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Tandem Repeats Provide Evidence for Convergent Evolution to Similar Protein Structures.

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Structural similarity does not always imply homology. Some protein structures with high similarity may be analogous due to convergent evolution, especially those with repeated sequences.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology
  • Evolutionary Biology

Background:

  • Homology is traditionally inferred from sequence similarity, supported by decades of statistical frameworks.
  • Advances in protein structure prediction allow homology inference beyond sequence alignment limits.
  • Nearly identical protein structures can exist with undetectable sequence similarity, challenging traditional homology assessment.

Purpose of the Study:

  • To investigate the presence of analogous proteins (structurally similar but not homologous) within large databases of predicted protein structures.
  • To assess whether structural similarity alone is a reliable indicator of homology, especially when sequence similarity is low.
  • To determine if convergent evolution can produce analogous protein structures that might be misidentified as homologous.

Main Methods:

  • Analyzed Foldseek clusters of predicted protein structures to identify pairs lacking sequence-level homology support.
  • Examined strong structure matches (template modeling score ≥ 0.5) for the absence of sequence homology.
  • Investigated structures with predicted repeats and sequence-level tandem repeats to assess their potential to cause spurious matches.
  • Compared genealogies of tandem repeat units to infer homology or analogy in highly similar structures.

Main Results:

  • Approximately 2.6% of Foldseek clusters showed no sequence-level homology support, including about 1% of strong structure matches.
  • Strong structural matches lacking sequence homology were enriched in proteins with predicted repeats, potentially leading to spurious findings.
  • Many tandem repeat units within these structures exhibited genealogies inconsistent with a shared common ancestor, indicating analogy.

Conclusions:

  • A significant subset of highly similar protein structures may be analogous, not homologous, challenging the assumption that structural resemblance guarantees shared ancestry.
  • Caution is advised when inferring homology solely from structural similarity, particularly in the absence of supporting sequence evidence.
  • The presence of repeats can contribute to structural convergence and lead to misidentification of homology.