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Related Experiment Videos

An insight into domain combinations.

G Apic1, J Gough, S A Teichmann

  • 1MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK. apic@mrc-lmb.cam.ac.uk

Bioinformatics (Oxford, England)
|July 27, 2001
PubMed
Summary
This summary is machine-generated.

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Protein structural domains are combined in diverse ways across genomes, forming scale-free networks. This study analyzes domain combinations in Eubacteria, Archaea, and Eukaryota, revealing insights into protein evolution and structural genomics.

Area of Science:

  • Structural biology
  • Bioinformatics
  • Genomics

Background:

  • Proteins are built from structural domains, which are also evolutionary units.
  • A limited set of domain families are duplicated and combined to form the proteome of a genome.
  • Gene duplication, recombination, fusion, and fission drive the creation of new genes and proteins.

Purpose of the Study:

  • To survey protein domain combinations across seven genomes from Eubacteria, Archaea, and Eukaryota.
  • To understand the evolutionary processes shaping protein structure and function.
  • To investigate the combinatorial behavior of protein domain superfamilies.

Main Methods:

  • Utilized domain and superfamily definitions from the Structural Classification of Proteins (SCOP) database.

Related Experiment Videos

  • Mapped pairs of adjacent domains in genome sequences based on their superfamily combinations.
  • Analyzed domain repeats and compared genomic domain combinations with those in the Protein Data Bank (PDB).

    • Main Results:

    • Identified 624 out of 764 SCOP superfamilies within the studied genomes.
    • Observed 585 distinct pairwise combinations of these 624 domain families.
    • Found that most domain families combine with only one or two others, exhibiting a scale-free network pattern.
    • Noted a few highly versatile domain families with extensive combinatorial behavior.

    Conclusions:

    • Protein domain combinations in genomes follow a scale-free network architecture, suggesting underlying evolutionary principles.
    • The findings provide insights into the modular evolution of proteins and have implications for structural genomics.
    • Comparative analysis of genomic and PDB domain combinations aids in understanding protein structure and function relationships.