Explanation for the non-specificity of small peptide-antibody interaction

Abstract

Testing the reactivity of synthetic peptides with monoclonal antibodies provides information on protein-protein interactions. Starting from a minimal basis, that is considering dipeptide-antibody interactions, binding occurs in a reproducible manner. With no knowledge of the testing antibody specificity, peptide length is the only parameter which can be easily handled. Best binding dipeptides are then extended by adding one aminoacid to either end, and the process goes on with best binding tri, tetra, etc., -peptides. Such a process would be well founded if specificity was gained at each step. In fact, a computer analysis of experimental results shows that binding of dipeptide tends to be independent from the specificity of the antibody. An ad hoc method mainly based on ranking and sorting operations, assesses predominant factor(s) accounting for dipeptide reactivity. Moreover, properties of dipeptides are not generalisable to tripeptides. The continuity of the extension process cannot be assumed.