Nevertheless, not all the observations can be explained by postulating a disruptive activity of DM on one or multiple H-bonds. In particular, the evidence that the destabilization Saracatinib of single H-bonds has a cooperative effect on peptide
stability [44, 45] is hard to reconcile with the sequence-independent j factor. Moreover, different reports have shown that complexes unable to form the H-bond at position β81,[46-48] as well as any other conserved H-bonds, are still susceptible to DM-mediated peptide release. A model of DM activity that is becoming increasingly accepted postulates that DM would recognize a specific and flexible conformation of class II, rather than a kinetically unstable pMHCII. The first evidence in support of this model was gained through the analysis of a mutant DR1, DR1βG86Y. This mutant remains permanently in a receptive form when empty, most likely because the tyrosine substituting Idasanutlin the wild-type glycine fills the P1 pocket and prevents the flexible N-terminal region from collapsing. DR1βG86Y forms only short-lived complexes with the peptide but features low affinity for DM. As the conformations of the mutant DR1 and wild-type (wt)DR1 bound to low-affinity peptides feature different
levels of rigidity, and DM was shown to interact preferentially with the latter, it was proposed that the flexibility present in the wtDR1 loosely bound to a low-affinity peptide was determinant for DM/pDR1 interaction. If conformational traits of the pMHCII complex are crucial for the interaction with DM, the next step towards a comprehensive model of DM activity is defining the structure of the DM-labile conformer. Our inability to resolve the crystal structure of the DM/pMHCII triad suggests a great structural flexibility of the pMHCII complex targeted by DM. However, two reports have provided important insights into the conformational aspects that render a pMHCII complex amenable to DM-mediated peptide exchange. The first was based on the analysis of αF54-substituted the DR1 molecules.
These mutants were shown to be more susceptible to DM-mediated peptide release than wtDR1 bound to a high-affinity peptide, they featured increased affinity for DM, and increased peptide vibration, especially in the H-bonding network at the N-terminal site of the complex. The crystal structure of the mutant MHCII identified peculiar structural features at this site of the pMHCII dyad, in particular a reorientation of the α45–50 region and changes in the flanking extended strand regions (α39–44 and α51–54). Importantly, the aforementioned molecular dynamics studies have predicted that the wtDR1 may also assume a conformation that resembles the one shown by the αF54C mutant.