Use of functional polymorphisms to elucidate the peptide binding site of the transporter associated with antigen processing (TAP) complexes (APP5P.101)

Abstract

Abstract The major histocompatibility (MHC) class I antigen presentation pathway plays an important role in alerting the immune system to virally infected and transformed cells. TAP translocates peptides from the cytosol to the endoplasmic reticulum lumen for peptide loading onto MHC class I molecules. The peptide specificity of TAP has been correlated with the antigenic peptide repertoire of MHC class I molecules in several species, but the precise location of the peptide binding site of TAP is unknown. Polymorphisms in rat and chicken TAPs influence peptide transport selectivity. Combining homology modeling of TAP with experimental measurements of peptide binding selectivity, we demonstrate several residues of rat TAP that are critical for the recognition of basic or hydrophobic residues at the peptide C-terminus, as well as of side chains near the peptide N-terminal and central regions. Based on these interaction sites of peptides with rat TAP, we propose models for rat, chicken and human TAPs in complex with selected peptides. The bound peptides adopt bent conformations and occupy a site near the cytosolic membrane surface, which is similar to that for glutathione derivatives in the NaAtm1 transporter, highlighting conserved elements of bacterial detoxification and eukaryotic immunity-related proteins. These experimentally verified models will facilitate the development of improved epitope discovery tools for assessments of CD8+ T cell prevalence and function in diseases.