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Reassessing the exon-foldon correspondence using frustration analysis.

Ezequiel A Galpern1,2, Hana Jaafari3,4, Carlos Bueno3

  • 1Protein Physiology Lab, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina.

Proceedings of the National Academy of Sciences of the United States of America
|July 2, 2024
PubMed
Summary
This summary is machine-generated.

Exons may act as protein folding modules, with conserved exons showing independent foldability. This suggests a link between gene structure (exons) and protein evolution, though other factors can influence protein folding.

Keywords:
energy landscapeexonfoldonprotein folding

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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Protein folding and evolution are interconnected processes.
  • Exons, the coding regions of genes, are investigated as potential functional units in protein structure.

Purpose of the Study:

  • To explore the hypothesis that exons serve as protein folding modules (foldons).
  • To analyze exon-exon boundary conservation and independent foldability within protein families.

Main Methods:

  • Analysis of genomic exon-intron organization and protein sequence data for 38 conserved protein families.
  • Application of energy landscape theory to assess exon foldon-like behavior.
  • Identification of exon boundary hotspots for protein domain partitioning.

Main Results:

  • Deviations from exponential decay in exon size distribution suggest evolutionary selection.
  • Conserved exons exhibit a tendency towards independent foldability, supporting the exon-foldon hypothesis.
  • Minimal common exons often correspond to uninterrupted secondary structure elements (alpha/beta).

Conclusions:

  • Evidence supports the concept of exons as protein folding modules, particularly conserved ones.
  • Evolutionary selection acts on exon size and organization.
  • While exon-foldon correspondence is common, other functional constraints (e.g., active sites) can override this pattern in specific protein families.