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Amino acid difference formula to help explain protein evolution.

R Grantham

    Science (New York, N.Y.)
    |September 6, 1974
    PubMed
    Summary
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    Amino acid differences are best predicted by composition, polarity, and molecular volume, not just genetic code changes. This suggests that mutations leading to dissimilar amino acids are uncommon in protein evolution.

    Area of Science:

    • Biochemistry and Molecular Biology
    • Evolutionary Biology
    • Genetics

    Background:

    • Protein residue substitution frequencies are key to understanding evolutionary relationships.
    • Previous models often focused on genetic code changes (mutations) rather than physicochemical properties.

    Purpose of the Study:

    • To develop and validate a formula for quantifying amino acid differences.
    • To determine which properties best predict observed substitution frequencies.
    • To assess the role of genetic vs. physicochemical factors in amino acid substitutions.

    Main Methods:

    • Developed a formula combining amino acid composition, polarity, and molecular volume.
    • Correlated formulaic differences with empirical protein residue substitution frequencies.

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  • Compared these correlations with those based on minimum base changes in codons.

    • Main Results:

    • A formula integrating composition, polarity, and molecular volume showed strong correlation with substitution frequencies.
    • Physicochemical differences explained substitution patterns better than minimum base changes.
    • High correlation coefficients indicate that fixation of mutations between dissimilar amino acids is rare.

    Conclusions:

    • Amino acid substitution patterns are primarily driven by physicochemical properties, not solely by genetic code.
    • The developed formula provides a robust measure of amino acid divergence.
    • Understanding these drivers is crucial for evolutionary and protein engineering studies.