A novel computer algorithm improves antibody epitope prediction using affinity-selected mimotopes: A case study using monoclonal antibodies against the West Nile virus E protein

Abstract

Understanding antibody function is often enhanced by knowledge of the specific binding epitope. Here, we describe a computer algorithm that permits epitope prediction based on a collection of random peptide epitopes (mimotopes) isolated by antibody affinity purification. We applied this methodology to the prediction of epitopes for five monoclonal antibodies against the West Nile virus (WNV) E protein, two of which exhibit therapeutic activity in vivo. This strategy was validated by comparison of our results with existing F(ab)-E protein crystal structures and mutational analysis by yeast surface display. We demonstrate that by combining the results of the mimotope method with our data from mutational analysis, epitopes could be predicted with greater certainty. The two methods displayed great complementarity as the mutational analysis facilitated epitope prediction when the results with the mimotope method were equivocal and the mimotope method revealed a broader number of residues within the epitope than the mutational analysis. Our results demonstrate that the combination of these two prediction strategies provides a robust platform for epitope characterization.

Characterizing Complex Polysera Produced by Antigen-Specific Immunization through the Use of Affinity-Selected Mimotopes

“…We have observed similar outcomes using monoclonal antibodies directed against the West Nile virus E protein [9]. The differences in epitope selection noted in this manuscript probably reflect differences in conformation of the soluble and cell-attached proteins which alter the way the protein is bound by antigen-specific B cells.…”

Bioinformatics Resources and Tools for Conformational B-Cell Epitope Prediction

“…In 2007, Bublil et al applied this method to conformational B-cell epitope prediction and presented the tool as Mapitope [70]. A continuous work by Denisova et al took all possible space pairs, including pairs separated by one residue, two residues, three residues, and so on in mimotopes into account and identified epitopes by pattern recognition theory [71–73]. This method is specially designed for elucidating epitope specificity within antiserum.…”

Generation and characterization of a monoclonal antibody against duck Tembusu virus envelope protein

“…Therefore, the need for development of alternative ways against TMUV appeared to gain high priority. Monoclonal antibodies have become a powerful tool to study protein structure and have been widely used to diagnose and treat a variety of infectious agents (Denisova et al 2008, Shen et al 2009, Sukupolvi-Petty et al 2010. The mAb 3E9 presented herein may advantageously be used to treat or prevent DTMUV infection in mice, for this reason, mAb 3E9 may further be developed as a therapeutic antibody to treat DTMUV in ducks after further investigation.…”