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An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins.

Janelle Nunez-Castilla1, Jessica Siltberg-Liberles2

  • 1Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.

Methods in Molecular Biology (Clifton, N.J.)
|July 23, 2020
PubMed
Summary

This study introduces a simple method for protein evolutionary analysis, focusing on disordered protein regions. It guides researchers in analyzing protein evolution and disorder changes across species using the p53 family as a model.

Keywords:
ConservationEvolutionIDPIDRIUPredPhylogenetic treeProteinProtein family

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Area of Science:

  • Evolutionary biology
  • Protein bioinformatics
  • Molecular evolution

Background:

  • Intrinsically disordered protein regions play crucial roles in cellular functions.
  • Understanding the evolutionary dynamics of these regions is essential for deciphering protein function and evolution.
  • Current methods for analyzing disordered regions within an evolutionary context are complex and time-consuming.

Purpose of the Study:

  • To present a straightforward protocol for the evolutionary analysis of proteins, with a specific focus on disordered regions.
  • To guide researchers in identifying homologous sequences, refining datasets, and constructing phylogenetic trees.
  • To enable the investigation of evolutionary changes in disorder content and site-specific disorder conservation.

Main Methods:

  • Utilized the p53 protein family as a model system for demonstrating the protocol.
  • Employed database searches for homologous sequences and dataset refinement.
  • Constructed phylogenetic trees to establish the evolutionary context.
  • Performed multiple sequence alignment and partitioned data for disorder content analysis.
  • Investigated site-specific disorder conservation and disorder-to-order transitions.

Main Results:

  • Successfully demonstrated an easy-to-follow protocol for evolutionary analysis of protein disordered regions.
  • Showcased how to partition phylogenetic data to study changes in disorder content across evolutionary history.
  • Provided insights into site-specific conservation patterns of disordered regions within the p53 family.

Conclusions:

  • The presented protocol simplifies the evolutionary analysis of protein disordered regions, making it accessible to a wider range of researchers.
  • This approach facilitates a deeper understanding of the evolutionary forces shaping protein disorder and its functional implications.
  • The method allows for the evaluation of disorder-to-order transitions, offering new perspectives on protein evolution.