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Related Experiment Videos

Circularly permuted proteins in the protein structure database.

J Jung1, B Lee

  • 1Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA.

Protein Science : a Publication of the Protein Society
|August 22, 2001
PubMed
Summary
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Circularly permuting protein sequences reveals extensive structural similarities. This systematic search found that nearly half of all protein domains can be structurally superimposed with another domain after sequence permutation, uncovering hidden protein homologies.

Area of Science:

  • Structural bioinformatics
  • Protein sequence analysis
  • Computational biology

Background:

  • Proteins can exhibit homology even after circular permutation of their amino acid sequence.
  • Previous identifications of circularly permuted proteins relied on sequence or structural comparisons.
  • A systematic search was needed to quantify the prevalence of such proteins.

Purpose of the Study:

  • To systematically identify protein pairs in a large database that are structurally superimposable after circular permutation of one sequence.
  • To determine the frequency of circular permutation-induced structural similarity across protein domains.
  • To discover novel instances of circularly permuted proteins, especially those with remote homology.

Main Methods:

  • Utilized the SCOP 90% identity domain database for comprehensive analysis.

Related Experiment Videos

  • Developed and applied criteria for structural superimposability after sequence circular permutation.
  • Performed systematic structural comparisons on a large scale to identify matching protein pairs.

    • Main Results:

    • 47% of all protein domains were found to be structurally superimposable to at least one other domain after circular permutation.
    • Many symmetric proteins superimpose both with and without sequence permutation.
    • 412 out of 3035 domains are nonsymmetric and become superimposable only after circular permutation, including many previously undetected remote homology cases.

    Conclusions:

    • Circular permutation is a common phenomenon that reveals significant, often hidden, structural relationships between proteins.
    • The study significantly expands the known set of circularly permuted proteins, highlighting their importance in protein evolution and function.
    • This systematic approach provides a powerful tool for discovering distant protein homologies.