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Evaluation of compositional nonrandomness in proteins

R Holmquist

    Journal of Molecular Evolution
    |October 6, 1978
    PubMed
    Summary
    This summary is machine-generated.

    The finite sampling component of Q, a measure of protein nonrandomness, was recalculated using natural amino acid abundances. This revised calculation significantly lowered the estimate of selective effects (Qc), suggesting minimal adjustments from average protein composition are needed for biological function.

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    Area of Science:

    • Biochemistry
    • Evolutionary Biology
    • Bioinformatics

    Background:

    • The measure of nonrandomness in protein amino acid composition (Q) may have been underestimated.
    • Previous calculations relied on genetic code table frequencies instead of natural amino acid abundances.

    Purpose of the Study:

    • To quantitatively estimate the finite sampling component of Q using natural amino acid abundances.
    • To reassess the measure of selective effects (Qc) based on actual amino acid occurrence in proteins.

    Main Methods:

    • Recalculating the finite sampling component of Q using average natural abundances of 20 amino acids.
    • Estimating Qc values for 81 protein families based on their mean composition.

    Main Results:

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    • The average Qc value was reduced from 24.3 to 9.7.
    • The standard deviation of Qc values was found to be 12.5.
    • Individual Qc values for 81 protein families were provided.

    Conclusions:

    • The revised mean Qc value of 9.7 indicates minimal selective adjustments from average protein composition are necessary for biological functions.
    • This value significantly differs from zero, suggesting that small deviations from natural amino acid abundances are selected for in a Darwinian sense.