Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Packing interactions in the apomyglobin folding intermediate

Abstract

The contribution of specific packing to the stability of the sperm whale apomyoglobin intermediate has been studied by urea denaturation monitored by circular dichroism and fluorescence. Mutations disrupting native packing sites within the subdomain formed by the A, G and H helices destabilize the intermediate, in contrast to the conclusion drawn from earlier studies of pH-induced unfolding. Based on these results, the intermediate is proposed to be stabilized by both partially formed native-like tertiary, and non-specific hydrophobic interactions forming a subdomain folding intermediate. The results help to explain how the intermediate acquires its structure and stability.

This is a preview of subscription content, access via your institution

Access options

Buy this article

USD 39.95

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

References

  1. Hughson, F.M., Barrick, D. & Baldwin, R.L. Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis. Biochemistry 30, 4113–4118 (1991).

    Article  CAS  Google Scholar 

  2. Barrick, D. & Baldwin, R.L. The molten globule intermediate of apomyoglobin and the process of protein folding. Protein Sci. 2, 869–876 (1993).

    Article  CAS  Google Scholar 

  3. Griko, Y.V., Privalov, P.L., Venyaminov, S.Y. & Kutyshenko, V.P. Thermodynamic study of the apomyoglobin structure. J. Mol. Biol. 202, 127–138 (1988).

    Article  CAS  Google Scholar 

  4. Cocco, M.J. & Lecomte, J.T. The native state of apomyoglobin described by proton NMR spectroscopy: interaction with the paramagnetic probe HyTEMPO and the fluorescent dye ANS. Protein Sci. 3, 267–281 (1994).

    Article  CAS  Google Scholar 

  5. Cocco, M.J. & Lecomte, J.T. Characterization of hydrophobic cores in apomyoglobin: a proton NMR spectroscopy study. Biochemistry 29, 11067–11072 (1990).

    Article  CAS  Google Scholar 

  6. Goto, Y. & Fink, A.L. Phase diagram for acidic conformational states of apomyoglobin. J. Mol. Biol. 214, 803–805 (1990).

    Article  CAS  Google Scholar 

  7. Griko, Y.V. & Privalov, P.L. Thermodynamic puzzle of apomyoglobin unfolding. J. Mol. Biol. 235, 1318–1325 (1994).

    Article  CAS  Google Scholar 

  8. Nishii, I., Kataoka, M. & Goto, Y. Thermodynamic stability of the molten globule states of apomyoglobin. J. Mol. Biol. 250, 223–238 (1995).

    Article  CAS  Google Scholar 

  9. Loh, S.N., Kay, M.S. & Baldwin, R.L. Structure and stability of a second molten globule intermediate in the apomyoglobin folding pathway. Proc. Natl. Acad. Sci. USA 92, 5446–5450 (1995).

    Article  CAS  Google Scholar 

  10. Kataoka, M. . et al. Structural characterization of the molten globule and native states of apomyoglobin by solution X-ray scattering. J. Mol. Biol. 249, 215–228 (1995).

    Article  CAS  Google Scholar 

  11. Hughson, F.M., Wright, P.E. & Baldwin, R.L. Structural characterization of a partly folded apomyoglobin intermediate. Science 249, 1544–1548 (1990).

    Article  CAS  Google Scholar 

  12. Jennings, P.A. & Wright, P.E. Formation of a molten globule intermediate early in the kinetic folding pathway of apomyoglobin. Science 262, 892–896 (1993).

    Article  CAS  Google Scholar 

  13. Weaver, D. Hydrophobic interaction between globin helices. Biopolymers 32, 477–490 (1992).

    Article  CAS  Google Scholar 

  14. Richmond, T.J. & Richards, F.M. Packing of alpha-helices: geometrical constraints and contact areas. J. Mol. Biol. 119, 537–555 (1978).

    Article  CAS  Google Scholar 

  15. Waltho, J.P., Feher, V.A., Merutka, G., Dyson, H.J. & Wright, P.E. Peptide models of protein folding initiation sites. 1. Secondary structure formation by peptides corresponding to the G- and H-helices of myoglobin. Biochemistry 32, 6337–6347 (1993).

    Article  CAS  Google Scholar 

  16. Barrick, D. & Baldwin, R.L. Three-state analysis of sperm whale apomyoglobin folding. Biochemistry 32, 3790–3796 (1993).

    Article  CAS  Google Scholar 

  17. Santoro, M.M. & Bolen, D.W. Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl alpha-chymotrypsin using different denaturants. Biochemistry 27, 8063–8068 (1988).

    Article  CAS  Google Scholar 

  18. Pace, C.N., Shirley, B.A. & Thomson, J.A. . in Protein Structure (ed. Creighton, T.E.) 311–330 (IRL Press, New York, (1992).

    Google Scholar 

  19. Ramsay, G., lonescu, R. & Eftink, M.R. Modified spectrophotometer for multi-dimensional circular dichroism/fluorescence data acquisition in titration experiments: application to the pH and guanidine-HCI induced unfolding of apomyoglobin. Biophys. J. 69, 701–707 (1995).

