Are residues in a protein folding nucleus evolutionarily conserved?

Area of Science:

• Molecular Biology
• Evolutionary Biology
• Biophysics

Background:

• Understanding the interplay between protein folding and evolution is crucial.
• Previous studies on folding nucleus residue conservation yielded conflicting results.
• Existing methods often rely on entropy measurements from multiple sequence alignments.

Purpose of the Study:

• To investigate the evolutionary conservation of protein folding nucleus residues using a novel evolutionary model.
• To differentiate between mutations fixed by evolution versus those fixed by chance.
• To assess the correlation between kinetic properties of folding nucleus residues and their evolutionary selection pressure.

Main Methods:

• Employed a continuous time Markov model of codon substitution.
• Incorporated codon frequency bias, transition-transversion bias, and phylogenetic information.
• Estimated selection pressure using the omega (ω) ratio of synonymous to non-synonymous substitutions (dN/dS) via PAML.
• Conducted randomization tests to compare folding nucleus residue conservation with the whole protein.

Main Results:

• Little correlation was observed between experimental phi-values (measuring kinetic participation) and omega-values (measuring selection pressure).
• Randomization tests did not indicate significantly higher conservation of folding nucleus residues compared to other protein residues.
• The study found no evidence of enhanced evolutionary conservation for folding nucleus residues at the codon substitution level.

Conclusions:

• Folding nucleus residues do not appear to be under stronger evolutionary constraint than other residues, based on codon substitution analysis.
• The findings challenge the assumption that functionally critical residues in protein folding are necessarily more conserved evolutionarily.
• Reconstructed ancestral residues offer potential avenues for future experimental validation of folding behavior.