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.

  • Letter
  • Published:

Crystal structure of a stable dimer reveals the molecular basis of serpin polymerization

Nature volume 455, pages 1255–1258 (2008)Cite this article

Abstract

Repeating intermolecular protein association by means of β-sheet expansion is the mechanism underlying a multitude of diseases including Alzheimer’s, Huntington’s and Parkinson’s and the prion encephalopathies1. A family of proteins, known as the serpins, also forms large stable multimers by ordered β-sheet linkages leading to intracellular accretion and disease2. These ‘serpinopathies’ include early-onset dementia caused by mutations in neuroserpin, liver cirrhosis and emphysema caused by mutations in α1-antitrypsin (α1AT), and thrombosis caused by mutations in antithrombin3. Serpin structure and function are quite well understood, and the family has therefore become a model system for understanding the β-sheet expansion disorders collectively known as the conformational diseases4. To develop strategies to prevent and reverse these disorders, it is necessary to determine the structural basis of the intermolecular linkage and of the pathogenic monomeric state. Here we report the crystallographic structure of a stable serpin dimer which reveals a domain swap of more than 50 residues, including two long antiparallel β-strands inserting in the centre of the principal β-sheet of the neighbouring monomer. This structure explains the extreme stability of serpin polymers, the molecular basis of their rapid propagation, and provides critical new insights into the structural changes which initiate irreversible β-sheet expansion.

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

Figure 1: Crystallographic structures of active, latent and self-terminating dimer of the serpin antithrombin.
Figure 2: Biochemical properties of serpin polymers and the M* state.
Figure 3: Models of the serpin polymer and the M* state.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited in the Protein Data Bank under the accession code 2ZNH.

References

  1. Harrison, R. S., Sharpe, P. C., Singh, Y. & Fairlie, D. P. Amyloid peptides and proteins in review. Rev. Physiol. Biochem. Pharmacol. 159, 1–77 (2007)

    CAS  PubMed  Google Scholar 

  2. Lomas, D. A. & Carrell, R. W. Serpinopathies and the conformational dementias. Nature Rev. Genet. 3, 759–768 (2002)

    Article  CAS  Google Scholar 

  3. Lomas, D. A. et al. Molecular mousetraps and the serpinopathies. Biochem. Soc. Trans. 33, 321–330 (2005)

    Article  CAS  Google Scholar 

  4. Carrell, R. W. & Lomas, D. A. Conformational disease. Lancet 350, 134–138 (1997)

    Article  CAS  Google Scholar 

  5. Sharp, H. L., Bridges, R. A., Krivit, W. & Freier, E. F. Cirrhosis associated with α1-antitrypsin deficiency: a previously unrecognized inherited disorder. J. Lab. Clin. Med. 73, 934–939 (1969)

    CAS  PubMed  Google Scholar 

  6. Lomas, D. A., Evans, D. L., Finch, J. T. & Carrell, R. W. The mechanism of Z α1-antitrypsin accumulation in the liver. Nature 357, 605–607 (1992)

    Article  ADS  CAS  Google Scholar 

  7. Lomas, D. A. et al. Polymerisation underlies α1-antitrypsin deficiency, dementia and other serpinopathies. Front. Biosci. 9, 2873–2891 (2004)

    Article  CAS  Google Scholar 

  8. Huntington, J. A., Read, R. J. & Carrell, R. W. Structure of a serpin-protease complex shows inhibition by deformation. Nature 407, 923–926 (2000)

    Article  ADS  CAS  Google Scholar 

  9. Gettins, P. G. Serpin structure, mechanism, and function. Chem. Rev. 102, 4751–4804 (2002)

    Article  CAS  Google Scholar 

  10. Im, H., Ahn, H. Y. & Yu, M. H. Bypassing the kinetic trap of serpin protein folding by loop extension. Protein Sci. 9, 1497–1502 (2000)

    Article  CAS  Google Scholar 

  11. Corral, J. et al. Mutations in the shutter region of antithrombin result in formation of disulfide-linked dimers and severe venous thrombosis. J. Thromb. Haemost. 2, 931–939 (2004)

    Article  CAS  Google Scholar 

  12. Dafforn, T. R., Mahadeva, R., Elliott, P. R., Sivasothy, P. & Lomas, D. A. A kinetic mechanism for the polymerization of α1-antitrypsin. J. Biol. Chem. 274, 9548–9555 (1999)

    Article  CAS  Google Scholar 

  13. Kim, D. & Yu, M. H. Folding pathway of human α1-antitrypsin: characterization of an intermediate that is active but prone to aggregation. Biochem. Biophys. Res. Commun. 226, 378–384 (1996)

    Article  CAS  Google Scholar 

  14. Devlin, G. L., Chow, M. K., Howlett, G. J. & Bottomley, S. P. Acid denaturation of α1-antitrypsin: characterization of a novel mechanism of serpin polymerization. J. Mol. Biol. 324, 859–870 (2002)

    Article  CAS  Google Scholar 

  15. Tew, D. J. & Bottomley, S. P. Probing the equilibrium denaturation of the serpin α1-antitrypsin with single tryptophan mutants; evidence for structure in the urea unfolded state. J. Mol. Biol. 313, 1161–1169 (2001)

    Article  CAS  Google Scholar 

  16. Egelund, R. et al. A regulatory hydrophobic area in the flexible joint region of plasminogen activator inhibitor-1, defined with fluorescent activity-neutralizing ligands. Ligand-induced serpin polymerization. J. Biol. Chem. 276, 13077–13086 (2001)

    Article  CAS  Google Scholar 

  17. Zhou, A. & Carrell, R. W. Dimers initiate and propagate serine protease inhibitor polymerisation. J. Mol. Biol. 375, 36–42 (2008)

    Article  CAS  Google Scholar 

  18. Yu, M. H., Lee, K. N. & Kim, J. The Z type variation of human α1-antitrypsin causes a protein folding defect. Nature Struct. Biol. 2, 363–367 (1995)

    Article  CAS  Google Scholar 

  19. James, E. L., Whisstock, J. C., Gore, M. G. & Bottomley, S. P. Probing the unfolding pathway of α1-antitrypsin. J. Biol. Chem. 274, 9482–9488 (1999)

    Article  CAS  Google Scholar 

  20. Kjoller, L. et al. Conformational changes of the reactive-centre loop and β-strand 5A accompany temperature-dependent inhibitor-substrate transition of plasminogen-activator inhibitor 1. Eur. J. Biochem. 241, 38–46 (1996)

    Article  CAS  Google Scholar 

  21. Jung, C. H., Na, Y. R. & Im, H. Retarded protein folding of deficient human α1-antitrypsin D256V and L41P variants. Protein Sci. 13, 694–702 (2004)

    Article  CAS  Google Scholar 

  22. Bennett, M. J., Sawaya, M. R. & Eisenberg, D. Deposition diseases and 3D domain swapping. Structure 14, 811–824 (2006)

    Article  CAS  Google Scholar 

  23. Liu, Y. & Eisenberg, D. 3D domain swapping: as domains continue to swap. Protein Sci. 11, 1285–1299 (2002)

    Article  CAS  Google Scholar 

  24. James, E. L. & Bottomley, S. P. The mechanism of α1-antitrypsin polymerization probed by fluorescence spectroscopy. Arch. Biochem. Biophys. 356, 296–300 (1998)

    Article  CAS  Google Scholar 

  25. Pearce, M. C., Cabrita, L. D., Ellisdon, A. M. & Bottomley, S. P. The loss of tryptophan 194 in antichymotrypsin lowers the kinetic barrier to misfolding. FEBS J. 274, 3622–3632 (2007)

