Study proposes new bioinformatic approach to design better vaccines
These discrepancies between previous and current results could be explained as follows: pentapeptides are recognized by T cell receptors , but longer peptides are needed for attachment in the MHC protein groove []. The specificity of the bond between the MHC protein and the neighboring amino acids of the T-cell-recognized pentapeptide might be relatively low.
The fact that many potential T cell targets were not detected in any immunogenic peptides can be explained easily, as discussed above. More interesting is the existence of about one-half of immunogenic peptides that do not contain any potential pentapeptide T cell targets. As discussed in the previous paragraphs, it is possible that hexapeptides, rather than pentapeptides—or, even more probably, both hexapeptides and pentapeptides—are the genuine targets of T cell recognition.
It is also probable that, due to polymorphism in most human proteins, some pentapeptides are missing in the protein vocabulary of some individuals, including the individual whose proteome was used for the construction of peptide vocabularies in the present study . In future studies, or when designing vaccines, it might be helpful to prepare a more representative human peptide vocabulary by using the proteomes of several individuals of different ethnic origins.
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