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Compact units in proteins.

M H Zehfus, G D Rose

    Biochemistry
    |September 23, 1986
    PubMed
    Summary
    This summary is machine-generated.

    A new coefficient of compactness measure identifies compact protein units, analogous to protein domains. This method accurately distinguishes native from misfolded proteins, revealing hierarchical organization and potential folding pathways.

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    Area of Science:

    • Structural biology
    • Computational biology
    • Biophysics

    Background:

    • Protein domains are fundamental units of protein structure and function.
    • Identifying protein domains is crucial for understanding protein folding and evolution.
    • Existing methods using only backbone atoms struggle to differentiate native from misfolded proteins.

    Purpose of the Study:

    • Introduce a novel geometric measure, the coefficient of compactness, to identify compact protein units.
    • Demonstrate the coefficient of compactness's ability to identify protein domains and their hierarchical organization.
    • Validate the method's sensitivity in distinguishing native from misfolded protein structures.

    Main Methods:

    • Calculated the coefficient of compactness based on solvent-accessible surface area and volume for continuous polypeptide segments.

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  • Applied the measure to lysozyme and ribonuclease to identify compact units.
  • Compared identified units with known protein domains, subdomains, and modules.
  • Tested the method's ability to differentiate native from deliberately misfolded proteins.

    • Main Results:

    • The coefficient of compactness successfully identified compact segments corresponding to protein domains.
    • Larger compact units identified by this measure align with conventional protein domains.
    • The method effectively differentiated between native and misfolded protein structures, unlike backbone-only methods.
    • Identified compact units exhibited a hierarchical organization.

    Conclusions:

    • The coefficient of compactness is a robust measure for identifying protein domains and structural units.
    • This method offers a sensitive approach to detect protein misfolding.
    • The hierarchical organization of compact units suggests potential protein folding pathways that warrant experimental investigation.