Journal de protéomique et bioinformatique
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Main Pathways of Proteome Simplification in Alphaherpesviruses Under the Influence of the Strong Mutational GC-pressure

Vladislav V. Khrustalev and Eugene V. Barkovsky

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%.