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Related Experiment Videos

Proteomic traces of speciation.

Eric J Deeds1, Boris Shakhnovich, Eugene I Shakhnovich

  • 1Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue Cambridge, MA 02138, USA.

Journal of Molecular Biology
|April 21, 2004
PubMed
Summary

Protein domain evolution follows a scale-free network pattern. A divergent model, incorporating speciation, accurately explains structural proteome overlap, challenging convergent evolution theories.

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Area of Science:

  • Evolutionary Biology
  • Bioinformatics
  • Structural Bioinformatics

Background:

  • The protein domain universe graph (PDUG) exhibits a scale-free network structure.
  • Previous studies suggested a divergent model could explain this scale-free nature.
  • The possibility of a convergent model remained unresolved.

Purpose of the Study:

  • To differentiate between convergent and divergent models of protein structural evolution.
  • To analyze organism-specific proteome subgraphs within the PDUG.
  • To assess the consistency of evolutionary models with observed proteome structures.

Main Methods:

  • Partitioned the PDUG into organismal subgraphs based on proteome occurrence.
  • Analyzed the scale-free properties of these organismal subgraphs.
  • Tested predictions of simple and biased convergent models against subgraph data.
  • Developed and tested a divergent model incorporating speciation mechanisms.

Main Results:

  • Organismal subgraphs of the PDUG also exhibit scale-free properties.
  • Simple and biased convergent models were inconsistent with observed subgraph features.
  • A divergent model augmented with speciation mechanisms successfully reproduced organismal subgraph characteristics.
  • Speciation events are crucial for explaining non-random structural proteome overlap.

Conclusions:

  • Divergent evolution, including speciation, is a more plausible explanation for protein structural evolution patterns than convergent evolution.
  • Dynamic models incorporating speciation can account for the observed distributions of structural similarity within proteomes.
  • Findings impact the understanding of protein evolution and the broader study of organismal evolution.

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