The availability of crystal structures for several

DR molecules in complex with relevant epitopes and the relative facility to purify large amounts of these proteins in a stable form have led to a focus Veliparib of the analysis of DM on the interaction with these specific alleles. A significant deviation from this trend is constituted by a recent report showing that DR, DQ and DP differ markedly in their requirements for Ii and DM, despite having 70% amino acid sequence similarity. For instance, it seems that Ii is sufficient for DQ to attain a stable SDS conformation in the absence of DM, and SDS-stable DQ5 dimers can be identified through dimer-specific antibodies recognizing the stable conformation. These observations are consistent FK506 with studies conducted on DQ alleles, suggesting that DM-independent antigen presentation by these MHCII may constitute a risk factor for autoimmune disease.[67] Therefore it appears that DM can interact and function on a variety of MHCII alleles; however, the actual requirement of DM for efficient antigen presentation may be isotype-specific. We are not fully aware of the reasons as to how and why the effect of DM on epitope selection differs on an allele basis. If DM recognizes a flexible conformation of the pMHCII complex and promotes a destabilization of the interactions near the P1 pocket, it is plausible

that DM-independent alleles may feature an increased rigidity related to a specific pocket structure that renders such alleles a

low-affinity (or overall ‘insensitive’) target of DM activity. Structural analysis and in vivo studies of these different isotypes will contribute to increase our understanding of the different paths of epitope selection Lonafarnib molecular weight and it will indicate whether we need alternative mechanisms to explain the outcome of DM interaction with different MHCII alleles. Moreover, a deeper analysis of the molecular properties of DP and DQ conformation and stability and their looser DM requirement for proper trafficking may offer an explanation as to why some autoimmune diseases are linked to these alleles. An interesting aspect of the interaction between DM and MHCII that has not received enough attention is the dependence on protonation of DM function. It has been evident since the initial studies that the ability of DM to promote peptide exchange has an optimum at pH 4·5–5·5 and it is dramatically weakened at pH 7. Through time-resolved fluorescence anisotropy and fluorescence binding studies with 8-anilinonaphthalene-1-sulphonate, conformational rearrangements of DM and HLA-DR3 promoted by pH changes were probed. With this approach it was shown that both molecules increased their degree of non-polarity upon protonation, and that the interaction between DM and DR limited the exposure of these pH-sensitive non-polar areas to solvent.