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Related Experiment Videos

Structural characterization of genomes by large scale sequence-structure threading.

Artem Cherkasov1, Steven J M Jones

  • 1Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada. artc@interchange.ubc.ca

BMC Bioinformatics
|April 6, 2004
PubMed
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Sequence-structure threading successfully characterized protein folds in over 60% of eukaryotic, archaeal, and bacterial proteomes. This large-scale genomic analysis reveals universal patterns in protein architecture and distribution across life.

Area of Science:

  • Structural bioinformatics
  • Genomics
  • Computational biology

Background:

  • Utilized sequence-structure threading for comprehensive structural characterization.
  • Analyzed complete proteomes from 37 diverse organisms (archaea, bacteria, eukaryotes).
  • Total dataset comprised 167,888 genes from various species, including human and mouse.

Purpose of the Study:

  • To evaluate the performance and general applicability of sequence-structure threading for large-scale genomic studies.
  • To establish protein fold repertoires across different superkingdoms.
  • To investigate the distribution patterns of protein classes, architectures, and topologies.

Main Methods:

  • Applied sequence-structure threading to analyze complete proteomes.
  • Classified protein structures using the CATH 2.4 database.

Related Experiment Videos

  • Performed statistical analysis on genomic occurrences of protein superfamilies and topologies.

    • Main Results:

    • Assigned protein folds to over 60% of eukaryotic, 68% of archaeal, and 70% of bacterial proteomes.
    • Identified "alpha and beta" as the most abundant CATH class, "3-Layer (aba) Sandwich" as the most common architecture, and Rossmann fold as the most frequent topology.
    • Characterized repertoires of protein classes, architectures, and topologies for diverse organisms.

    Conclusions:

    • Genomic occurrences of protein superfamilies and topologies exhibit power-law distributions.
    • Established double logarithmic "frequency - genomic occurrence" dependences characteristic of scale-free systems.
    • Demonstrated the power-law nature of protein distribution across individual organisms and superkingdoms.