Traditionally the method based on expressed peptides is used to find antigen epitope, but it is not that good for spatial epitope. Is there any better method?
I think there is a set of reliable methods to determinae that, all based on mutagenesis. If you have the recombinant whole antigen and you manage to discover clusters of residues close in the 3D structure (although perhaps far in the sequece. that cannot be replaced without loosing recognition by a given antibody, you are describing the epitope in an accurate way. Tolerated substitutions at these positions even tell you what properties re important for antibody binding. For instance, some residues can only be replaced by aromatic, or positive, or negative or hydrophobic residues.
If you want to test multiple mutated variants of the antigen in a simple way, phage display or yeast display can help to do it in a high throughput manner. There are different approaches. The one I use is the combination of antigen phage display and extensive mutagenesis.
Gertrudis has the right answer. From 3D modeling you can get some hints about what conformational epitopes are possible, to help you with the mutagenesis experiments. In my hands ~85% of monoclonal antibodies are specific for conformational epitopes. However, MAb raised against peptides generally bind to sequential epitopes.
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