Optimal Length of Peptides for MHC Class II Interaction

Completely randomized synthetic peptide amide libraries from 7 to 15 amino acids (Xt-X15) were synthesized and applied to elucidate an ideal peptide length applicable in competition studies with HLA-DR1 (Fig. 11.3). A minimal length of peptide amides comprising 11 amino acids was found to be promising in assays with DR1 molecules [66]. 

The activity of a sublibrary is only governed by the amino acid residue in the defined sequence position, whereas the remaining 10 randomized positions provide an averaged contribution to binding. Thus, by summarizing the rel C values of the 220 sublibraries in an Activity Pattern [66], the contribution of any amino acid side chain in any sequence 

Our interpretation of results from competition studies DR2b and with peptide libraries allowed us to describe a new interesting phenomena, called translational invariance e.g., sublibraries carrying aliphatic residues in position 2 showed comparable competitions as those with aliphatic side chains in position 3 (Fig. 11.4). Similar results were obtained for 

In order to avoid translational invariance when studying peptide binding to class II molecules with peptide libraries, two approaches would be possible. First, the incorporation of more than one defined residue in the undecapeptide library, e.g., a common hydro-phobic residue in the first anchor position of DR-ligands, would prevent translational invariance. However, universal applicability of the peptide library approach would be lost, 

1 Tolerance to Amino Acid Variations in a HLA Class 11 Ligand 

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