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Atomic size packing defects in proteins.

M L Connolly

    International Journal of Peptide and Protein Research
    |October 1, 1986
    PubMed
    Summary
    This summary is machine-generated.

    This study examined 20 protein structures, finding most are well-packed with few atomic-sized defects. Hydrophobic atoms like carbon and sulfur often surround these rare packing defects in proteins.

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    Area of Science:

    • Structural biology
    • Protein structure analysis

    Background:

    • Proteins are essential biological macromolecules with complex three-dimensional structures.
    • Understanding protein packing is crucial for comprehending their stability and function.
    • Previous studies suggested proteins are generally well-packed, but larger sample sizes are needed.

    Purpose of the Study:

    • To investigate the presence and characteristics of atomic-scale packing defects in high-resolution protein structures.
    • To confirm or refute the hypothesis that proteins are predominantly well-packed.
    • To identify the chemical nature of atoms surrounding any observed packing defects.

    Main Methods:

    • Analysis of 20 three-dimensional refined high-resolution protein structures.
    • Systematic examination for packing defects of atomic size or larger.

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  • Identification and characterization of atoms adjacent to packing defects.
  • Tabulation of internal water molecules within the protein structures.

    • Main Results:

    • Out of 20 proteins analyzed, 12 showed no packing defects.
    • 6 proteins contained a single packing defect, and 2 proteins had 2 or 3 defects.
    • Atoms surrounding packing defects were predominantly hydrophobic (carbon or sulfur).
    • The number of internal water molecules varied significantly, ranging from 0 to 28 per protein.

    Conclusions:

    • The findings support previous research indicating that proteins are generally well-packed structures.
    • The prevalence of hydrophobic residues around packing defects suggests a role in maintaining structural integrity.
    • The variability in internal water content highlights diverse strategies for protein internal organization.