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The 'knotting' problem in proteins. Loop penetration.

M H Klapper, I Z Klapper

    Biochimica Et Biophysica Acta
    |November 20, 1980
    PubMed
    Summary
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    Protein knotting is redefined as loop penetration. Analysis of disulfide-containing proteins suggests loop penetration occurs randomly, challenging the notion that it is a rare phenomenon in protein structures.

    Area of Science:

    • Biochemistry
    • Structural Biology
    • Computational Biology

    Background:

    • The 'knotting' problem in proteins describes complex topological structures.
    • Understanding protein topology is crucial for predicting protein function and stability.
    • Current models may underestimate the prevalence of certain topological features like loop penetration.

    Purpose of the Study:

    • To redefine protein knotting using the concept of loop penetration.
    • To investigate the occurrence and distribution of loop penetration in disulfide-containing proteins.
    • To challenge the prevailing view on the rarity of loop penetration in proteins.

    Main Methods:

    • Representing disulfide-containing proteins as linear graphs.
    • Analyzing the planarity of these graph representations.

    Related Experiment Videos

  • Correlating graph non-planarity with three-dimensional loop penetrations.
  • Comparing observed loop penetration frequency with random pairing models.

    • Main Results:

    • Proteins with nonplanar graph representations exhibit loop penetrations in their 3D structure.
    • The observed frequency of loop penetration in disulfide-containing proteins aligns with random sulfhydryl group pairing.
    • Loop penetration appears to be more common than previously assumed.

    Conclusions:

    • Loop penetration is a more general concept than protein knotting.
    • The occurrence of loop penetration is consistent with random topological processes.
    • The prevalence of loop penetration in proteins warrants re-evaluation.