Frequently Asked Questions

Q: But B-cell epitopes are three dimensional….
A: Certainly many antibody binding sites are conformational. But any 3-D epitope is made up of multiple linear epitopes brought into contact with each other by the folding of the protein molecule. Some linear B-cell epitopes or B-cell contacts are as short as 2-3 amino acids. By combining uTOPE™ plots of B cell-epitopes with structural models it is possible to demonstrate how linear B-cell epitopes, usually with predicted MHC binding sites immediately adjacent to them, come together to form 3D epitopes.

Q: What about glycosylation?
A: uTOPE™ analysis maps the peptide epitopes in proteins. It does not map glycotopes. Glycosylation of a protein is highly dependent on the growth or nutritional milieu and varies. Amino acid sequences are “hard coded” in the genome. Glycosylation is largely removed in the lysosomes of antigen presenting cells so has little impact on MHC binding. We focus on the underlying amino acid sequence and then examine whether there might be potential glycosylation sites which may affect antibody binding.

Q: Proteins need to be broken apart for MHC presentation, how do you address this?
A: Initial disruption of proteins may occur outside or inside antigen presenting cells by the action of enzymes such as serine proteases or arginine endopeptidase (AEP). After the tertiary structure is opened up, cathepsins play a major role in protein cleavage for MHC binding. uTOPE™ analysis predicts cathepsin cleavage site probability for cathepsin B, L and S.

Q: How have you validated uTOPE™ analysis?
A: uTOPE™ analysis has been validated by comparison with experimental results generated internally and by others. B-cell epitope predictions have been compared to binding of linear peptide arrays. uTOPE™ analysis  has been compared to prior methods of predicting both MHC binding and B cell epitopes and shown to have better repeatability. This is addressed in our publications.