Fig. 8: Favored amino acid positions within the HLA-A*02:01 peptide-binding pocket.
From: Opening opportunities for Kd determination and screening of MHC peptide complexes
Native MS confirms Leu-2 in the B pocket and Val-9 in the F pocket respectively as the main anchor positions of the pMHC. The analysis of truncated NV9 variants reveals that Val-2 is also a favored binding site. Moreover, Met-5 or Val-5, as well as Val-6, also contribute significantly to binding under certain circumstances. Among the anchor residues, Leu-2 contributes significantly more to the binding than Val-9. Concerning the termini, the N-terminus is of greater importance for binding than the C-terminus.
