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antigen presentation by major histocompatibility complex (MHC) class I proteins initiates CD8<sup>+</sup> T cell-mediated immunity against pathogens and cancers. MHC I molecules typically bind peptides with 9 amino acids in length with both ends tucked inside the major A and F binding pockets. It has been known for a while that longer peptides can also bind by either bulging out of the groove in the middle of the peptide or by binding in a zigzag fashion inside the groove. In a recent study, we identified an alternative binding conformation of naturally occurring peptides from <i>Toxoplasma gondii</i> bound by HLA-A*02:01. These peptides were extended at the C terminus (P\u03a9) and contained charged amino acids not more than 3 residues after the anchor amino acid at P\u03a9, which enabled them to open the F pocket and expose their C-terminal extension into the solvent. Here, we show that the mechanism of F pocket opening is dictated by the charge of the first charged amino acid found within the extension. Although positively charged amino acids result in the Tyr-84 swing, amino acids that are negatively charged induce a not previously described Lys-146 lift. Furthermore, we demonstrate that the peptides with alternative binding modes have properties that fit very poorly to the conventional MHC class I pathway and suggest they are presented via alternative means, potentially including cross-presentation via the MHC class II pathway.","bibjson":{"author":[{"initials":"SG","lastname":"Remesh","name":"Remesh SG"},{"initials":"M","lastname":"Andreatta","name":"Andreatta M"},{"initials":"G","lastname":"Ying","name":"Ying G"},{"initials":"T","lastname":"Kaever","name":"Kaever T"},{"initials":"M","lastname":"Nielsen","name":"Nielsen M"},{"initials":"C","lastname":"McMurtrey","name":"McMurtrey C"},{"initials":"W","lastname":"Hildebrand","name":"Hildebrand W"},{"initials":"B","lastname":"Peters","name":"Peters B"},{"initials":"DM","lastname":"Zajonc","name":"Zajonc DM"}],"identifier":[{"id":"10.1074/jbc.M117.776542","type":"doi"},{"id":"28179428","type":"pubmed"}],"issue":["13"],"journal":{"iso_abbreviation":"J. Biol. 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