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In silico evolution of globular protein folds from random sequences.

Harutyun Sahakyan1, Sanasar G Babajanyan1, Yuri I Wolf1

  • 1Computational Biology Branch, Division of Intramural Research, National Library of Medicine, NIH, Bethesda, MD 20894.

Proceedings of the National Academy of Sciences of the United States of America
|June 30, 2025
PubMed
Summary

Protein Fold Evolution Simulator (PFES) models how protein folds evolve from random sequences. Stable protein folds can emerge relatively quickly, suggesting an easier evolutionary path than previously thought.

Keywords:
fold nucleationmolecular dynamicsprotein evolutionprotein foldsprotein structure prediction

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Area of Science:

  • Computational Biology
  • Protein Evolution
  • Bioinformatics

Background:

  • The origin and evolution of protein folds remain a fundamental challenge in biology.
  • Understanding how simple protein structures arise from random sequences is crucial for deciphering evolutionary processes.

Purpose of the Study:

  • To develop a computational tool, the Protein Fold Evolution Simulator (PFES), for simulating protein fold evolution.
  • To investigate the evolutionary trajectory of protein folds from random amino acid sequences under selective pressures.
  • To determine the efficiency and speed of protein fold evolution.

Main Methods:

  • Simulated evolution of globular protein folds from random amino acid sequences using atomistic detail.
  • Introduced random mutations in protein sequences and evaluated their structural effects.
  • Applied selective pressures for stability and protein-protein interactions to guide evolution.
  • Tracked evolutionary history and quantified amino acid replacements per site.

Main Results:

  • Demonstrated the evolution of stable, globular protein folds from random sequences, both as monomers and in complexes.
  • Reproduced the evolution of known natural protein folds and generated novel, previously undiscovered folds.
  • Showed that simple globular protein folds evolve with an average of 1.15 to 3 amino acid replacements per site, with some evolving as rapidly as 0.2 replacements per site.

Conclusions:

  • Protein folds can evolve from random sequences more easily and rapidly than suggested by comparisons with conserved proteins since the Last Universal Common Ancestor.
  • PFES provides a valuable platform for testing hypotheses related to protein fold evolution and exploring the emergence of novel protein structures.