The semiautomatic database Epitome collects structure-inferred antigenic residues in proteins that are involved in interaction with residues on antibody CDRs, and it provides information of corresponding paratope
This indicated that the peptides recognized structures in the paratope
that do not participate in antigen binding or that the epitopes were different and mainly determined by the three-dimensional structure of PSA.
In light of these results, we can postulate degradation of the mAb and E2 when they are not bound to each other, but an epitope-paratope protection against the deleterious effect of the cross-linking agents induced by the Fenton-like reaction when the mAb-E2 complex is formed (the paratope
being defined as the part of the antibody molecule directly in contact with the epitope).
In a practical sense, it is not be possible to distinguish an idiotope from a paratope
because the binding sites are equivalent.
Knowledge of the chemistry of the antigen-antibody reaction, the contribution of different binding forces, the spatial orientation of critical elements of the molecular structure, and the ultimate definition of definitive epitope and paratope
regions has been gleaned from fundamental techniques such as x-ray diffraction, nuclear magnetic resonance, elipsometry, and mass spectrometry (8), together with the experience gained from the clinical application of assays and their subsequent refinement.
We developed a bsMAb incorporating in one arm of the molecule an anti-PSA paratope
and in the other an anti-peroxidase binding site.