Comparison of scales of amino acid side chain properties by conservation during evolution of four proteins

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Abstract
As the amino acid sequence of a given protein changes along the phylogenetic tree, enough of the overall folding pattern must be conserved to ensure that the protein still fulfils its biological function. Eighteen published scales which tabulate various side chain properties are compared here by computing the variance of each scale when applied to each of several protein families. The conservation of each scale of side chain properties is examined for the 20 627 residues in 60 mammalian myoglobins, 31 mammalian ribonucleases, insulin A and B chains (29 sequences each), 29 vertebrate and 28 plant cytochrome c's. Those scales which are the most highly conserved through the evolution of each protein family may well be the best predictors of protein folding patterns. The mean-area-buried scale and the optimized matching hydrophobicities scale are more conserved than other scales. An additional result is the relatively poor conservation across evolution of the Chou-Fasman secondary structure predictors.
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