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:

Restored heptad pattern continuity does not alter the folding of a four-α-helix bundle

Nature Structural Biology volume 1, pages 706–716 (1994)Cite this article

Abstract

The sequences of α-helical coiled-coils and bundles are characterized by a specific pattern of hydrophobic and hydrophilic residues which is repeated every seven residues. Highly conserved breaks in this pattern frequently occur in segments of otherwise continuous heptad substructures. The hairpin bend of the ROP protein coincides with such a break and provides a model system for the study of the structural effects induced by heptad discontinuities. The structure of a ROP mutant which re-establishes a continuous heptad pattern, shows insignificant changes relative to the wild-type protein, as is also reflected in its conformational stability, spectroscopic properties and unfolding behaviour. Thus, formation of α-α-hairpin bends may occur both in the presence and absence of heptad breaks.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Similar content being viewed by others

References

  1. DeGrado, W.F., Wasserman, Z.R. & Lear, J.D. Protein design, a minimalist approach. Science 243, 622–628 (1989).

    Article  CAS  Google Scholar 

  2. Cohen, C. & Parry, D.A.D. α-Helical coiled coils and bundles: How to design an α-helical protein. Proteins Struct. Funct. Genet. 7, 1–15 (1990).

    Article  CAS  Google Scholar 

  3. Hecht, M., Richardson, J.S., Richardson, D.C. & Ogden, R.C. De novo design, expression, and characterization of Felix: A four-helix bundle protein of native-like sequence. Science 249, 884–891 (1990).

    Article  CAS  Google Scholar 

  4. Morii, H., Ichimura, K. & Uedaira, H. Asymmetric inclusion by the Novo designed proteins: Fluorescence probe studies on amphiphilic α-helix bundles. Prot. Struct. Funct. Genet. 11, 133–141 (1991).

    Article  CAS  Google Scholar 

  5. Kamtekar, S., Sciffer, J.M., Xiong, H., Babik, J. & Hecht, M.H. Protein design by binary patterning of polar and nonpolar amino acids. Science 262, 1680–1685 (1993).

    Article  CAS  Google Scholar 

  6. Paliakasis, C.D. & Kokkinidis, M. Relationships between sequence and structure for the four-α-helix bundle tertiary motif in proteins. Prot. Engng. 5, 739–748 (1992).

    Article  CAS  Google Scholar 

  7. Chou, K.C., Maggiora, G.M., Scheraga, H.A. Role of loop-helix interactions in stabilizing four-helix bundle proteins. Proc. natn. Acad. Sci. U.S.A., 89, 7315–7319 (1992).

    Article  CAS  Google Scholar 

  8. Steif, C., et al. Subunit interactions provide a significant contribution to the stability of the dimeric four-α-helical-bundle protein Rop. Biochemistry 32, 3867–3876 (1993).

    Article  CAS  Google Scholar 

  9. Crick, F.H.C. The packing of α-helices: Simple coiled coils. Acta crystallogr. 6, 689–697 (1953).

    Article  CAS  Google Scholar 

  10. Lupas, A., Van Dyke, M. & Stock, J. Predicting coiled coils from protein sequences. Science 252, 1162–1164 (1991).

    Article  CAS  Google Scholar 

  11. Cohen, C. & Parry, D.A.D. α-helical coiled coils- A widespread motif in proteins. Trends biochem. Sci. 11, 245–248 (1986).

    Article  CAS  Google Scholar 

  12. Banner, D.W., Kokkinidis, M. & Tsernoglou, D. Structure of the ColE1 Rop protein at 1.7 Å resolution. J. molec. Biol. 196, 657–675 (1987).

    Article  CAS  Google Scholar 

  13. Chou, K.C. The role of loops in stabilizing bundle motif protein structures. Prot. Engng., 4, 849–850 (1991).

    Article  CAS  Google Scholar 

  14. Paliakasis, C.D. & Kokkinidis, M. The stability of the four-α-helix bundle motif in proteins. Prot. Engng. 4, 849–850 (1991).

    Article  CAS  Google Scholar 

  15. Brunet, A.P. et al. The role of turns in the structure of an α-helical protein. Nature, 364, 355–358 (1993).

    Article  CAS  Google Scholar 

  16. Castagnoli, L., Vetriani, C. & Cesareni, G. Linking an easily detectable phenotype to the folding of a common structural motif. Selection of rare turn mutations that prevent the folding of Rop. J. molec. Biol. 237, 378–387 (1994).

