Sub-unit vaccines are synthetic or recombinant peptides representing T- or B-cell epitopes of major protein antigens from a particular pathogen. Epitope selection requires the synthesis of peptides that overlap the protein sequences and screening for the most effective ones. In this study a new method of immunogenic peptide selection based on the analysis of information structure of protein sequences is suggested. The analysis of known B-cell epitope location in the information structure of Aspergillus fumigatus proteins Asp f 2 and Asp f 3 has shown that epitopes are scattered along the sequences of proteins for the exception of sites with Increased Degree Information Coordination (IDIC). Based on these results peptides from different allergens such as Asp f 2, Der p 1, and Fel d 1 were selected and produced in a recombinant form in the context of yeast virus-like particles (VLPs). Immunization of mice with VLPs containing peptides form allergens has induced the production of IgG able to recognize full-length antigens. This result suggests that the analysis of information structure of proteins can be used for the selection of peptides possessing cryptic B-cell epitope activity.
Journal of Bioinformatics and Computational Biology Vol. 4, No. 2, (2006), pp. 389–402.

A comparison of the location of B-cell epitopes and information structure (IS) of protein sequences was attempted. Analysis of 62 known B-cell epitopes located in five different proteins showed that they concentrated in IS sites with increased degree of information coordination. Based on the analysis of IS six peptides from two proteins were selected and produced in a recombinant form as yeast virus-like particles (VLPs). Immunization of mice with recombinant VLP-peptides has induced the production of IgG capable of recognizing full-length antigens. This result suggests that the analysis of IS of proteins can be useful in the selection of peptides possessing cryptic B-cell epitope activity.
Vaccine 2007 vol. 25(14), pp. 2688-2697