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Roles of solvent accessibility and gene expression in modeling protein sequence evolution.

Kuangyu Wang1, Shuhui Yu2, Xiang Ji1

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Summary

This study introduces a new codon substitution model considering protein structure and gene expression. Gene expression, not protein structure, more strongly influences codon choice, impacting evolutionary rate estimates.

Keywords:
codon usagegene expressionprotein evolutionprotein structurescaled selection coefficientsolvent accessibility

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Area of Science:

  • Evolutionary biology
  • Computational biology
  • Molecular evolution

Background:

  • Protein evolution models often overlook functional and structural constraints.
  • Relative solvent accessibility (RSA) and gene expression are key factors influencing protein evolution.

Purpose of the Study:

  • To develop a probabilistic framework for codon substitution incorporating RSA and gene expression.
  • To create a new codon substitution model for estimating evolutionary parameters.

Main Methods:

  • Explored the relationship between RSA, codon usage, and gene expression.
  • Constructed a probabilistic framework to determine amino acid and codon probabilities based on RSA and gene expression.
  • Developed a new codon substitution model to estimate 2N s (product of effective population size and relative fitness difference).

Main Results:

  • Both RSA and gene expression correlate with amino acid frequencies.
  • Gene expression is more strongly related to the relative probability of synonymous codons than RSA.
  • Estimates of 2N s were concentrated around 0, suggesting limited variability.

Conclusions:

  • The proposed framework provides insights into the interplay of structural and functional constraints in protein evolution.
  • Gene expression plays a more significant role than RSA in determining codon usage.
  • Further research is needed to understand the observed lack of variability in 2N s estimates.