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Related Experiment Videos

Selecting protein targets for structural genomics of Pyrobaculum aerophilum: validating automated fold assignment

P Mallick1, K E Goodwill, S Fitz-Gibbon

  • 1UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, Department of Chemistry and Biochemistry, Molecular Biology Institute, Box 951570, University of California, Los Angeles, CA 90095-1570, USA.

Proceedings of the National Academy of Sciences of the United States of America
|March 8, 2000
PubMed
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Researchers analyzed protein folds in the Pyrobaculum aerophilum genome, identifying known and novel protein structures. This study aids in selecting targets for structural determination, advancing our understanding of archaeal biology.

Area of Science:

  • Structural bioinformatics
  • Genomics
  • Archaea biology

Background:

  • The genome of the hyperthermophilic archaeon Pyrobaculum aerophilum has been sequenced.
  • Understanding protein structures is crucial for deciphering biological functions.
  • A significant portion of sequenced genomes remains structurally uncharacterized.

Purpose of the Study:

  • To assign three-dimensional protein folds to all open reading frames (ORFs) in the Pyrobaculum aerophilum genome.
  • To estimate the confidence level for each fold assignment.
  • To identify proteins with novel folds not yet present in structural databases.

Main Methods:

  • Utilized binary hypothesis testing to assign protein folds and estimate confidence levels.
  • Conducted separate statistical tests to determine the probability of novel folds.

Related Experiment Videos

  • Integrated fold assignment data with homology searches against the Online Mendelian Inheritance in Man (OMIM) database and other protein databases.

    • Main Results:

    • 916 out of 2,130 predicted non-transmembrane proteins were assigned a known fold with 90% confidence, and 245 with 99% confidence.
    • 286 proteins were predicted to have novel folds with 90% confidence, and 14 with 99% confidence.
    • The study provides a curated list of potential targets for crystallographic or NMR structure determination.

    Conclusions:

    • Statistically robust methods can effectively assign protein folds and identify novel structures within a newly sequenced genome.
    • The findings facilitate the selection of high-priority targets for experimental structure determination.
    • This work contributes to the structural and functional annotation of the Pyrobaculum aerophilum proteome.