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evo3D: a generalised framework for structure-informed evolutionary analysis, implemented in R.

Bradley K Broyles1, Qixin He1

  • 1Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.

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Summary
This summary is machine-generated.

Evolutionary analyses are enhanced by considering protein 3D structure. The evo3D R package offers a flexible framework for structure-informed evolutionary analysis, revealing conserved spatial neighborhoods missed by linear methods.

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Area of Science:

  • Molecular Evolution
  • Structural Biology
  • Bioinformatics

Background:

  • Traditional evolutionary analyses focus on linear protein sequences, often missing critical structure-based selection pressures.
  • Previous structure-informed methods used fixed 3D windows, limiting analytical flexibility and scope.
  • A need exists for a generalized framework to integrate protein structure into evolutionary studies.

Purpose of the Study:

  • To introduce evo3D, a generalized R package for structure-informed evolutionary analysis.
  • To enable flexible analysis of evolutionary patterns within 3D protein structures.
  • To overcome limitations of previous methods by supporting diverse statistics and structural complexities.

Main Methods:

  • Developed the evo3D R package, a generalized framework for structure-informed evolutionary analysis.
  • Implemented extraction of structure-informed multiple sequence alignment subsets (spatial haplotypes).
  • Provided flexible spatial windowing (fixed-count, fixed-distance) and analysis modes (residue, codon) applicable to monomers, multimers, and interfaces.

Main Results:

  • Demonstrated evo3D's utility in identifying conserved spatial neighborhoods in Hepatitis C virus E1/E2 complex, missed by linear methods.
  • Evaluated evo3D's scalability using the Chikungunya virus E1/E2 assembly.
  • Confirmed evo3D's ability to streamline evolutionary pattern evaluation within 3D structural contexts.

Conclusions:

  • evo3D provides a formalized and accessible framework for structure-informed evolutionary genetic analysis.
  • The package removes technical barriers, enabling broader application in molecular evolution research.
  • evo3D facilitates the direct evaluation of evolutionary patterns within 3D structural contexts.