A method for estimation of immunogenic determinants mutability: case studies of HIV1 gp120 and diphtheria toxin
There is a need for the method which helps to choose the less mutable immunogenic determinant for the design of recombinant or synthetic vaccines and ELISA test-systems. With the help of our method based on the directional mutational pressure theory one is able to estimate direction of symmetric and asymmetric mutational pressure in a gene coding for a protein of interest, and to find out which of its immunogenic determinants are less prone to missense mutations and so, to immune escaping. Three original computer algorithms (“VVK Sliding Window”, “VVK VarInvar” and “VVK Protective Buffer” available via www.barkovsky.hotmail.ru) have been created to perform all the necessary calculations and tests. “VVK Sliding Window” calculates nucleotide usage in fourfold and twofold degenerated sites, as well as usage of missense, nonsense and synonymous sites for each kind of nucleotide mutation along the length of a coding region, while “VVK Protective Buffer” calculates those indexes in a set of sequences. “VVK VarInvar” calculates percentage of variable sites in a set of aligned sequences, as well as nucleotide usage in invariable sites. We tested our method on HIV1 gp120 protein and on diphtheria toxin. The less mutable epitopes have been found for both proteins. Finally, we showed that antibodies recognizing the less mutable epitope of gp120 can be found in 80,22% of HIV1-infected persons.