Abstract
We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations, one based on relative amino-acid rates and the other based on site-specific codon rates measured as dN/dS. In addition to describing the specific analysis protocols we recommend, we also provide a code repository containing scripts to facilitate these kinds of analyses.
Highlights
Different sites within a protein-coding gene evolve at different rates1,2
Protein structure has been found to play a major role in shaping protein evolutionary rates across the entire protein sequence, because the imperative for a protein to stably fold produces an overarching evolutionary constraint
Protocols In the following, we provide four separate protocols to (i) measure relative amino acid rates, (ii) measure site-specific codon evolutionary rates, (iii) measure structural quantities such as relative solvent accessibility (RSA) and weighted contact number (WCN), and (iv) combine the measured quantities into a combined analysis
Summary
Measuring evolutionary rates of proteins in a structural context [version 1; peer review: 4 approved].
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