The impact of human leukocyte antigen (HLA) micropolymorphism on ligand specificity within the HLA-B*41 allotypic family

Abstract Background. Polymorphic differences between human leucocyte antigen (HLA) molecules affect the specificity and conformation of their bound peptides and lead to differential selection of the T-cell repertoire. Mismatching during allogeneic transplantation can therefore lead to immunological reactions. Design and methods. We investigated the structure-function relationships of six members of the HLA-B*41 allelic group that differ by six polymorphic amino acids, including positions 80, 95, 97 and 114 within the antigen binding cleft. Peptide-binding motifs for B*4101, *4102, *4103, *4104, *4105 and *4106 were determined by sequencing self-peptides from recombinant B*41 molecules by ESI-MS-MS fragmentation. The crystal structures of HLA-B*4103 bound to a natural 16-mer self-ligand (AEMYGSVTEHPSPSPL) and HLA-B*4104 bound to a natural 11-mer self-ligand (HEEAVSVDRVL) were solved. Results. Peptide analysis revealed that all B*41 alleles have an identical p2 anchor (Glu), but differ in their choice of C-terminal p_anchor (Pro, Val, Leu). Additionally, B*4104 displayed a greater preference for long peptides (>10 residues) when compared to the other B*41 allomorphs, while the longest peptide to be eluted from the allelic group (a 16mer) was obtained from B*4103. The crystal structures of HLA-B*4103 and HLA-B*4104 revealed that both alleles interact in a highly conserved manner with the terminal regions of their respective ligands, while micropolymorphism-induced changes in the steric and electrostatic properties of the Ag-binding cleft account for differences in peptide repertoire and auxiliary anchoring. Conclusions. Differences in peptide repertoire, and peptide length specificity reflect the significant functional evolution of these closely related allotypes and signal their importance in allogeneic transplantation, especially B*4103 and B*4104, which accommodate longer peptides, creating structurally distinct pHLA-I (peptide-HLA) ligands.