Molecular basis for the recognition and cleavages of IGF-II, TGF-alpha, and amylin by human insulin-degrading enzyme

J Mol Biol. 2010 Jan 15;395(2):430-43. doi: 10.1016/j.jmb.2009.10.072. Epub 2009 Nov 5.


Insulin-degrading enzyme (IDE) is involved in the clearance of many bioactive peptide substrates, including insulin and amyloid-beta, peptides vital to the development of diabetes and Alzheimer's disease, respectively. IDE can also rapidly degrade hormones that are held together by intramolecular disulfide bond(s) without their reduction. Furthermore, IDE exhibits a remarkable ability to preferentially degrade structurally similar peptides such as the selective degradation of insulin-like growth factor (IGF)-II and transforming growth factor-alpha (TGF-alpha) over IGF-I and epidermal growth factor, respectively. Here, we used high-accuracy mass spectrometry to identify the cleavage sites of human IGF-II, TGF-alpha, amylin, reduced amylin, and amyloid-beta by human IDE. We also determined the structures of human IDE-IGF-II and IDE-TGF-alpha at 2.3 A and IDE-amylin at 2.9 A. We found that IDE cleaves its substrates at multiple sites in a biased stochastic manner. Furthermore, the presence of a disulfide bond in amylin allows IDE to cut at an additional site in the middle of the peptide (amino acids 18-19). Our amylin-bound IDE structure offers insight into how the structural constraint from a disulfide bond in amylin can alter IDE cleavage sites. Together with NMR structures of amylin and the IGF and epidermal growth factor families, our work also reveals the structural basis of how the high dipole moment of substrates complements the charge distribution of the IDE catalytic chamber for the substrate selectivity. In addition, we show how the ability of substrates to properly anchor their N-terminus to the exosite of IDE and undergo a conformational switch upon binding to the catalytic chamber of IDE can also contribute to the selective degradation of structurally related growth factors.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Amyloid / chemistry
  • Amyloid / genetics
  • Amyloid / metabolism*
  • Amyloid beta-Peptides / chemistry
  • Amyloid beta-Peptides / genetics
  • Amyloid beta-Peptides / metabolism
  • Binding Sites / genetics
  • Crystallography, X-Ray
  • Humans
  • In Vitro Techniques
  • Insulin / chemistry
  • Insulin / genetics
  • Insulin / metabolism
  • Insulin-Like Growth Factor II / chemistry
  • Insulin-Like Growth Factor II / genetics
  • Insulin-Like Growth Factor II / metabolism*
  • Insulysin / chemistry*
  • Insulysin / genetics
  • Insulysin / metabolism*
  • Islet Amyloid Polypeptide
  • Models, Molecular
  • Molecular Sequence Data
  • Multiprotein Complexes
  • Peptide Fragments / chemistry
  • Peptide Fragments / genetics
  • Peptide Fragments / metabolism
  • Sequence Homology, Amino Acid
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
  • Static Electricity
  • Substrate Specificity
  • Tandem Mass Spectrometry
  • Transforming Growth Factor alpha / chemistry
  • Transforming Growth Factor alpha / metabolism*


  • Amyloid
  • Amyloid beta-Peptides
  • Insulin
  • Islet Amyloid Polypeptide
  • Multiprotein Complexes
  • Peptide Fragments
  • Transforming Growth Factor alpha
  • amyloid beta-protein (1-40)
  • amyloid beta-protein (1-42)
  • Insulin-Like Growth Factor II
  • Insulysin

Associated data

  • PDB/2WK3
  • PDB/3E4Z
  • PDB/3E50
  • PDB/3HGZ