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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a

Sandeep Chakraborty1, Basuthkar J Rao1, Nathan Baker2

  • 1Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.

Intrinsically Disordered Proteins
|November 4, 2014
PubMed
Summary

This study introduces STEEP, a novel method for protein phylogenetic analysis that uses electrostatic properties alongside structural alignment. STEEP improves the accuracy of evolutionary relationship detection, especially for divergent protein sequences.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Phylogenetic analysis of proteins relies on multiple sequence alignment (MSA), which can be challenging with highly divergent sequences.
  • Existing structural alignment methods do not utilize electrostatic properties to identify relationships between spatially equivalent residues.

Purpose of the Study:

  • To develop a new methodology for multiple sequence alignment (MSA) that incorporates electrostatic properties.
  • To enhance the detection of evolutionary relationships in proteins with significant sequence divergence.

Main Methods:

  • Developed STEEP (Structural and Electrostatic property-based alignment), a method for MSA using electrostatic properties as a discriminator.
  • Performed multiple structural superimposition to create a spatial framework for residue comparison.
  • Generated phylogenetic trees using PhyML based on STEEP-derived MSAs for serine and metallo-β-lactamase superfamilies.

Main Results:

  • STEEP successfully identified evolutionary relationships in protein superfamilies, corroborating accepted phylogenetic trees.
  • The method demonstrated its ability to act as a functional classifier by using electrostatic congruence.
  • Identified specific residues whose alignment differs with and without electrostatic properties, suggesting targets for directed evolution.

Conclusions:

  • STEEP is a unique phylogenetic method that leverages electrostatic congruence to identify mutations potentially causing functional divergence.
  • The study hypothesizes that active site information is sufficient for inferring the correct phylogeny of related proteins.