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.

  • Timeline
  • Published:

From the first protein structures to our current knowledge of protein folding: delights and scepticisms

Abstract

Every breakthrough that opens new vistas also removes the ground from under the feet of other scientists. The scientific joy of those who have seen the new light is accompanied by the dismay of those whose way of life has been changed for ever. The publication of the first structures of proteins at atomic resolution 50 years ago astounded and inspired scientists in every field, but caused others to flee or scoff. That advance and every subsequent paradigm-shifting breakthrough in protein science have met with some resistance before universal acceptance. I relate these events and their impact on the field of protein folding.

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

Access options

Buy this article

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

Figure 1: Three-dimensional structure of myoglobin.
Figure 2: Max Perutz and John Kendrew.
Figure 3: The pathway of folding of the Engrailed homeodomain of Drosophila melanogaster.

References

  1. Kendrew, J. C. et al. A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature 181, 662–666 (1958).

    Article  CAS  Google Scholar 

  2. Perutz, M. F. et al. A three-dimensional fourier synthesis at 5.5-Å resolution, obtained by X-ray analysis. Nature 185, 416–422 (1960).

    Article  CAS  Google Scholar 

  3. Blake, C. C. et al. Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Å resolution. Nature 206, 757–761 (1965).

    Article  CAS  Google Scholar 

  4. Matthews, B. W., Sigler, P. B., Henderson, R. & Blow, D. M. Three-dimensional structure of tosyl-α-chymotrypsin. Nature 214, 652–656 (1967).

    Article  CAS  Google Scholar 

  5. Wyckoff, H. W. et al. The structure of ribonuclease-S at 3.5 Å resolution. J. Biol. Chem. 242, 3984–3988 (1967).

    CAS  PubMed  Google Scholar 

  6. Lipscomb, W. N., Hartsuck, J. A., Quiocho, F. A. & Reeke, G. N. Jr. The structure of carboxypeptidase A. IX. The x-ray diffraction results in the light of the chemical sequence. Proc. Natl Acad. Sci. USA 64, 28–35 (1969).

    Article  CAS  Google Scholar 

  7. Arnone, A. et al. A high resolution structure of an inhibitor complex of the extracellular nuclease of Staphylococcus aureus. I. Experimental procedures and chain tracing. J. Biol. Chem. 246, 2302–2316 (1971).

    CAS  PubMed  Google Scholar 

  8. Perutz, M. F. Stereochemistry of cooperative effects in haemoglobin. Nature 228, 726–739 (1970).

    Article  CAS  Google Scholar 

  9. Epstein, C. J., Goldberger, R. F. & Anfinsen, C. B. The genetic control of tertiary protein structure. Model systems. Cold Spring Harb. Symp. Quant. Biol. 28, 439–449 (1963).

    Article  CAS  Google Scholar 

  10. Levinthal, C. in Mossbauer Spectroscopy in Biological Systems (eds Debrunner, P. et al.) 22–24 (University of Illinois Press, Urbana, Illinois, 1969).

    Google Scholar 

  11. Ptitsyn, O. B. Stages in the mechanism of self-organization of protein molecules. Dokl. Akad. Nauk SSSR 210, 1213–1215 (1973) (in Russian).

    CAS  PubMed  Google Scholar 

  12. Kim, P. S. & Baldwin, R. L. Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu. Rev. Biochem. 51, 459–489 (1982).

    Article  CAS  Google Scholar 

  13. Karplus, M. & Weaver, D. L. Diffusion-collision model for protein folding. Biopolymers 18, 1421–1437 (1979).

    Article  CAS  Google Scholar 

  14. Dolgikh, D. A. et al. α-Lactalbumin: compact state with fluctuating tertiary structure? FEBS Lett. 136, 311–315 (1981).

    Article  CAS  Google Scholar 

  15. Creighton, T. E. The two-disulphide intermediates and the folding pathway of reduced pancreatic trypsin inhibitor. J. Mol. Biol. 95, 167–199 (1975).

    Article  CAS  Google Scholar 

  16. Cohen, S. N., Chang, A. C., Boyer, H. W. & Helling, R. B. Construction of biologically functional bacterial plasmids in vitro. Proc. Natl Acad. Sci. USA 70, 3240–3244 (1973).

    Article  CAS  Google Scholar 

  17. Shortle, D. A genetic system for analysis of staphylococcal nuclease. Gene 22, 181–189 (1983).

    Article  CAS  Google Scholar 

  18. Perry, L. J., Heyneker, H. L. & Wetzel, R. Non-toxic expression in Escherichia coli of a plasmid-encoded gene for phage T4 lysozyme. Gene 38, 259–264 (1985).

    Article  CAS  Google Scholar 

  19. Hartley, R. W. Barnase and barstar. Expression of its cloned inhibitor permits expression of a cloned ribonuclease. J. Mol. Biol. 202, 913–915 (1988).

    Article  CAS  Google Scholar 

  20. Sanger, F. et al. Nucleotide sequence of bacteriophage ϕ X174 DNA. Nature 265, 687–695 (1977).

    Article  CAS  Google Scholar 

  21. Hutchison, C. A., et al. Mutagenesis at a specific position in a DNA sequence. J. Biol. Chem. 253, 6551–6560 (1978).

    CAS  PubMed  Google Scholar 

  22. Winter, G., Fersht, A. R., Wilkinson, A. J., Zoller, M. & Smith, M. Redesigning enzyme structure by site-directed mutagenesis: tyrosyl tRNA synthetase and ATP binding. Nature 299, 756–758 (1982).

    Article  CAS  Google Scholar 

  23. Matouschek, A., Kellis, J. T. Jr., Serrano, L. & Fersht, A. R. Mapping the transition state and pathway of protein folding by protein engineering. Nature 340, 122–126 (1989).

    Article  CAS  Google Scholar 

  24. Fersht, A. R., Leatherbarrow, R. J. & Wells, T. N. Structure–activity relationships in engineered proteins: analysis of use of binding energy by linear free energy relationships. Biochemistry 26, 6030–6038 (1987).

    Article  CAS  Google Scholar 

  25. Itzhaki, L. S., Otzen, D. E. & Fersht, A. R. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254, 260–288 (1995).

    Article  CAS  Google Scholar 

  26. Daggett, V. & Fersht, A. R. Is there a unifying mechanism for protein folding? Trends Biochem. Sci. 28, 18–25 (2003).

    Article  CAS  Google Scholar 

  27. Levitt, M. & Lifson, S. Refinement of protein conformations using a macromolecular energy minimization procedure. J. Mol. Biol. 46, 269–279 (1969).

    Article  CAS  Google Scholar 

  28. McCammon, J. A., Gelin, B. R. & Karplus, M. Dynamics of folded proteins. Nature 267, 585–590 (1977).

    Article  CAS  Google Scholar 

  29. Daggett, V. & Fersht, A. The present view of the mechanism of protein folding. Nature Rev. Mol. Cell Biol. 4, 497–502 (2003).

    Article  CAS  Google Scholar 

  30. Williamson, M. P., Havel, T. F. & Wuthrich, K. Solution conformation of proteinase inhibitor IIA from bull seminal plasma by 1H nuclear magnetic resonance and distance geometry. J. Mol. Biol. 182, 295–315 (1985).

    Article  CAS  Google Scholar 

  31. Baum, J., Dobson, C. M., Evans, P. A. & Hanley, C. Characterization of a partly folded protein by NMR methods: studies on the molten globule state of guinea pig α-lactalbumin. Biochemistry 28, 7–13 (1989).

    Article  CAS  Google Scholar 

  32. Bax, A. & Grishaev, A. Weak alignment NMR: a hawk-eyed view of biomolecular structure. Curr. Opin. Struct. Biol. 15, 563–570 (2005).

    Article  CAS  Google Scholar 

  33. Religa, T. L., Markson, J. S., Mayor, U., Freund, S. M. & Fersht, A. R. Solution structure of a protein denatured state and folding intermediate. Nature 437, 1053–1056 (2005).

