Linear models of ovine IgG1 and IgG2 subclasses and predicted pepsin cleavage sites

Highly purified specific Fab antibody fragments derived from sheep have a long history of therapeutic use as safe and effective emergency medicines. In more recent years simple low-cost methods have been developed, which take advantage of the ability of pepsin under optimally controlled conditions to preferentially digest ovine IgG within the Fc region to produce F(ab')2 and easy to remove low MW Fc sub-fragments. Despite these developments no information is currently available on the pepsin digestion of ovine IgG at the amino acid level hindering the development of improved F(ab')2 processing methods. To gain knowledge of the fragments properties we have constructed linear models of ovine IgG1 and IgG2 subclasses, starting from the gamma-1 and gamma-2 chain amino acid sequences, which also incorporate the inter- and intra-chain disulphide bonds. Any potential pepsin cleavage site was initially predicted in silico, then high probability points identified for each of the molecules and mapped onto the individual models. A theoretical order of digestion was subsequently constructed, which appeared to agree with the experimental data, suggesting an accurate prediction model for ovine IgG1 and IgG2 subclasses. These findings lay the foundations for a more detailed analysis of pepsin cleavage fragments in the future. Additionally, the F(ab')2 generated following pepsin digestion were predicted to contain subclass unique C-terminal octapeptide neoepitopes, despite the high 89% sequence identity of the intact gamma-1 and gamma-2 chain constant regions. These neoepitopes have the potential to be utilised for identification purposes once confirmed experimentally.