A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices.

ABSTRACT: Proteins evolve under a myriad of biophysical selection pressures that collectively control the patterns of amino acid substitutions. These evolutionary pressures are sufficiently consistent over time and across protein families to produce substitution patterns, summarized in global amino acid substitution matrices such as BLOSUM, JTT, WAG, and LG, which can be used to successfully detect homologs, infer phylogenies, and reconstruct ancestral sequences. Although the factors that govern the variation of amino acid substitution rates have received much attention, the influence of thermodynamic stability constraints remains unresolved. Here we develop a simple model to calculate amino acid substitution matrices from evolutionary dynamics controlled by a fitness function that reports on the th

SUBMITTER: Norn C 

PROVIDER: S-EPMC8442976 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature