Substitution Models of Protein Evolution with Selection on Enzymatic Activity.

ABSTRACT: Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme-substrate complex as

SUBMITTER: Ferreiro D 

PROVIDER: S-EPMC10873502 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature