Testing for the Time Dependent Transition from a Rates Across Sites Model to a Covarion Model of Protein Evolution

Tisdell, Makayla
Protein-coding gene sequences typically evolve constrained by the requirements for a protein to fold into its three dimensional structure. These constraints can dictate evolutionary rates at different sites, where residues in the hydrophobic core of a protein typically evolve more slowly than those on the surface. The exceptions to this are surface residues involved directly in functions of the protein such as binding, which are also conserved. A gamma distribution of rates across sites is typically used to describe the process of protein evolution in what is called the rates across sites model. It has been proposed that this model is violated when the function of a protein changes. It has alternatively been proposed that protein structure leads to violations of the gamma distribution over increasing evolutionary time. I hypothesized that the rate of the transition is fold-dependent and that different protein folds will move from an RAS model to a Covarion model at different rates. In preliminary analysis, an equal rates rather than a RAS model was supported which suggests the energy function used in the evaluation of protein folding should be modified before further analysis.
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