    Article  CAS  Google Scholar 

  26. Pedersen, K. E. et al. Plasminogen activator inhibitor-1 polymers, induced by inactivating amphipathic organochemical ligands. Biochem. J. 372, 747–755 (2003)

    Article  CAS  Google Scholar 

  27. Crowther, D. C., Serpell, L. C., Dafforn, T. R., Gooptu, B. & Lomas, D. A. Nucleation of α1-antichymotrypsin polymerization. Biochemistry 42, 2355–2363 (2003)

    Article  CAS  Google Scholar 

  28. Davis, R. L. et al. Familial dementia caused by polymerization of mutant neuroserpin. Nature 401, 376–379 (1999)

    ADS  CAS  PubMed  Google Scholar 

  29. Soto, C. et al. β-sheet breaker peptides inhibit fibrillogenesis in a rat brain model of amyloidosis: implications for Alzheimer’s therapy. Nature Med. 4, 822–826 (1998)

    Article  CAS  Google Scholar 

  30. Olson, S. T., Bjork, I. & Shore, J. D. Kinetic characterization of heparin-catalyzed and uncatalyzed inhibition of blood coagulation proteinases by antithrombin. Methods Enzymol. 222, 525–559 (1993)

    Article  CAS  Google Scholar 

  31. Stock, D., Perisic, O. & Lowe, J. Robotic nanolitre protein crystallisation at the MRC Laboratory of Molecular Biology. Prog. Biophys. Mol. Biol. 88, 311–327 (2005)

    Article  CAS  Google Scholar 

  32. Leslie, A. W. G. in Joint CCP4 and ESF-EACMB Newsletter on Protein Crystallography (Daresbury Laboratory, 1992)

    Google Scholar 

  33. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C. & Read, R. J. Likelihood-enhanced fast translation functions. Acta Crystallogr. D 61, 458–464 (2005)

    Article  Google Scholar 

  34. Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D. 54, 905–921 (1998)

    Article  CAS  Google Scholar 

  35. McRee, D. E. A visual protein crystallographic software system for X11/XView. J. Mol. Graph. 10, 44–46 (1992)

    Article  Google Scholar 

  36. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

    Article  Google Scholar 

  37. Lovell, S. C. et al. Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins 50, 437–450 (2003)

    Article  CAS  Google Scholar 

  38. DeLano, W. L. The PyMOL Molecular Graphics System. <http://www.pymol.org> (2002)

  39. Zhou, A., Carrell, R. W. & Huntington, J. A. The serpin inhibitory mechanism is critically dependent on the length of the reactive center loop. J. Biol. Chem. 276, 27541–27547 (2001)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank R. Carrell, D. Crowther and D. Lomas for their comments on the manuscript. We are also grateful to J. Löwe for access to the robotic crystallisation facility in the MRC-LMB, and to M. Weldon for N-terminal sequencing. This work was supported by the National Institutes of Health (USA) and the Uehara Memorial Foundation (Japan, to M.Y.), and J.A.H. is a senior MRC non-clinical fellow. Data were collected at beamlines I02 and I04 at the Diamond Light Source and we acknowledge the support of L. Duke, G. Evans, R. Flaig, J. Sandy and T. Sorensen.

Author information

Authors and Affiliations

  1. Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK,

    Masayuki Yamasaki, Wei Li, Daniel J. D. Johnson & James A. Huntington

Authors
  1. Masayuki Yamasaki
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wei Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Daniel J. D. Johnson
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. James A. Huntington
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to James A. Huntington.

Supplementary information

Supplementary Information

This file contains Supplementary Table 1 and Supplementary Figures 1 and 2 with Legends (PDF 469 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yamasaki, M., Li, W., Johnson, D. et al. Crystal structure of a stable dimer reveals the molecular basis of serpin polymerization. Nature 455, 1255–1258 (2008). https://doi.org/10.1038/nature07394

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature07394

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

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