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Related Experiment Videos

Quantifying the similarities within fold space.

Andrew Harrison1, Frances Pearl, Richard Mott

  • 1Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, Gower Street, UK. harry@biochem.ucl.ac.uk

Journal of Molecular Biology
|November 6, 2002
PubMed
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This study introduces "gregariousness," a new measure of fold similarity, revealing that protein fold space is continuous for some structures but discrete for others. This impacts how we understand protein structural relationships.

Area of Science:

  • Structural Bioinformatics
  • Computational Biology
  • Protein Science

Background:

  • Understanding protein fold similarity is crucial for deciphering evolutionary relationships and functional mechanisms.
  • Existing methods often treat protein folds as discrete entities, potentially oversimplifying the complex relationships within protein structure databases.

Purpose of the Study:

  • To investigate whether protein folds are best represented as discrete entities or as a continuum connected by common structural motifs.
  • To develop and apply a novel statistical measure, "gregariousness," to quantify fold similarity and explore the topology of protein fold space.

Main Methods:

  • Utilized the GRATH algorithm for graph-based comparison of protein domain structures within the CATH database.
  • Introduced and applied a new metric, "gregariousness," to measure the extent of structural overlap between folds.

Related Experiment Videos

  • Performed statistical analysis on fold similarity distributions to assess significance.

    • Main Results:

    • Identified "gregarious folds" that share significant structural overlap (≥40%) with many other folds, often containing common super-secondary structural motifs.
    • Found that most highly gregarious folds (matching ≥20% of other folds) are alpha-beta proteins with sandwich-like arrangements.
    • Observed that low gregariousness is associated with distinctive folds and unusual motif packing, as seen in superhelices.

    Conclusions:

    • Protein fold space can be viewed as continuous for certain architectural arrangements, like alpha-beta sandwiches, where super-secondary motifs bridge fold groups.
    • Other regions of fold space exhibit more discrete topologies, with limited similarity between folds, suggesting varied organizational principles.