Peptide Libraries for the Investigation of TAP

In comparison to a reporter peptide, the affinity of human TAP for a totally degenerate nonapeptide library was found to be 17-fold lower [20]. Single amino acid substitutions in the high-affinity reporter peptides resulted in only two- to three-fold differences in transport rates, but in up to 80-fold differences as revealed by the use of synthetic peptide libraries. 

A complete map of the fine specificity of human TAP was obtained by testing nonapeptide sublibraries [20]. The most pronounced effects for side-chain substitutions were found for the C-terminus where aromatic, aliphatic, and positively charged residues were preferred (Table 11.1).The amino-terminal region (positions one to three) also proved to be important. 

These results verified the results obtained with totally randomized undecapeptide libraries and pentadecapeptide libraries characterized by one position occupied by D-ami-no acids [21]. Interestingly, TAP can accommodate peptides with bulky or non natural side chains, and even branched peptides [21,22]. 

The C-terminal amino acid residues preferred by TAP match with those generated by the proteolytic activities of the proteasome [23], as well as with C-terminal anchors used by most human class I molecules (database S YFPEITHI www.medizin.uni-tuebingen.de/ sfb510/index.html) [24]. 

MHC class I molecules are folded by support of a variety of chaperones, e.g., calnexin, calreticulin, tapasin. The class II pathway has to exclude the presentation of peptides of intracellular origin. Therefore, in the ER MHC class II molecules remain associated with the invariant chain Ii, where the CLIP region of Ii occupies the peptide-binding cleft [27]. CLIP is removed from the MHC in the MHC class II compartment MIIC [28], MHC class II molecules adopt a conformational change upon loading with peptides that allows the sorting to the cell surface. 

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