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Protein folds and functions

A C Martin1, C A Orengo, E G Hutchinson

  • 1Department of Biochemistry and Molecular Biology, University College, London, UK.

Structure (London, England : 1993)
|August 4, 1998
PubMed
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Protein structure (fold) is not strongly linked to enzyme class, but is highly correlated with the type of ligand bound. This finding aids in understanding protein function and evolution.

Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • The exponential growth of 3D protein structure data necessitates understanding structure-function relationships.
  • Structural classification databases (SCOP, CATH, DALI) enable large-scale analysis of protein folds and functions.

Purpose of the Study:

  • To investigate the relationship between protein fold, function, and bound ligands using structural classification data.
  • To determine if protein function, specifically enzyme classification, correlates with protein fold or bound ligand.

Main Methods:

  • Utilized a relational database of the CATH (Class, Architecture, Topology, Homologous superfamily) structural classification.
  • Generated and analyzed protein fold distributions for selected protein sets.

Related Experiment Videos

  • Correlated fold distributions with protein function (EC number) and bound ligand information.

    • Main Results:

    • Protein fold distributions did not clearly reflect different enzyme classes.
    • The type of bound ligand demonstrated a significant impact on fold distributions.
    • Top-level enzyme classification (EC number) showed weak correlation with protein fold.

    Conclusions:

    • Protein fold is more closely related to the type of ligand a protein binds than its broad enzymatic function.
    • Specific residues, not overall fold, are primarily responsible for enzyme activity.
    • Structural classification data facilitates novel analyses of protein structure-function relationships.