Epitopes applications

The most frequent application of SPOT-synthesis has been in the preparation of peptide arrays for the identification of linear B-cell epitopes. If the protein antigen is known, a set of overlapping peptides that encompass the entire sequence can be readily synthesized and assayed for binding of antibody (Reineke et al., 1999). The individual residues critical for binding can then be determined by SPOT-synthesis of peptides containing amino acid substitutions. 

Whereas molecular design is a strategy applicable to the chemical level of epitope-paratope interactions, it cannot be used for optimizing the many cellular interactions required for achieving an immune response that leads to infectivity neutralization of a pathogen. As a result, the future development of vaccines will continue to rely more on the empirical testing of the protection afforded by candidate vaccine preparations than on the rational design of biomolecules defined in a reductionist manner by their chemical structure. 

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