A structure for the trimeric MHC class II-associated invariant chain transmembrane domain

Andreas Kukol*, Jaume Torres, Isaiah T. Arkin

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

39 Scopus citations


The major histocompatibility complex (MHC)-associated invariant chain (Ii) contains a single transmembrane domain that forms trimers. Ii is involved in the assembly of the MHC and antigen presentation, and is thus central to the function of the immune system. Here, we show by attenuated total reflectance, Fourier transform infrared (ATR-FTIR) spectroscopy that the transmembrane domain is α-helical and we provide a structural model of the transmembrane domain obtained by a combination of site-specific infrared dichroism and molecular dynamics (MD) simulations. This work resolves the backbone structure of a transmembrane peptide by multiple 13C==18O labelling at ten different residues. A second purely computational approach, based on MD simulations of Ii transmembrane homologous sequences, yields a similar structure that is consistent with our experimental results. The structure presented forms a left-handed coiled coil with an average helix tilt of 13(±6)°; the residue Gln47 implicated in trimer formation forms strong interhelical contacts, Thr50 points to the inside of the trimeric coil and forms a network of hydrogen bonds.

Original languageAmerican English
Pages (from-to)1109-1117
Number of pages9
JournalJournal of Molecular Biology
Issue number5
StatePublished - 2002

Bibliographical note

Funding Information:
This work was supported by grants from the Welcome Trust and BBSRC to I.T.A.


  • Associated invariant chain
  • FTIR spectroscopy
  • Molecular dynamics
  • Site-specific dichroism
  • Transmembrane protein


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