Peptide binding to MHC class I is determined by individual pockets in the binding groove.
H-2Kb and HLA-A2 are MHC4 class I molecules with a similar overall structure. Important differences between these two class I molecules reside in the structure of the individual pockets in the antigenic-peptide-binding groove. H-2Kb, which has a deep C pocket, binds specifically peptides with a tyrosine or a phenylalanine at position 5. In contrast, HLA-A2 has a shallow C pocket, which cannot accommodate large side chains at position 5. Site-directed mutagenesis was used to generate a chimera between the murine H-2Kb and the human HLA-A2 [H-2Kb/HLA-A2(C')]. The structure of this chimera is similar to H-2Kb except 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-2Kb-binding peptides [VSV (52-59), OVA (257-264), and MCMV pp89 (168-176)], revealed that the deep C pocket of H-2Kb was crucial for high-affinity binding. While a peptide, VSV (52-59), was found to bind with severalfold lower 'affinity' to H-2Kb/HLA-A2(C') than to the wild-type H-2Kb, a VSV analogue with the tyrosine in position 5 (Tyr5) substituted with an alanine was found to bind with a similar 'affinity' to both MHC class I molecules. Computer-aided modelling of the H-2Kb/HLA-A2(C') complex indicates that the VSV (52-59) peptide probably binds to the chimeric MHC molecule with the peptide side chain of anchor residue Tyr5 pointing away from the groove. These results confirm a role of the individual pockets in determining peptide-binding affinity and specificity and suggest that this may be accomplished by changes in side-chain orientation.
Johansen
T E
TE
Department of Pathology and Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA.
McCullough
K
K
Catipovic
B
B
Su
X M
XM
Amzel
M
M
Schneck
J P
JP
D000818:Animals; D000911:Antibodies, Monoclonal; D002460:Cell Line; D002478:Cells, Cultured; D006183:H-2 Antigens / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015789:HLA-A2 Antigen / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D051379:Mice; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D009841:Oligonucleotides / Q000737:chemistry; D009842:Oligopeptides / Q000378:metabolism*; D010047:Ovalbumin / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D011993:Recombinant Fusion Proteins / Q000737:chemistry* / Q000378:metabolism; D013329:Structure-Activity Relationship; D014162:Transfection; D014764:Viral Proteins / Q000378:metabolism
D000911:Antibodies, Monoclonal; D006183:H-2 Antigens; C032876:H-2Kb protein, mouse; D015789:HLA-A2 Antigen; D009841:Oligonucleotides; D009842:Oligopeptides; D011993:Recombinant Fusion Proteins; D014764:Viral Proteins; D010047:Ovalbumin