Prediction of the Interaction between NK Cell Receptor KIR2DS4 and HLA-C*05-Peptide Complex

The ability of NK cells to establish antigen-specific responses has been demonstrated in various infections. NK cell receptors of the diverse family of Killer-cell Immunoglobulin-like Receptors (KIR) interact with HLA class I molecules, and this interaction is peptide-dependent. The activating receptor KIR2DS4 enables NK cell degranulation following interaction with specific peptides presented within HLA-C*05. However, the mechanism underlying the differential NK cell response depending on a peptide remains poorly understood and lacks explanation based on the structure of ligand-receptor interaction. Using AlphaFold 3, we generated models of KIR2DS4-peptide-HLA-C*05 complexes to analyze the contact interfaces. We confirmed the substantial role of the aromatic ring in the 8th amino acid residue of peptide sequences in mediating interactions with KIR2DS4. Even with the same amino acid residue at position 8, different peptides exhibited variability in polar contacts with KIR2DS4. Our results may contribute to the prediction of KIR-HLA interactions and facilitate the identification of specific peptides capable of activating NK cells.