Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme

  1. Zhening Zhang
  2. Wenguang G Liang
  3. Lucas J Bailey
  4. Yong Zi Tan
  5. Hui Wei
  6. Andrew Wang
  7. Mara Farcasanu
  8. Virgil A Woods
  9. Lauren A McCord
  10. David Lee
  11. Weifeng Shang
  12. Rebecca Deprez-Poulain
  13. Benoit Deprez
  14. David R Liu
  15. Akiko Koide
  16. Shohei Koide
  17. Anthony A Kossiakoff
  18. Sheng Li  Is a corresponding author
  19. Bridget Carragher  Is a corresponding author
  20. Clinton S Potter  Is a corresponding author
  21. Wei-Jen Tang  Is a corresponding author
  1. New York Structural Biology Center, United States
  2. The University of Chicago, United States
  3. University of California, San Diego, United States
  4. Argonne National Laboratory, United States
  5. Université de Lille, France
  6. Harvard University, United States
  7. New York University, United States

Abstract

Insulin degrading enzyme (IDE) plays key roles in degrading peptides vital in type 2 diabetes, Alzheimer's, inflammation, and other human diseases. However, the process through which IDE recognizes peptides that tend to form amyloid fibrils remained unsolved. We used cryoEM to understand both the apo- and insulin-bound dimeric IDE states, revealing that IDE displays a large opening between the homologous ~55 kDa N- and C-terminal halves to allow selective substrate capture based on size and charge complementarity. We also used cryoEM, X-ray crystallography, SAXS, and HDX-MS to elucidate the molecular basis of how amyloidogenic peptides stabilize the disordered IDE catalytic cleft, thereby inducing selective degradation by substrate-assisted catalysis. Furthermore, our insulin-bound IDE structures explain how IDE processively degrades insulin by stochastically cutting either chain without breaking disulfide bonds. Together, our studies provide a mechanism for how IDE selectively degrades amyloidogenic peptides and offers structural insights for developing IDE-based therapies.

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Article and author information

Author details

  1. Zhening Zhang

    National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Wenguang G Liang

    Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Lucas J Bailey

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Yong Zi Tan

    National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6656-6320
  5. Hui Wei

    National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Andrew Wang

    Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Mara Farcasanu

    Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Virgil A Woods

    Department of Medicine, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Lauren A McCord

    Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. David Lee

    Department of Medicine, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Weifeng Shang

    BioCAT, Argonne National Laboratory, Argonne, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Rebecca Deprez-Poulain

    U1177 - Drug and Molecules for Living Systems, Université de Lille, Lille, France
    Competing interests
    The authors declare that no competing interests exist.
  13. Benoit Deprez

    U1177 - Drug and Molecules for Living Systems, Université de Lille, Lille, France
    Competing interests
    The authors declare that no competing interests exist.
  14. David R Liu

    Department of Chemistry and Chemical Biology, Harvard University, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Akiko Koide

    Perlmutter Cancer Center, New York University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  16. Shohei Koide

    Perlmutter Cancer Center, New York University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  17. Anthony A Kossiakoff

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  18. Sheng Li

    Department of Medicine, University of California, San Diego, La Jolla, United States
    For correspondence
    s4li@ucsd.edu
    Competing interests
    The authors declare that no competing interests exist.
  19. Bridget Carragher

    National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
    For correspondence
    bcarr@nysbc.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0624-5020
  20. Clinton S Potter

    National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
    For correspondence
    cpotter@nysbc.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2394-0831
  21. Wei-Jen Tang

    Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States
    For correspondence
    wtang@bsd.uchicago.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8267-8995

Funding

National Institutes of Health (GM81539)

  • Wei-Jen Tang

Defense Advanced Research Projects Agency (N66001-14-2-4053)

  • David R Liu

Simons Foundation (349247)

  • Bridget Carragher
  • Clinton S Potter

National Institutes of Health (GM121964)

  • Wei-Jen Tang

National Institutes of Health (GM103310)

  • Bridget Carragher
  • Clinton S Potter

National Institutes of Health (R35 GM118062)

  • David R Liu

Howard Hughes Medical Institute

  • David R Liu

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Sriram Subramaniam, National Cancer Institute, United States

Publication history

  1. Received: November 15, 2017
  2. Accepted: March 28, 2018
  3. Accepted Manuscript published: March 29, 2018 (version 1)
  4. Version of Record published: April 20, 2018 (version 2)

Copyright

© 2018, Zhang et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Zhening Zhang
  2. Wenguang G Liang
  3. Lucas J Bailey
  4. Yong Zi Tan
  5. Hui Wei
  6. Andrew Wang
  7. Mara Farcasanu
  8. Virgil A Woods
  9. Lauren A McCord
  10. David Lee
  11. Weifeng Shang
  12. Rebecca Deprez-Poulain
  13. Benoit Deprez
  14. David R Liu
  15. Akiko Koide
  16. Shohei Koide
  17. Anthony A Kossiakoff
  18. Sheng Li
  19. Bridget Carragher
  20. Clinton S Potter
  21. Wei-Jen Tang
(2018)
Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme
eLife 7:e33572.
https://doi.org/10.7554/eLife.33572
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