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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Structural Phylogenetics with Confidence.

Ashar J Malik1,2, Anthony M Poole3,4,5, Jane R Allison3,4,5,6

  • 1Centre for Theoretical Chemistry and Physics, School of Natural and Computational Sciences, Massey University Auckland, Auckland, New Zealand.

Molecular Biology and Evolution
|April 18, 2020
PubMed
Summary
This summary is machine-generated.

Structural phylogenetics offers insights into deep protein evolution when sequence data is insufficient. This study introduces a method to assess confidence in structural phylogenies, aiding evolutionary reconstruction.

Keywords:
deep evolutionphylogeneticsprotein structure

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Area of Science:

  • * Computational biology and structural bioinformatics.
  • * Evolutionary biology and molecular evolution.

Background:

  • * Sequence-based homology searches and phylogenetic methods are limited for evaluating deep evolutionary relationships due to low sequence similarity.
  • * Protein structures are more conserved than sequences, offering an alternative for uncovering deep evolutionary signals.
  • * Existing protein structure databases (SCOP, CATH) lack detailed evolutionary relationship descriptions within hierarchical levels.

Purpose of the Study:

  • * To address limitations in applying structural data to deep phylogeny, specifically assessing sensitivity to protein length/shape and developing statistical support for structural phylogenies.
  • * To evaluate the impact of protein length and shape variations on phylogenies derived from pairwise structural comparisons.
  • * To present a novel method for assessing confidence in structural phylogenies.

Main Methods:

  • * Analysis of phylogenies derived from pairwise structural comparisons, considering protein length and shape variations.
  • * Utilizing molecular dynamics (MD) and Monte Carlo (MC) simulations to generate protein shape fluctuations.
  • * Developing a confidence assessment method for structural phylogenies based on simulated shape fluctuations.

Main Results:

  • * Structural phylogenetics is most effective for proteins of similar lengths.
  • * Shape fluctuations from MD simulations affect pairwise comparisons but do not eliminate evolutionary signal.
  • * A new method for assessing statistical confidence in structural phylogenies has been developed.

Conclusions:

  • * Structural phylogenetics is a valuable tool for inferring deep evolutionary relationships in proteins.
  • * The developed confidence assessment method enhances the reliability of structural phylogenies.
  • * This approach will aid in reconstructing evolutionary relationships within protein superfamilies and organizing the protein universe.