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Related Experiment Videos

Protein function space: viewing the limits or limited by our view?

Jeroen Raes1, Eoghan Donal Harrington, Amoolya Hardev Singh

  • 1European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

Current Opinion in Structural Biology
|June 19, 2007
PubMed
Summary
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Estimating the limits of protein function space is challenging. While many proteins have known functions, new sequencing data reveals an increasing number of novel protein families, obscuring the boundaries of protein space.

Area of Science:

  • Proteomics and Bioinformatics
  • Genomics and Metagenomics

Background:

  • The finite number of protein functions on Earth suggests limits to protein space.
  • Biological knowledge and protein sequence data are expanding exponentially.
  • Computational methods are crucial for investigating protein function coverage.

Purpose of the Study:

  • To explore the estimation of protein function space limits.
  • To investigate the functional coverage of protein sequences using computational approaches.
  • To reconcile the increasing number of known protein functions with the emergence of novel protein families.

Main Methods:

  • Analysis of protein functional assignments in completely sequenced genomes.
  • Investigation of protein functional coverage in metagenomics surveys.

Related Experiment Videos

  • Utilizing computational methods to assess large-scale sequencing data.

    • Main Results:

    • Approximately 85% of proteins in sequenced genomes have assigned functional features.
    • Functional coverage estimation in metagenomics is less certain due to environmental and analytical complexities.
    • Continued sequencing consistently reveals an increasing number of novel protein families.

    Conclusions:

    • Global knowledge of protein functions is substantial but faces challenges in metagenomic contexts.
    • The emergence of novel protein families complicates the understanding of protein space boundaries.
    • Reconciling current functional knowledge with new discoveries is necessary to define the limits of protein space.