To overcome these problems, promising T cell epitopes that bind to several HLA alleles for maximal population coverage should be selected [ 16], and a large variety of HIV sequences should be considered in the design of a HIV vaccine.
Lastly, since a single pathogenic protein can give rise to several epitopes that bind different MHC molecules that are characteristic of each individual, there is a need for a high-throughput screening system that incorporates cell cultures and antigen presentation via professional antigen-presenting cells.
However, our study has shown that by large scale bioinformatics analysis it is possible to identify CD4+ T cell epitopes that promiscuously bind to several MHC class II alleles thus have potential for maximal population coverage.
They bind to three distinct epitopes: epitope I (1a2y and 1jhl), epitope II (1p2c and 2iff) and epitope III (1j1x) (see Supplementary Section 5).
As a test case we have picked lysozyme and the five distinct antibodies that bind to three different epitopes: epitope I (1a2y and 1jhl), epitope II (2iff and 1p2c) and epitope III with 1j1x (see Supplementary Section 5).
Two of these antibodies bind to conserved epitopes in the gp120 subunit, b12 and 2G12 [25], [25]; and two bind to conserved, contiguous epitopes in the gp41 subunit, 2F5 and 4E10 [27], [27].
The method is based on the two murine monoclonal antibodies that bind to different epitopes of insulin, but do not bind to proinsulin.
