How to determine amino acid sequence of peptide bound by MHC I

Ian A. York iayork at
Mon Nov 15 12:26:24 EST 1999

In article <38303a39.9690549 at news>, Kevin Ault <kevin-ault at> wrote:
>Is there a similar body of literature for MHC II?  -  Kevin Ault 

Yes, though there isn't quite as much.  The procedure is tricker for
MHC II.  MHC I-associated peptides as homogenous, or close to homogenous,
in length.  That means you can elute the peptides and then sequence them
as apool, and you will still see patterns quite easily; anchor residues
at, say, position two and nine will show up as a limited diversity of
amino acids at those positions.  In contrast, MHC class I binds peptides
of varying lengths; although the anchor residues are still present, then
ends of the peptides overhang the molecules, so that the anchor residues
might be at position 9 and 14 for one peptide and 6 and 11 for another.
nevertheless the procedure can be done.  

I believe the first motif sequencing from MHC class II was

Nature 1991 Oct 17;353(6345):622-7 
Sequence analysis of peptides bound to MHC class II molecules.
Rudensky AYu, Preston-Hurlburt P, Hong SC, Barlow A, Janeway CA Jr

A useful review for both types is

Annu Rev Immunol 1994;12:181-207 
Structure of peptides associated with class I and class II MHC
Engelhard VH

    Ian York   (iayork at  <>
    "-but as he was a York, I am rather inclined to suppose him a
     very respectable Man." -Jane Austen, The History of England

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