    Article  CAS  Google Scholar 

  20. Barrick, D., Hughson, F.M. & Baldwin, R.L. Molecular mechanisms of acid denaturation. The role of histidine residues in the partial unfolding of apomyoglobin. J. Mol. Biol. 237, 588–601 (1994).

    Article  CAS  Google Scholar 

  21. Kiefhaber, T. & Baldwin, R.L. Intrinsic stability of individual alpha helices modulates structure and stability of the apomyoglobin molten globule form. J. Mol. Biol. 252, 122–132 (1995).

    Article  CAS  Google Scholar 

  22. Bashford, D., Chothia, C. & Lesk, A.M. Determinants of a protein fold. Unique features of the globin amino acid sequences. J. Mol. Biol. 196, 199–216 (1987).

    Article  CAS  Google Scholar 

  23. Takano, T. Structure of myoglobin refined at 2.0 Å resolution. I. Crystallographic refinement of metmyoglobin from sperm whale. J. Mol. Biol. 110, 537–568 (1977).

    Article  CAS  Google Scholar 

  24. Garcia, M.B., Chen, L.X., March, K.L., Gurd, R.S. & Gurd, F.R. Electrostatic interactions in sperm whale myoglobin. Site specificity, roles in structural elements, and external electrostatic potential distributions. J. Biol. Chem. 260, 14070–14082 (1985).

    Google Scholar 

  25. Hargrove, M.S. et al. Stability of myoglobin: a model for the folding of heme proteins. Biochemistry 33, 11767–11775 (1994).

    Article  CAS  Google Scholar 

  26. Wu, L.C., Peng, Z.Y. & Kim, P.S. Bipartite structure of the alpha-lactalbumin molten globule. Nature Struct. Biol. 2, 281–286 (1995).

    Article  CAS  Google Scholar 

  27. Peng, Z.Y., Wu, L.C., Schulman, B.A. & Kim, P.S. Does the molten globule have a native-like tertiary fold? Phil. Trans. R. Soc. Lond. B348, 43–47 (1995).

    Google Scholar 

  28. Morozova, L.A., Haynie, D.T., Arico-Meundel, C., Dael, H.V & Dobson, C.M. Structural basis of the stability of a lysozyme molten globule. Nature Struct. Biology 2, 871–875 (1995).

    Article  CAS  Google Scholar 

  29. Tirado-Rives, J. & Jorgensen, W. Molecular dynamics simulations of the unfolding of apomyoglobin in water. Biochemistry 32, 4175–4184 (1993).

    Article  CAS  Google Scholar 

  30. Marmorino, J.L. & Pielak, G.J. A native tertiary interaction stabilizes the A state of cytochrome c. Biochemistry 34, 3140–3143 (1995).

    Article  CAS  Google Scholar 

  31. Lin, L., Pinker, R.J., Forde, K., Rose,, G.D & Kallenbach, N.R. Molten globular characteristics of the native state of apomyoglobin. Nature Struct. Biol. 1, 447–452 (1994).

    Article  CAS  Google Scholar 

  32. Cocco, M.J., Kao, Y.H., Philips, A.T. & Lecomte, J.T. Structural comparison of apomyoglobin and metaquomyoglobin: pH titration of histidines by NMR spectroscopy. Biochemistry 31, 6481–6491 (1992).

    Article  CAS  Google Scholar 

  33. Shin, H.C. et al. Peptide models of protein folding initiation sites. 3. The G-H helical hairpin of myoglobin. Biochemistry 32, 6356–6364 (1993).

    Article  CAS  Google Scholar 

  34. Springer, B.A. & Sligar, S.G. High-level expression of sperm whale myoglobin in Escherichia coli. Proc. Natl. Acad. Sci. USA 84, 8961–8965 (1987).

    Article  CAS  Google Scholar 

  35. Landt, O., Grunert, H.P. & Hahn, U. A general method for rapid site-directed mutagenesis using the polymerase chain reaction. Gene 96, 125–128 (1990).

    Article  CAS  Google Scholar 

  36. Sambrook, J., Fritsch, E.F. & Maniatis., T. Molecular cloning : a laboratory manual (Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y, 1989).

    Google Scholar 

  37. Fanelli, A.R., Antonini, E. & Caputo, A. Studies on the structure of hemoglobin. I. Physicochemical Properties of Human Globin. Biochim. Biophys. Acta. 30, 608–615 (1958).

    Article  CAS  Google Scholar 

  38. Edelhoch, H. Spectroscopic determination of tryptophan and tyrosine in proteins. Biochemistry 6, 1948–1954 (1967).

    Article  CAS  Google Scholar 

  39. Kraulis, P. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kay, M., Baldwin, R. Packing interactions in the apomyglobin folding intermediate. Nat Struct Mol Biol 3, 439–445 (1996). https://doi.org/10.1038/nsb0596-439

Download citation

  • Issue date:

  • DOI: https://doi.org/10.1038/nsb0596-439

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing