Potential binding modes of beryllium with the class II major histocompatibility complex HLA-DP: a combined theoretical and structural database study

In an effort to understand the molecular basis of chronic beryllium disease (CBD), a study of the chemical relationship between beryllium, antigen, and the major histocompatibility complex II, HLA-DP, was undertaken. A homology model of the HLA-DP protein was developed. An analysis of the sequences of HLA-DPB1 and HLA-DPA1 alleles most common among CBD patients revealed several carboxylate rich regions in the peptide-binding cleft. These regions contain many hard Lewis base sites that may provide bonding opportunities for beryllium, a hard Lewis acid. Quantum chemistry calculations and structural database results support the presence of beryllium clusters, bridged by carboxylate, hydroxo, and/or oxo ligands, in the HLA-DP binding cleft. These results strongly suggest that beryllium clusters are an integral part of the antigen, and may even act solely as antigen. This work provides an initial model for thinking about beryllium interactions with proteins relevant to CBD and other metal-induced diseases.