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Naturally occurring circular permutations in proteins.

S Uliel1, A Fliess, R Unger

  • 1Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 52900, Israel.

Protein Engineering
|October 2, 2001
PubMed
Summary
This summary is machine-generated.

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Researchers identified 25 protein pairs with circular permutations using a novel screening algorithm. This finding suggests circular permutations in proteins are rare and likely arise from functional unit fusion, not local genetic manipulation.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Circular permutation defines a specific relationship between protein sequences where N- and C-terminal regions are swapped.
  • Detecting such relationships is crucial for understanding protein evolution and function.

Purpose of the Study:

  • To develop and apply a computational method for identifying circularly permuted protein pairs.
  • To assess the prevalence of circular permutation in protein databases.

Main Methods:

  • A fast screening algorithm, a variation of dynamic programming string matching with sequence doubling, was developed.
  • Candidate pairs were validated using exhaustive string matching and manual inspection with dotplots.
  • Searches were conducted in the Swissprot and Pfam databases.

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Main Results:

  • Twenty-five independent protein pairs related by circular permutation were identified in Swissprot.
  • These pairs were categorized based on functional similarity.
  • A systematic search in Pfam yielded only seven additional candidates, none matching the initial definition.

Conclusions:

  • The low number of identified cases suggests that mechanisms for inducing local genetic manipulation leading to circular permutation are unlikely.
  • Observed instances of circular permutation appear to predominantly result from the fusion of functional protein units.