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Related Experiment Videos

Comparing function and structure between entire proteomes.

J Liu1, B Rost

  • 1CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.

Protein Science : a Publication of the Protein Society
|September 22, 2001
PubMed
Summary
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Bioinformatics analysis of 29 proteomes reveals eukaryotes have more long proteins and distinct membrane protein structures compared to prokaryotes and archaea. Overall amino acid composition remains similar across kingdoms.

Area of Science:

  • Comparative genomics
  • Proteomics
  • Bioinformatics

Background:

  • Over 30 organisms have been fully sequenced, providing a rich dataset for comparative analysis.
  • Understanding proteome diversity across the three domains of life (eukaryotes, prokaryotes, archaea) is crucial for evolutionary and functional insights.

Purpose of the Study:

  • To analyze 29 proteomes from eukaryotes, prokaryotes, and archaea using bioinformatics tools.
  • To compare protein characteristics, including length, amino acid composition, transmembrane helices, coiled-coil proteins, secretion, and structural families across the three kingdoms.

Main Methods:

  • Utilized a variety of simple bioinformatics tools for proteome analysis.
  • Analyzed 29 representative proteomes from eukaryotes, prokaryotes, and archaea.

Related Experiment Videos

  • Compared protein length, amino acid composition, transmembrane helix content, coiled-coil protein presence, secretion prediction, and structural homology.

    • Main Results:

    • Eukaryotes possess a higher proportion of long proteins compared to prokaryotes and archaea.
    • Amino acid composition is largely conserved across the three kingdoms.
    • While overall transmembrane helix content is similar, eukaryotes show more proteins with seven transmembrane helices, and prokaryotes with six and 12.
    • Eukaryotes have twice the percentage of coiled-coil proteins (10%) compared to prokaryotes and archaea (4%-5%).
    • Approximately 15%-25% of proteins are predicted to be secreted in eukaryotes and prokaryotes.
    • 10% of proteins lack known homologs, and 30%-40% belong to large structural families (>100 members).
    • Eukaryotes exhibit a higher proportion of proteins involved in environmental communication.

    Conclusions:

    • Comparative proteome analysis reveals kingdom-specific differences in protein features, particularly in eukaryotes.
    • The study provides insights into protein structure, function, and evolution across diverse life forms.
    • Predictions suggest a potential universe of 1200-2600 protein folds.