Article | Published:

Structural characterization of a misfolded intermediate populated during the folding process of a PDZ domain

Nature Structural & Molecular Biology volume 17, pages 14311437 (2010) | Download Citation

Abstract

Incorrectly folded states transiently populated during the protein folding process are potentially prone to aggregation and have been implicated in a range of misfolding disorders that include Alzheimer's and Parkinson's diseases. Despite their importance, however, the structures of these states and the mechanism of their formation have largely escaped detailed characterization because of their short-lived nature. Here we present the structures of all the major states involved in the folding process of a PDZ domain, which include an off-pathway misfolded intermediate. By using a combination of kinetic, protein engineering, biophysical and computational techniques, we show that the misfolded intermediate is characterized by an alternative packing of the N-terminal β-hairpin onto an otherwise native-like scaffold. Our results suggest a mechanism of formation of incorrectly folded transient compact states by which misfolded structural elements are assembled together with more extended native-like regions.

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Acknowledgements

We acknowledge financial support from the Italian Ministero dell'Istruzione dell'Università e della Ricerca (2007B57EAB_004, 20074TJ3ZB_005, RBRN07BMCT_007) (S.G., Y.I., C.T.-A., M.B.), the Wenner Green Foundations (Y.I.), the Istituto Pasteur-Fondazione Cenci Bolognetti (Y.I.), European Molecular Biology Organization (Y.I.), Engineering and Physical Sciences Research Council (A.D.S.), Biotechnology and Biological Sciences Research Council (M.V.) and the Royal Society (M.V.).

Author information

Author notes

    • Ylva Ivarsson

    Present address: Department of Human Genetics, Katholieke Universiteit Leuven, Herestraat, Leuven, Belgium.

    • Stefano Gianni
    •  & Ylva Ivarsson

    These authors contributed equally to this work.

Affiliations

  1. Istituto Pasteur–Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Università di Roma 'La Sapienza', Rome, Italy.

    • Stefano Gianni
    • , Ylva Ivarsson
    • , Carlo Travaglini-Allocatelli
    •  & Maurizio Brunori
  2. Department of Chemistry, University of Cambridge, Cambridge, UK.

    • Alfonso De Simone
    •  & Michele Vendruscolo

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Contributions

S.G., Y.I., C.T.-A. and M.B. conceived and designed the experimental work; A.D.S. and M.V. conceived and designed the computational work; Y.I. expressed and purified the protein samples; S.G. and Y.I. conducted the experiments; A.D.S. did the simulations; S.G., Y.I., A.D.S., C.T.-A., M.B. and M.V. analyzed the data and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Michele Vendruscolo.

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DOI

https://doi.org/10.1038/nsmb.1956

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