T-cell epitope processing (the epitope flanking regions matter).

Epitopes presented by major histocompatibility complex (MHC) class I molecules for cytotoxic T-lymphocyte (CTL) recognition are derived mainly from cytosolic proteins. Antigen presentation on the cell surface requires correct processing of epitopes by the proteasome, cytosolic and endoplasmic reticulum (ER) aminopeptidases, efficient TAP transport, and sufficient binding to MHC class I molecules. The efficiency of the epitope generation depends not only on the epitope itself but also on its flanking regions. To investigate preferences at the C-terminal epitope extension on processing and presentation, the SIINFEKL (S8L) epitope can be used as a model epitope. By exchanging the amino acids at the C-terminus of S8L, their influence on the presentation of S8L can be analyzed.