Anti-HLA-E mAb 3D12 mimics MEM-E/02 in binding to HLA-B and HLA-C alleles: Web-tools validate the immunogenic epitopes of HLA-E recognized by the antibodies

HLA-E shares several peptide sequences with HLA-class Ia molecules. Therefore, anti-HLA-E antibodies that recognize the shared sequences may bind to HLA-class Ia alleles. This hypothesis was validated with a murine anti-HLA-E monoclonal antibody (mAb) MEM-E/02, which reacted with microbeads coated with several HLA-B and HLA-C antigens. In this report, the hypothesis was reexamined with another mAb 3D12, considered to be specific for HLA-E. The antibody binding is evaluated by measuring mean fluorescence index [MFI] with Luminex Multiplex Flow-Cytometric technology. The peptide-inhibition experiments are carried out with synthetic shared peptides, most prevalent to HLA-E and HLA-Ia alleles. The results showed that mAb 3D12 simulated MEM-E/02 in recognizing several HLA-B and HLA-C antigens. Both 3D12 and MEM-E/02 did not bind to HLA-A, HLA-F and HLA-G molecules. As observed with MEM-E/02, binding of 3D12 to HLA-E is inhibited by the peptides sequences 115QFAYDGKDY123 and 137DTAAQI142. Decrease in binding of mAb 3D12 to HLA class Ia, after heat treatment of antigen coated microbeads, supports the contention that the epitope may be located at the outside of the “thermodynamically stable” α-helix conformations of HLA-E. Several sequence and structure-based web-tools were employed to validate the discontinuous epitopes recognized by the mAbs. The scores obtained by these web-tools distinguished the shared peptide sequences that inhibited the mAb binding to HLA-E. Furthermore, ElliPro web tool points out that both mAbs recognize the conformational discontinuous epitopes (the shared inhibitory peptide sequences) in the secondary structure of the HLA-E molecule. The study favors the contention that the domain of the shared inhibitory peptide sequences may be the most immunogenic site of HLA-E molecule. It also postulates and clarifies that amino acid substitution on or near the binding domains may account for the lack of cross reactivity of 3D12 and MEM-E/02 with HLA-A, HLA-F and HLA-G molecules.