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Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context.

Zhengyuan O Wang1, David D Pollock

  • 1Department of Biological Sciences and Biological Computing and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA.

Journal of Molecular Evolution
|October 24, 2007
PubMed
Summary

Amino acid residue coevolution in cytochrome c oxidase subunit I varies by structural and functional context. Coevolutionary signals are strongest in transmembrane regions, suggesting global constraints and a critical role for proton channel H.

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Area of Science:

  • Molecular Evolution
  • Protein Structure and Function
  • Bioinformatics

Background:

  • Amino acid residue coevolution patterns are context-dependent, influenced by structural and functional environments.
  • Previous analyses of coevolution have yielded varied results due to differing techniques and protein contexts.
  • Understanding context dependence is crucial for interpreting coevolutionary signals within individual proteins.

Purpose of the Study:

  • To further analyze residue coevolution in cytochrome c oxidase subunit I (COI) sequences from vertebrates.
  • To investigate how structural and functional contexts influence coevolutionary patterns within COI.
  • To explore the relationship between coevolution, residue properties, and functional elements like proton channels.

Main Methods:

  • Utilized a statistically robust phylogeny-based maximum likelihood ratio method.
  • Analyzed coevolutionary signals in 231 vertebrate cytochrome c oxidase subunit I sequences.
  • Correlated coevolution with residue proximity (C(alpha) distances), structural regions (surface, transmembrane), and physicochemical properties (polarity, hydrophobicity, volume).

Main Results:

  • A strong overall coevolutionary signal was detected in vertebrate COI sequences.
  • Coevolution within structural regions correlated significantly with C(alpha) distances between residues.
  • The transmembrane region exhibited the strongest coevolutionary signal, with greater residue distances, suggesting global constraints.
  • Coevolution related to polarity and hydrophobicity in the transmembrane region showed a tendency to colocalize with proton channel H.
  • Coevolutionary patterns were strongly influenced by domain structure and residue physicochemical characteristics.

Conclusions:

  • Coevolutionary patterns in cytochrome c oxidase subunit I are highly dependent on protein structure, residue properties, and functional context.
  • The transmembrane region's strong coevolutionary signal suggests maintenance of global structural and functional constraints.
  • Proximity to functional sites, specifically proton channel H, appears critical, potentially indicating a more significant functional role for this channel.