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Accelerated disassembly of IgE–receptor complexes by a disruptive macromolecular inhibitor

Nature volume 491, pages 613617 (22 November 2012) | Download Citation

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IgE antibodies bind the high-affinity IgE Fc receptor (FcεRI), found primarily on mast cells and basophils, and trigger inflammatory cascades of the allergic response1,2. Inhibitors of IgE–FcεRI binding have been identified and an anti-IgE therapeutic antibody (omalizumab) is used to treat severe allergic asthma3,4. However, preformed IgE–FcεRI complexes that prime cells before allergen exposure dissociate extremely slowly5 and cannot be disrupted by strictly competitive inhibitors. IgE-Fc conformational flexibility indicated that inhibition could be mediated by allosteric or other non-classical mechanisms6,7,8. Here we demonstrate that an engineered protein inhibitor, DARPin E2_79 (refs 9, 10, 11), acts through a non-classical inhibition mechanism, not only blocking IgE–FcεRI interactions, but actively stimulating the dissociation of preformed ligand–receptor complexes. The structure of the E2_79–IgE-Fc3-4 complex predicts the presence of two non-equivalent E2_79 sites in the asymmetric IgE–FcεRI complex, with site 1 distant from the receptor and site 2 exhibiting partial steric overlap. Although the structure is indicative of an allosteric inhibition mechanism, mutational studies and quantitative kinetic modelling indicate that E2_79 acts through a facilitated dissociation mechanism at site 2 alone. These results demonstrate that high-affinity IgE–FcεRI complexes can be actively dissociated to block the allergic response and suggest that protein–protein complexes may be more generally amenable to active disruption by macromolecular inhibitors.

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Change history

  • 22 November 2012

    This article was originally incorrectly listed under Planetary Sciences. The subject terms have since been corrected.


Primary accessions

Protein Data Bank

Data deposits

The structure factors and model for the E2_79–C335 IgE complex have been deposited in the Protein Data Bank under accession code 4GRG.


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We thank B. Wurzburg and other past and present members of the Jardetzky Laboratory. This research was supported in part by an NIH research grant (AI-18939) and an American Asthma Foundation Senior Investigator Award as well as the Swiss National Science Foundation grant number 310030_127350 to T.S.J. We also thank C. A. Dahinden and B. M. Stadler and members of their groups for valuable discussions. Furthermore, we thank M. J. Baumann for technical support and Molecular Partners AG, especially P. Amstutz, M. T. Stumpp, P. Forrer and D. Steiner, for placing DARPin libraries at our disposal and providing scientific support.

Author information

Author notes

    • Beomkyu Kim
    •  & Alexander Eggel

    These authors contributed equally to this work.


  1. Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA

    • Beomkyu Kim
    • , Svetlana S. Tarchevskaya
    •  & Theodore S. Jardetzky
  2. Institute of Immunology, University of Bern, CH-3010 Bern, Switzerland

    • Alexander Eggel
    •  & Monique Vogel
  3. Max-Planck-Institut fur Molekulare Physiologie, Otto-Hahn-Str. 11, 44227 Dortmund, Germany

    • Heino Prinz


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B.K., A.E., S.S.T. and T.S.J. designed and performed experiments. B.K., A.E., S.S.T., H.P. and T.S.J. analysed data. B.K., S.S.T., A.E., M.V. and T.S.J. contributed reagents. B.K., S.S.T., A.E., M.V., H.P. and T.S.J. discussed/commented on results and edited the manuscript. B.K., A.E. and T.S.J. wrote the manuscript and Supplementary Information, and prepared the figures.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Theodore S. Jardetzky.

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    Supplementary Information

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