    Article  CAS  Google Scholar 

  34. Korzhnev, D. M. & Kay, L. E. Probing invisible, low-populated states of protein molecules by relaxation dispersion NMR spectroscopy: an application to protein folding. Acc. Chem. Res. 41, 442–451 (2008).

    Article  CAS  Google Scholar 

  35. Hvidt, A. & Linderstrøm-Lang, K. Exchange of hydrogen atoms in insulin with deuterium atoms in aqueous solutions. Biochim. Biophys. Acta 14, 574–575 (1954).

    Article  CAS  Google Scholar 

  36. Englander, S. W., Mayne, L., Bai, Y. & Sosnick, T. R. Hydrogen exchange: the modern legacy of Linderstrøm-Lang. Protein Sci. 6, 1101–1109 (1997).

    Article  CAS  Google Scholar 

  37. Levitt, M. & Chothia, C. Structural patterns in globular proteins. Nature 261, 552–558 (1976).

    Article  CAS  Google Scholar 

  38. Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

    Article  CAS  Google Scholar 

  39. Petsko, G. A. An idea whose time has gone. Genome Biol. 8, 107 (2007).

    Article  Google Scholar 

  40. Banci, L. et al. An idea whose time has come. Genome Biol. 8, 408 (2007).

    Article  Google Scholar 

  41. Moult, J. et al. Critical assessment of methods of protein structure prediction — Round VII. Proteins 69 (Suppl. 8), 3–9 (2007).

    Article  CAS  Google Scholar 

  42. Daggett, V. & Levitt, M. Protein unfolding pathways explored through molecular dynamics simulations. J. Mol. Biol. 232, 600–619 (1993).

    Article  CAS  Google Scholar 

  43. Mayor, U. et al. The complete folding pathway of a protein from nanoseconds to microseconds. Nature 421, 863–867 (2003).

    Article  CAS  Google Scholar 

  44. Vendruscolo, M., Paci, E., Dobson, C. M. & Karplus, M. Three key residues form a critical contact network in a protein folding transition state. Nature 409, 641–645 (2001).

    Article  CAS  Google Scholar 

  45. Gianni, S. et al. Unifying features in protein-folding mechanisms. Proc. Natl Acad. Sci. USA 100, 13286–13291 (2003).

    Article  CAS  Google Scholar 

  46. Fink, A. L. Natively unfolded proteins. Curr. Opin. Struct. Biol. 15, 35–41 (2005).

    Article  CAS  Google Scholar 

  47. Wells, M. et al. Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain. Proc. Natl Acad. Sci. USA 105, 5762–5767 (2008).

    Article  CAS  Google Scholar 

  48. Chiti, F. & Dobson, C. M. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem. 75, 333–366 (2006).

    Article  CAS  Google Scholar 

  49. Jones, P. T., Dear, P. H., Foote, J., Neuberger, M. S. & Winter, G. Replacing the complementarity-determining regions in a human antibody with those from a mouse. Nature 321, 522–525 (1986).

    Article  CAS  Google Scholar 

  50. Jiang, L. et al. De novo computational design of retro-aldol enzymes. Science 319, 1387–1391 (2008).

    Article  CAS  Google Scholar 

  51. Rothlisberger, D. et al. Kemp elimination catalysts by computational enzyme design. Nature 453, 190–195 (2008).

    Article  Google Scholar 

  52. Maxam, A. M. & Gilbert, W. A new method for sequencing DNA. Proc. Natl Acad. Sci. USA 74, 560–564 (1977).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

I thank the Medical Research Council for 40 years of funding, without which this article would not have been written.

Author information

Authors and Affiliations

Authors

Related links

Related links

FURTHER INFORMATION

Alan Fersht's homepage

European Bioinformatics Institute

National Center for Biotechnology Information

Protein Structure Initiative

Rights and permissions

Reprints and permissions

About this article

Cite this article

Fersht, A. From the first protein structures to our current knowledge of protein folding: delights and scepticisms. Nat Rev Mol Cell Biol 9, 650–654 (2008). https://doi.org/10.1038/nrm2446

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrm2446

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