of action based on structure of enzyme-thymidine 3'.5' bisphosphate-calcium ion complex at 1-5 Å resolution. Proc. Nat. Acad. Sci. U.S.A. 76, 2551-2555.
7. Creighton T. E. (1979), Electrophoresis analysis of the unfolding of proteins by urea. J. Mol. Biol. 129, 235-264.
8. Creighton, T. E. (1980). Kinetic study of protein unfolding and refolding using urea gradient electrophoresis. J Mol. Biol. 137, 61-80.
9. Creighton, T. E. (1986). Detection of folding intermediates using urea-gradient electrophoresis. Methods Enzymol, 131, 156-172.
10. Creighton, T. E. (1993). Proteins: Structures, Functions and Molecular Properties, 2nd edit. W.H. Freeman, New York.
11. Creighton, T. E. & Pain, R H. (1980). Enfolding and refolding of Staphylococcus aureus penicillinase by urea-gradient electrophoresis., J. Mol. Biol. 137, 431-436.
12. Dill, K. A. & Shortle, D, (1991). Denatured states of proteins. A nnu, Rev. Biochem, 60, 795-825.
13. Evans, P A., Kautz, R. A., Fox, R. O. & Dobson, C. M. (1989). A magnetization-transfer nuclear magnetic resonance study of the folding of staphylococcal nuclease. Biochemistry, 28, 362-370.
14. Ewbank, J. J. & Creighton, T. E. (1993). Structural characterization of the disulfide folding intermediates of bovine a-lactalbumin. Biochemistry, 32, 3694-3707.
15. Flanagan, J. M., Kataoka, M., Shortle, D. & Engelman, D. M. (1992). Truncated staphylococcal nuclease is compact but disordered. Proc. Nat. Acad. Sci., U.S.A. 89, 748-752.
16. Flanagan, J. M., Kataoka, M., Fujisawa, T. & Engelman, D. M. (1993). Mutations can cause large changes in the conformation of a denatured protein. Biochemistry, 32, 10359-10370.
17. Gittis, A. G., Stites, W. E. & Lattman, E. E. (1993). The phase transition between a compact denatured state and a random coil state in staphylococcal nuclease is first-order. J. Mol. Biol. 232, 718-724.
18. Goldenberg, D. R & Creighton, T. E. (1984), Gel electrophoresis in studies of protein conformation and folding. Anal. Biochem. 138-148.
19. Goldenberg, D. P & Zhang, J. X. (1993). Small effects of amino acid replacements on the reduced and unfolded state of pancreatic trypsin inhibitor. Proteins: Struct. Fund. Genet. 15, 322-329.
20. Green, S. M., Meeker, A. K. & 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.
21. Hamada, D., Hoshino, M., Kataoka, M., Fink, A. L. & Goto, Y. (1993). Intermediate conformational states of apocytochrome c. Biochemistry. 32, 10351-10358.
22. Hodel, A., Kautz, R. A., Jacobs, M. D. & Fox, R. O. (1993). Stress and strain in staphylococcal nuclease. Protein Sci. 2, 838-850.
23. Hodel, A., Kautz, R. A., Adelman, D. M. & Fox, R. O. (1994). The importance of anchorage in determining a strained loop conformation. Protein Sri. 3, 549-556.
24. Hollecker, M. & Creighton, T. E. (1982). Effect, on protein stability of reversing the charge on amino groups. Biochim. Biophys. Acta, 701, 395-404.
25. Hynes, T. R. & Fox, R. 0. (1991). The crystal structure of staphylococcal nuclease refined at 1-7 A resolution. Proteins: Struct. Fund. Genet. 10, 92-105.
26. Kemmink, J. & Creighton, T. E. (1993). Local conformations of peptides representing the entire sequence of bovine pancreatic trypsin inhibitor and their roles in folding. J. Mol. Biol, 234, 861-878.
27. Kuwajima, K. (1989). The molten globule as a clue for understanding the folding and eooperativity of globular-protein structure. Proteins: Struct. Fund, Genet. 6, 87-103.
