Binding of Longer Peptides to the H-2Kb Heterodimer Is Restricted to Peptides Extended at Their C Terminus: Refinement of the Inherent MHC Class I Peptide Binding Criteria

• Published in: The Journal of immunology (1950) 1999-10, Vol.163 (8), p.4434-4441
• Main Authors: Horig, Heidi, Young, Aideen C. M, Papadopoulos, Nicholas J, DiLorenzo, Teresa P, Nathenson, Stanley G
• Format: Article
• Language: English
• Subjects: Animals; Computer Simulation; Dimerization; Drug Design; Energy Metabolism; H-2 Antigens - chemistry; H-2 Antigens - metabolism; Macromolecular Substances; Mice; Models, Molecular; Oligopeptides - chemistry; Oligopeptides - immunology; Oligopeptides - metabolism; Peptide Fragments - chemistry; Peptide Fragments - immunology; Peptide Fragments - metabolism; Protein Binding - immunology; Protein Folding; Structure-Activity Relationship
• ISSN: 0022-1767; 1550-6606
• DOI: 10.4049/jimmunol.163.8.4434

MHC class I molecules usually bind short peptides of 8-10 amino acids, and binding is dependent on allele-specific anchor residues. However, in a number of cellular systems, class I molecules have been found containing peptides longer than the canonical size. To understand the structural requirements for MHC binding of longer peptides, we used an in vitro class I MHC folding assay to examine peptide variants of the antigenic VSV 8 mer core peptide containing length extensions at either their N or C terminus. This approach allowed us to determine the ability of each peptide to productively form Kb/beta2-microglobulin/peptide complexes. We found that H-2Kb molecules can accommodate extended peptides, but only if the extension occurs at the C-terminal peptide end, and that hydrophobic flanking regions are preferred. Peptides extended at their N terminus did not promote productive formation of the trimolecular complex. A structural basis for such findings comes from molecular modeling of a H-2Kb/12 mer complex and comparative analysis of MHC class I structures. These analyses revealed that structural constraints in the A pocket of the class I peptide binding groove hinder the binding of N-terminal-extended peptides, whereas structural features at the C-terminal peptide residue pocket allow C-terminal peptide extensions to reach out of the cleft. These findings broaden our understanding of the inherent peptide binding and epitope selection criteria of the MHC class I molecule. Core peptides extended at their N terminus cannot bind, but peptide extensions at the C terminus are tolerated.