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Swaps in protein sequences.

Amit Fliess1, Benny Motro, Ron Unger

  • 1Faculty of Life Science, Bar-Ilan University, Ramat-Gan, Israel.

Proteins
|July 12, 2002
PubMed
Summary
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Protein domain swaps are rare in evolution, challenging the idea of high modularity. Sequential constraints on domain order appear to be highly conserved, impacting protein evolution and engineering.

Area of Science:

  • Protein Evolution
  • Bioinformatics
  • Structural Biology

Background:

  • Protein evolution may involve domain or fragment order swaps.
  • Understanding protein swaps is crucial for theoretical insights and protein engineering applications.
  • Previous analyses faced challenges with repeats leading to false positives.

Purpose of the Study:

  • To systematically survey and quantify protein swaps in evolution.
  • To investigate the extent of domain or fragment order permutations in proteins.
  • To assess the frequency of swaps and their implications for protein modularity.

Main Methods:

  • Conducted a large-scale survey of protein pairs from the Swiss-Prot database.
  • Employed two main approaches: Pfam domain analysis and BLAST fragment comparison.

Related Experiment Videos

  • Developed algorithms to distinguish true swaps from duplications and used visual analysis to refine results.

    • Main Results:

    • Identified approximately 140 distinct cases of protein swaps in the Swiss-Prot database.
    • Many identified swaps represent novel examples not previously described.
    • The frequency of observed swaps is significantly lower than anticipated based on modularity assumptions.

    Conclusions:

    • Protein domain swaps are rare events in evolutionary history.
    • Contrary to expectations, proteins exhibit strong conservation of sequential domain order.
    • Sequential constraints play a significant role in protein evolution, limiting extensive module shuffling.