28. Loh, S. N., Prehoda, K. E., Wang, J. & Markley, J. L. (1993). Hydrogen exchange in unligated and ligated staphylococcal nuclease. Biochemistry, 32, 11022-11028.
29. 2+, and the inhibitor pd Tp, refined at 1-65 Â. Proteins: Struct. Fund, Genet. 3, 183-201.
30. Lyubimova, T., Caglio, S., Gelfi, C., Righetti, R G. & Rabilloud, T. (1993). Photopolymerizat. ion of polyacrylamide gels with methylene blue. Electrophoresis, 14, 40-50.
31. Privalov, P L. (1992). Physical basis of the stability of the folded con format ions of proteins. In Protein Folding (Creighton, T. E., ed.), 83-126, W H. Freeman & Co., New York.
32. Privalov, P L., Tiktopulo, E. L, Venuaminoy S. Y., Griko, Y. V, Makhatadze, G. I. & Khechinashvili N. X. (1989). Heat capacity and conformation of proteins in the denatured state. J. Mol. Biol. 205. 737-750.
33. Ptitsyn, O. B. (1992). The molten globule state. In Protein Folding (Creighton, T. E, ed.), 243-300, W H. Freeman & Co., New York.
34. Schellman, J. A. (1978). Solvent dénaturation. Biopolymers, 17, 1305-1322.
35. 2 +-liganding amino acid in staphylococcal nuclease. Biochemistry, 25, 68-77.
36. Shortle, D. (1989). Probing the determinants of protein folding and stability with amino acid substitutions. J. Biol. Chem. 264, 5315-5318.
37. Shortle, D. & Abeygunawardana, C. (1993). NMR analysis of the residual structure in the denatured state of an unusual mutant of staphylococcal nuclease. Structure, 1, 121-134.
38. Shortle, D. & Meeker, K. (1986). Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea dénaturation. Proteins: Struct. Fund. Genet. 1, 81-89.
39. Shortle, D. & Meeker, A. K. (1989). Residual structure in large fragments of staphylococcal nuclease: effects of amino acid substitutions. Biochemistry, 28, 936-944.
40. Shortle, D., Meeker, A. K. & Gerring, S. L. (1989), Effects of dénaturants at low concentrations on the reversible dénaturation of staphylococcal nuclease. Arch, Biochem, Biophys. 272, 103-113.
41. Shortle, D, Stites, W E. & Meeker, A. K. (1990). Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry, 29, 8033-8041.
42. Sondek, J. & Shortle, D. (1990). Accommodation of single amino acid insertions by the native state of staphylococcal nuclease. Proteins: Struct. Fund. Genet. 7, 299-305.
43. Sondek, J. & Shortle, D. (1992). Structural and energetic differences between insertions and substitutions in staphylococcal nuclease. Proteins: Struct. Fund. Genet, 13, 132-140.
44. Staniforth, R. A., Burston, S. G., Smith, C. U., Jackson, G. S., Badeoe, I. G., Atkinson, T., Holbrook, J. J. & Clarke, A. R. (1993). The energetics and eooperativity of protein folding: a simple experimental analysis based upon the solvation of internal residues. Biochemistry, 32, 3842-3851.
45. Stites, W E., Meeker, A. K. & Shortle, D. (1994). Evidence for strained interactions between side-chains and the polypeptide backbone. J. Mol. Biol. 235, 27-32.
46. Sugawara, T., Kuwajima, K. & Sugai, S. (1991). Folding of staphylococcal nuclease A studied by equilibrium and kinetic; circular diehroism spectra. Biochemistry, 30. 2698-2706.
47. Tanaka, A. Flanagan J. & Sturtevant, J. M. (1993). Thermal unfolding of staphylococcal nuclease and several mutant forms thereof studied by differential scanning calorimetry. Protein Sci. 2. 567-576.
48. Tucker R W. Hazen, E. E. & Cotton, F A. (1979). Staphylococcal nuclease reviewed: a prototypie study in contemporary enzymology. II. Solution studies of the nucleotide binding site and the effects of nucleotide binding. Mol Cell. Biochem. 23, 3-16.
49. + ternary complex. Biochemistry, 31. 921-936.