    Article  CAS  Google Scholar 

  17. Presnell, S.R. & Cohen, F.E. Topological distribution of four-α-helix bundles. Proc. natn. Acad. Sci. U.S.A., 86, 6592–6596 (1989).

    Article  CAS  Google Scholar 

  18. Baker, E.N. & Hubbard, R.E. Hydrogen bonding in globular proteins. Prog. Biophys. molec. Biol. 44, 97–179 (1984).

    Article  CAS  Google Scholar 

  19. Janin, J., Wodak, S., Levitt, M. & Maigret, B. Conformation of amino acid side-chains in proteins. J. molec. Biol. 125, 357–386 (1978).

    Article  CAS  Google Scholar 

  20. Robson, B. & Garnier, J. Introduction to proteins and protein engineering. (Elsevier Science publishers B.V. Amsterdam; 1986).

    Google Scholar 

  21. Thornton, J.M. et al. Analysis of errors found in protein structure coordinates in the Brookhaven Data Bank. Proceedings of the CCP4 Study Weekend, 26-27 January 1990, 39–52, (1990).

    Google Scholar 

  22. Efimov, A.V. Structure of α-α-hairpins with short connections. Prot. Engng. 4, 245–250 (1991).

    Article  CAS  Google Scholar 

  23. Smith, W.W., Burnett, R.M., Darling, G.D. & Ludwig, M.L. Structure of the semiquinone form of flavodoxin from clostridium MP. Extension of 1.8 Å resolution and some comparisons with the oxidized state. J. molec. Biol. 117 195–225 (1977).

    Article  CAS  Google Scholar 

  24. Reid, L.S. & Thornton, J.M. Rebuilding flavodoxin from Cα coordinates: a test study. Prot. Struct. Funct. Genet. 5, 170–182 (1989).

    Article  CAS  Google Scholar 

  25. Richardson, J.S. & Richardson, D.C. Amino acid preferencies for specific locations at the ends of α-helices. Science 240, 1648–1652 (1988).

    Article  CAS  Google Scholar 

  26. Serrano, L., Sancho, J., Hirchberg, M. & Fersht, A.R. α-Helix stability in proteins. I. Empirical correlations concerning substitution of side-chains at the N and C-caps and the replacement of Alanine by Glycine or Serine at solvent exposed surfaces. J molec. Biol. 227, 544–559 (1992).

    Article  CAS  Google Scholar 

  27. Arutyunyan, E.G., Kuranova, I.P., Vainshtein, B.K. & Steigemann, W. X-ray structure investigation of leghemoglobin. VI. structure of acetate-ferrileghemoglobin at a resolution of 2.0 Å. Kristallografiya, 25, 80–91 (1980).

    CAS  Google Scholar 

  28. Ploegman, J.H., Drenth, G., Kalk, K.H. & Hol, W.G.J. Structure of bovine liver rhodanese. I. Structure determination of 2.5 Å resolution and a comparison of the conformation and sequence of its two domains. J. molec. Biol. 123, 557–594 (1978).

    Article  CAS  Google Scholar 

  29. Wetlaufer, D. Prolyl isomerization: how significant for in vivo protein folding? Biopolymers 24, 251–255 (1985).

    Article  CAS  Google Scholar 

  30. Castagnoli, L. et al. Genetic and structural analysis of the ColE1 Rop (Rom) protein. EMBO J. 8, 621–629 (1989).

    Article  CAS  Google Scholar 

  31. Chang, C.T., Wu, C.-S.C. & Yang, J.T. Circular dichroic analysis of protein conformation: Inclusion of the β-turns. Anal. Biochem. 91, 13–31 (1978).

    Article  CAS  Google Scholar 

  32. Parry, D.A.D. & Fraser, R.D.B. Intermediate filament structure: 1. Analysis of IF protein sequence data. Int. J. biol. Macromol., 7, 203–213 (1985).

    Article  CAS  Google Scholar 

  33. Quax-Jeuken, Y.E.F.M., Quax, W.J. & Bloemendal, H. Primary and secondary structure of hamster vimentin predicted from the nucleotide sequence. Proc. natn. Acad. Sci. U.S.A. 80, 3548–3552 (1983).

    Article  CAS  Google Scholar 

  34. McLachlan, A.D. & Karn, J. Periodic features in the amino acid sequence of nematode myosin rod. J. molec. Biol. 164, 605–626 (1983).

    Article  CAS  Google Scholar 

  35. CCP4. The SERC (UK) Collaborative Computing Project No.4: A Suite of programmes for protein Crystallography, (distributed from Daresbury Laboratory, Warrington WA44AD, UK; 1979).

