We studied nucleotide usage biases in 4-fold degenerated sites of all the genes from leading and lagging strands of 30 bacterial genomes. The level of guanine in 4-fold degenerated sites (G4f) is significantly lower in genes from lagging strands than in genes from leading strands, probably because of the faster rates of guanine oxidation in single-stranded DNA leading to G to T transversions. The rates of cytosine deamination causing C to T transitions are also higher in lagging strands. We showed that the level of codons able to form stop-codons by the way of G to T transversions and C to T transitions is always higher than the level of codons able to form stop-codons by the way of C to A transversions and G to A transitions. This circumstance can be an explanation of the lower percent of ORFs in lagging strands of bacterial replichores than in leading strands.
The simplification of amino acid content distribution under the influence of the strong mutational pressure takes place in simplex and varicello viruses proteins coded by genes with GC-content higher than 60%. We proved this statement by the way of in-silico calculation of Shannon's entropy of amino acid content distribution in all proteins from ten completely sequenced simplex and varicello viruses. Entropy of amino acid content distribution decreases because of the growth of GARP (glycine, alanine, arginine and proline) usage due to the decrease not only in FYMINK (phenylalanine, tyrosine, methionine, isoleucine, asparagine and lysine) but also in other amino acids (coded by codons with average GC-content) usages. Threonine, serine, glutamine and cysteine are frequently substituted to GARP in proteins coded by genes with G+C higher than 60% (threonine and serine are substituted mostly to alanine while glutamine and histidine are substituted mostly to arginine). Cysteine, valine and leucine are frequently substituted to GARP only in proteins coded by genes with G+C higher than 80%, probably because of the higher radicalism of these substitutions. Levels of tryptophan, glutamic and aspartic acids do not decrease under the influence of GC-pressure even in proteins coded by genes with G+C higher than 80%.
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. Our method based on the directional mutational pressure theory includes two steps: estimation of symmetric and asymmetric mutational pressure directions in a gene coding for a protein of interest; and selection of regions coding for its immunogenic determinants which are less prone to missense mutation occurrence 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. Our method has been tested on HIV1 gp120 protein and on diphtheria toxin. The less mutable epitopes have been found for both proteins. Finally, it has been shown that antibodies recognizing the less mutable epitope of gp120 can be found in 80.22% of HIV1-infected persons
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.