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

New York Structural Biology Center, United States
The University of Chicago, United States
University of California, San Diego, United States
Argonne National Laboratory, United States
Université de Lille, France
Harvard University, United States
New York University, United States

Mar 29, 2018

Open access
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Abstract
Data availability
Article and author information
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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.

Data availability

The following data sets were generated

1. Tang WJ et al
(2018) IDE with insulin map
EMD-7041.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE Open(O)/partial-Open(pO) state map
EMD-7092.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE O/O state map
EMD-7065.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE pO/pO state map
EMD-7090.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE with insulin and FabH11-E map
EMD-7062.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE O/pO state with FabH11-E map
EMD-7093.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE O/O state with FabH11-E map
EMD-7066.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE pO/pO state with FabH11-E map
EMD-7091.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE with mostly insulin A chain model
EMDB:6B3Q.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE with mostly insulin B chain model
EMDB:6BFC.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE O/pO state model
EMDB:6BF8.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE O/O state model
EMDB:6B7Y.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE pO/pO state model
EMDB:6BF6.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE with insulin and FabH11-E model
EMDB:6B70.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE O/pO state with FabH11-E model
EMDB:6BF9.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE O/O state with FabH11-E model
EMDB:6B7Z.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE pO/pO state with FabH11-E model
EMDB:6BF7.

https://www.ebi.ac.uk/pdbe/
1. Tang WJ et al
(2018) IDE with insulin and Fab1 structure
PDB: 5WOB.

http://www.rcsb.org/
1. Tang WJ et al
(2018) IDE with amyloid β and Fab1 structure
PDB: 4M1C.

http://www.rcsb.org/
1. Tang WJ et al
(2018) IDE with insulin and Fab1E structure
PDB: 5CJO.

http://www.rcsb.org/
1. Tang WJ et al
(2018) IDE with FabH11-E structure
PDB: 5UOE.

http://www.rcsb.org/

Article and author information

Author details

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.
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.
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.
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.

"This ORCID iD identifies the author of this article:" 0000-0001-6656-6320
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.
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.
Mara Farcasanu

Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States

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The authors declare that no competing interests exist.
Virgil A Woods

Department of Medicine, University of California, San Diego, La Jolla, United States

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The authors declare that no competing interests exist.
Lauren A McCord

Ben-May Institute for Cancer Research, The University of Chicago, Chicago, United States

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The authors declare that no competing interests exist.
David Lee

Department of Medicine, University of California, San Diego, La Jolla, United States

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The authors declare that no competing interests exist.
Weifeng Shang

BioCAT, Argonne National Laboratory, Argonne, United States

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The authors declare that no competing interests exist.
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.
Benoit Deprez

U1177 - Drug and Molecules for Living Systems, Université de Lille, Lille, France

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The authors declare that no competing interests exist.
David R Liu

Department of Chemistry and Chemical Biology, Harvard University, Boston, United States

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The authors declare that no competing interests exist.
Akiko Koide

Perlmutter Cancer Center, New York University, New York, United States

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The authors declare that no competing interests exist.
Shohei Koide

Perlmutter Cancer Center, New York University, New York, United States

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The authors declare that no competing interests exist.
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.
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.
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.

"This ORCID iD identifies the author of this article:" 0000-0002-0624-5020
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.

"This ORCID iD identifies the author of this article:" 0000-0003-2394-0831
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.

"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

Sriram Subramaniam, National Cancer Institute, United States

Version history

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

Copyright

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.