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Related Experiment Videos

Domain rearrangements in protein evolution.

Asa K Björklund1, Diana Ekman, Sara Light

  • 1Stockholm Bioinformatics Center, Stockholm University, SE-10691 Stockholm, Sweden.

Journal of Molecular Biology
|October 4, 2005
PubMed
Summary

This study introduces domain distance to analyze multi-domain protein evolution, revealing indels are more frequent than repetitions and domain exchange is rare. This method aids in understanding protein family evolution.

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Most eukaryotic proteins consist of multiple domains, arising from gene fusions, deletions, and internal repetitions.
  • Understanding the evolutionary events shaping these multi-domain proteins is crucial for deciphering protein function and diversity.

Purpose of the Study:

  • To develop a novel quantitative measure, "domain distance," to analyze evolutionary events in multi-domain proteins.
  • To investigate the predominant evolutionary mechanisms (indels, repetitions, domain exchange) driving the evolution of multi-domain protein architectures.
  • To demonstrate the utility of domain distance in constructing evolutionary trees and studying specific protein families.

Main Methods:

  • Defined "domain distance" as the count of differing domains between two protein domain architectures.

Related Experiment Videos

  • Applied domain distance to analyze evolutionary events distinguishing proteins from their ancestors.
  • Correlated domain distance with sequence similarity and Gene Ontology (GO) semantic similarity.
  • Utilized domain distance to construct phylogenetic trees.

    • Main Results:

    • Indels (insertions/deletions) are more common evolutionary events than internal repetitions or domain exchange in multi-domain proteins.
    • Indels and repetitions primarily occur at the N- and C-termini, with fewer events occurring internally between domains.
    • The evolution of most multi-domain proteins can be explained by stepwise single-domain insertions, with tandem duplications observed for repeats.
    • Domain distance shows strong agreement with sequence and GO semantic similarity.
    • Domain distance effectively aids in building evolutionary trees.

    Conclusions:

    • Domain distance is a robust measure for quantifying evolutionary changes in protein domain architectures.
    • Stepwise domain insertion is a primary driver of multi-domain protein evolution.
    • The developed method provides valuable insights into the evolutionary history of protein families, exemplified by non-receptor tyrosine kinases and RhoGEFs.