Biological Sciences Division
Published March 29, 2018 | Version v1
Journal article Open

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

Creators

  • 1. New York Structural Biology Center
  • 2. University of Chicago
  • 3. Columbia University
  • 4. University of California, San Diego
  • 5. Argonne National Laboratory
  • 6. Institut Pasteur de Lille
  • 7. Harvard University
  • 8. New York University

Description

Insulin degrading enzyme (IDE) plays key roles in degrading peptides vital in type two 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:

Tang WJ (2018) IDE with insulin map Publicly available at the Electron Microscopy Data Bank (accession no. EMD-7041). http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-7041

Tang WJ (2018) IDE Open(O)/partial-Open(pO) state map Publicly available at the Electron Microscopy Data Bank (accession no. EMD-7092). http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-7092

Tang WJ (2018) IDE O/O state map Publicly available at the Electron Microscopy Data Bank (accession no. EMD-7065). http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-7065

Tang WJ (2018) IDE pO/pO state map Publicly available at the Electron Microscopy Data Bank (accession no. EMD-7090). http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-7090

Tang WJ (2018) IDE with insulin and FabH11-E map Publicly available at the Electron Microscopy Data Bank (accession no. EMD-7062). http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-7062

Tang WJ (2018) IDE O/pO state with FabH11-E map Publicly available at the Electron Microscopy Data Bank (accession no. EMD-7093). http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-7093

Tang WJ (2018) IDE O/O state with FabH11-E map Publicly available at the Electron Microscopy Data Bank (accession no. EMD-7066). http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-7066

Tang WJ (2018) IDE pO/pO state with FabH11-E map Publicly available at the Electron Microscopy Data Bank (accession no. EMD-7091). http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-7091

Tang WJ (2018) IDE with mostly insulin A chain model Publicly available at the Electron Microscopy Data Bank (accession no. 6b3q). http://www.ebi.ac.uk/pdbe/entry/pdb/6b3q

Tang WJ (2018) IDE with mostly insulin B chain model Publicly available at the Electron Microscopy Data Bank (accession no. 6BFC). http://www.ebi.ac.uk/pdbe/entry/pdb/6bfc

Tang WJ (2018) IDE O/pO state model Publicly available at the Electron Microscopy Data Bank (accession no. 6bf8). http://www.ebi.ac.uk/pdbe/entry/pdb/6bf8

Tang WJ (2018) IDE O/O state model Publicly available at the Electron Microscopy Data Bank (accession no. 6b7y). http://www.ebi.ac.uk/pdbe/entry/pdb/6b7y

Tang WJ (2018) IDE pO/pO state model Publicly available at the Electron Microscopy Data Bank (accession no. 6bf6). http://www.ebi.ac.uk/pdbe/entry/pdb/6bf6

Tang WJ (2018) IDE with insulin and FabH11-E model Publicly available at the Electron Microscopy Data Bank (accession no. 6b70). http://www.ebi.ac.uk/pdbe/entry/pdb/6b70

Tang WJ (2018) IDE O/pO state with FabH11-E model Publicly available at the Electron Microscopy Data Bank (accession no. 6bf9). http://www.ebi.ac.uk/pdbe/entry/pdb/6bf9

Tang WJ (2018) IDE O/O state with FabH11-E model Publicly available at the Electron Microscopy Data Bank (accession no. 6b7z). http://www.ebi.ac.uk/pdbe/entry/pdb/6b7z

Tang WJ (2018) IDE pO/pO state with FabH11-E model Publicly available at the Electron Microscopy Data Bank (accession no. 6bf7). http://www.ebi.ac.uk/pdbe/entry/pdb/6bf7

Tang WJ (2018) IDE with insulin and Fab1 structure Publicly available at the RCSB Protein Data Bank (accession no. 5WOB). http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5WOB

Tang WJ (2018) IDE with amyloid β and Fab1 structure Publicly available at the RCSB Protein Data Bank (accession no. 4M1C). https://www.rcsb.org/structure/4M1C

Tang WJ (2018) IDE with insulin and Fab1E structure Publicly available at the RCSB Protein Data Bank (accession no. 5CJO). https://www.rcsb.org/structure/5CJO

Tang WJ (2018) IDE with FabH11-E structure Publicly available at the RCSB Protein Data Bank (accession no. 5UOE). https://www.rcsb.org/structure/5UOE

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Additional details

Identifiers

DOI
10.7554/eLife.33572
Other
oai:uchicago.tind.io:10180

Funding

Agency for Science, Technology and Research
Defense Advanced Research Projects Agency
N66001-14-2-4053
National Institutes of Health
R35 GM118062
Howard Hughes Medical Institute
Simons Foundation
349247
National Institutes of Health
GM103310
National Institutes of Health
GM81539
National Institutes of Health
GM121964

UChicago Information

Division(s)
Biological Sciences Division
Department(s)
Ben May Department for Cancer Research, Biochemistry and Molecular Biology