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Related Experiment Videos

Review: what can structural classifications reveal about protein evolution?

C A Orengo1, I Sillitoe, G Reeves

  • 1Department of Biochemistry and Molecular Biology, University College, Gower Street, London, WC1E 6BT, United Kingdom.

Journal of Structural Biology
|September 12, 2001
PubMed
Summary

This review covers protein structure comparison and classification methods. It examines major classifications, evolutionary trends, and recent genomic analyses revealing fold usage patterns.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Evolutionary biology

Background:

  • Protein structure classification is crucial for understanding protein function and evolution.
  • Existing classification systems face challenges in comprehensive analysis of structural evolution.
  • Genomic data offers new avenues for expanding protein family classifications.

Purpose of the Study:

  • To review and compare existing methods for protein structure comparison and classification.
  • To discuss the hierarchies and populations within major protein structure classifications.
  • To explore recent advancements in protein classification using genomic data.

Main Methods:

  • Literature review of protein structure comparison and classification methodologies.

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  • Analysis of major protein structure classification databases (e.g., SCOP, CATH).
  • Review of studies employing genomic sequence analysis to identify protein relatives and evolutionary trends.

    • Main Results:

    • Discussion of the strengths and limitations of various protein structure comparison algorithms.
    • Examination of fold group and evolutionary family distributions in key classifications.
    • Identification of trends in protein fold usage and recurrence across different genomes.

    Conclusions:

    • Current classification methods provide valuable insights but have limitations for broad evolutionary analyses.
    • Genomic approaches significantly enhance the scope and accuracy of protein family classification.
    • Understanding protein fold usage and recurrence is key to deciphering protein structural evolution.