Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution

• DOI: 10.7717/peerj.5549
• Publication Date: 2018-10-05T08:49:34Z
• Authors: María José Jiméne...; Miguel Arenas; Ugo Bastolla
• Keywords: Sequence space; Substitution (logic); Sequence (biology)

The number of amino acids that occupy a given protein site during evolution reflects the selective constraints operating on site. This evolutionary variability is strongly influenced by structural properties in native structure, and it quantified either through sequence entropy or substitution rates. However, while only depends equilibrium frequencies acids, rate also exchangeability matrix describes mutations mathematical model process. Here we apply two variants with selection for stability, both against unfolding misfolding. Exploiting approximation independent sites, these models allow computing site-specific processes satisfy global folding stability. We find rates do not depend acting site, its entropy. In fact, polar sites evolve faster than hydrophobic even equal entropy, as consequence fact are characterized higher mutational ones. Accordingly, predicts more proteins tend to faster. Nevertheless, results change if compare under different mutation biases, such orthologous bacterial genomes. this case, genomes bias favor preferentially incorporating nucleotide Thymine frequent codons. appearingly contradictory result arises because buried occupied larger factors largely amplify between exposed have weaker effect. Thus, changes produce deep effects biophysical (hydrophobicity) (sequence rate) at same time. program Prot_evol implements freely available https://ub.cbm.uam.es/prot_fold_evol/prot_fold_evol_soft_main.php#Prot_Evol .