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Protein densities.

I D Kuntz, G M Crippen

    International Journal of Peptide and Protein Research
    |February 1, 1979
    PubMed
    Summary

    Calculating protein densities reveals significant internal variations. Low densities correlate with nonpolar sidechains, while high densities associate with protein backbone structures like helices and beta sheets.

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    Area of Science:

    • Biophysics
    • Structural Biology
    • Computational Biology

    Background:

    • Determining protein densities from atomic coordinates is complex.
    • Careful definition of the protein-solvent boundary is crucial for accurate calculations.
    • Interior protein densities can be estimated and compared with solvent accessibility data.

    Purpose of the Study:

    • To calculate and analyze internal protein densities using atomic coordinates.
    • To investigate the heterogeneity of densities within globular proteins.
    • To correlate local density variations with protein structural features and polarity.

    Main Methods:

    • Calculation of protein densities from provided atomic coordinates.
    • Analysis of density variations within the protein interior.
    • Comparison of calculated densities with solvent accessibility estimates.
    • Correlation analysis between local density, secondary structures, and sidechain composition.

    Main Results:

    • Protein interior exhibits significant density inhomogeneities (100-1000 A3).
    • Densities range from <0.5 g/cm3 to >3 g/cm3.
    • Low densities are linked to nonpolar sidechain clusters.
    • High densities are associated with protein backbone secondary structures (helices, beta sheets).
    • A correlation between local density and local polarity was observed.

    Conclusions:

    • Internal protein density is highly heterogeneous.
    • Specific structural elements like nonpolar clusters and secondary structures dictate local density.
    • Local density variations correlate with protein polarity, offering insights into protein structure-function relationships.

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