  36. Lim, V.I. Algorithms for prediction of α-helical and β-structural regions in globular proteins. J. molec. Biol. 88, 873–894 (1974).

    Article  CAS  Google Scholar 

  37. DeGrado, W.F. & Lear, J.D. Induction of peptide conformation of apolar/water interfaces. 1. A study with model peptides of designed hydrophobic periodicity. J. Am. chem. Soc. 107, 7684–7689 (1985).

    Article  CAS  Google Scholar 

  38. Lovejoy, B. et al. Crystal structure of a synthetic triple-stranded α-helical bundle. Science 259, 1288–1293 (1993).

    Article  CAS  Google Scholar 

  39. Tronrud, D.E., Ten Eyck, L.F. & Matthews, B.W. An efficient general-purpose least-squares refinement program for macromolecular structures. Acta crystallogr. A43, 489–501 (1987).

    Article  CAS  Google Scholar 

  40. Kokkinidis,M. et al. Correlation between protein stability and crystal properties of designed Rop variants. Prot. Struct. Funct. .Genet., 16 214–216 (1993).

    Article  CAS  Google Scholar 

  41. Matthews, B.W. Solvent content of protein crystals. J. molec. Biol. 33, 491–497 (1968).

    Article  CAS  Google Scholar 

  42. Brünger, A.T. X-PLOR Manual, v. 2.1, (Yale University, New Haven, U.S.A.; 1990).

    Google Scholar 

  43. Brünger, A.T. Extension of molecular replacement: a new search strategy based on Patterson correlation refinement. Acta crystallogr. A46, 46–57 (1990).

    Article  Google Scholar 

  44. Read, R.J. Improved Fourier coefficients for map using phases from partial structures with errors. Acta crystallogr. A42, 140–149 (1986).

    Article  CAS  Google Scholar 

  45. Jones, T.A. in FRODO: A graphics fitting program for macromolecule in computational crystallography. ed. Sayre, D. 303–317 (Clarendon press, Oxford; (1988).

    Google Scholar 

  46. Brünger, A.T., Krukowski, A. & Erickson, J. Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta crystallogr. A46, 585–593 (1990).

    Article  Google Scholar 

  47. Perkins, S.J. Protein volumes and hydration effects-The calculation of partial specific volumes, neutron scattering matchpoints and 280 nm Absorption coefficients for proteins and glycoproteins from amino acid sequences. Eur. J. Biochem. 157, 3867–3876 (1993).

    Google Scholar 

  48. Privalov, P.L., Plotnikov, V.V. & Filimonov, V.V. Precision scanning microcalorimeter for the study of liquids. J. chem. Thermodynamics 7, 41–47 (1975).

    Article  CAS  Google Scholar 

  49. Marky, L.A. & Breslauer, K.J. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers 26, 1601–1620 (1987).

    Article  CAS  Google Scholar 

  50. Yang, J.T., Wu, C.-S.C. & Martinez, H.M. Calculation of protein conformation from circular dichroism. Meth. Enzymol. 130, 208–269 (1986).

    Article  CAS  Google Scholar 

Download references

Author information

Author notes

  1. Demetrius Tsernoglou

    Present address: Università di Roma “La Sapienza”, Dept. of Biochemistry, Piazzale A. Moro 5, I-00185, Rome, Italy

Authors and Affiliations

  1. University of Crete, Dept. of Biology and IMBB, P.O. Box 1527, GR-71110, Heraklion, Crete, Greece

    Metaxia Vlassi & Michael Kokkinidis

  2. Institut für Physikalische Chemie der Westfälischen Wilhelms-Universität, Schlossplatz 4/7, D-48149, Münster, Germany

    Christian Steif, Peter Weber & Hans-Jürgen Hinz

  3. European Molecular Biology Laboratory, Meyerhofstr. 1, D-69012, Heidelberg, Germany

    Demetrius Tsernoglou

  4. EMBL, c/o DESY, Notkestrasse 85, D-22603, Hamburg, Germany

    Keith S. Wilson

Authors
  1. Metaxia Vlassi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Christian Steif
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Peter Weber
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Demetrius Tsernoglou
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Keith S. Wilson
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hans-Jürgen Hinz
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Michael Kokkinidis
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Vlassi, M., Steif, C., Weber, P. et al. Restored heptad pattern continuity does not alter the folding of a four-α-helix bundle. Nat Struct Mol Biol 1, 706–716 (1994). https://doi.org/10.1038/nsb1094-706

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsb1094-706

This article is cited by

Search

Advanced 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