Te. Johansen et al., PEPTIDE BINDING TO MHC CLASS-I IS DETERMINED BY INDIVIDUAL POCKETS INTHE BINDING GROOVE, Scandinavian journal of immunology, 46(2), 1997, pp. 137-146
H-2K(b) and HLA-A2 are MHC4 class I molecules with a similar overall s
tructure. Important differences between these two class I molecules re
side in the structure of the individual pockets in the antigenic-pepti
de-binding groove. H-2K(b), which has a deep C pocket, binds specifica
lly peptides with a tyrosine or a phenylalanine at position 5. In cont
rast, HLA-A2 has a. shallow C pocket, which cannot accommodate large s
ide chains at position 5. Site-directed mutagenesis was used to genera
te a chimera between the murine H-2K(b) and the human HLA-A2 [H-2K(b)/
HLA-A2(C')]. The structure of this chimera is similar to H-2K(b) excep
t for the region around the deep C pocket, where residues at positions
9, 97 and 99 were substituted with those bulkier residues from HLA-A2
. Peptide binding between this chimera and H-2K(b)-binding peptides [V
SV (52-59), OVA (257-264), and MCMV pp89 (168-176)], revealed that the
deep C pocket of H-2K(b) was crucial for high-affinity binding. While
a peptide, VSV (52-59), was found to bind with severalfold lower 'aff
inity' to H-2K(b)/HLA-A2(C') than to the wild-type H-2K(b), a VSV anal
ogue with the tyrosine in position 5 (Tyr5) substituted with an alanin
e was found to bind with a similar 'affinity' to both MHC class I mole
cules. Computer-aided modelling of the H-2K(b)/HLA-A2(C') complex indi
cates that the VSV (52-59) peptide probably binds to the chimeric MHC
molecule with the peptide side chain of anchor residue Tyr5 pointing a
way from the groove. These results confirm a role of the individual po
ckets in determining peptide-binding affinity and specificity and sugg
est that this may be accomplished by changes in side-chain orientation
.