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Related Experiment Videos

Imprint of evolution on protein structures.

Guido Tiana1, Boris E Shakhnovich, Nikolay V Dokholyan

  • 1Department of Physics and Istituto Nazionale di Fisica Nucleare, University of Milano, Via Celoria 16, 20133 Milan, Italy.

Proceedings of the National Academy of Sciences of the United States of America
|February 19, 2004
PubMed
Summary

This study simulates protein fold evolution using a lattice model, revealing that evolved protein structures become more designable over time. This trend holds true for real proteins, with eukaryotic proteins showing higher designability than prokaryotic ones.

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Area of Science:

  • Computational Biology
  • Protein Evolution
  • Biophysics

Background:

  • Understanding the evolutionary origins of protein folds is crucial for deciphering protein function and diversity.
  • Previous models have explored protein evolution, but a comprehensive simulation of fold emergence and designability is lacking.

Purpose of the Study:

  • To investigate the evolutionary trajectory of protein folds using a novel simulation approach.
  • To assess how protein 'designability' changes during simulated evolution.
  • To compare designability trends between simulated and real-world protein structures, including eukaryotic and prokaryotic domains.

Main Methods:

  • Utilized a three-dimensional lattice model to simulate divergent protein evolution.
  • Employed sequence duplication and point mutations to generate new protein sequences.

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  • Conducted kinetic folding simulations to test the stability and uniqueness of novel protein structures.
  • Assessed protein designability using established structural determinants and thermodynamic sampling.

    • Main Results:

    • Simulated evolution generated thousands of diverse protein structures.
    • Evolved protein structures demonstrated significantly higher designability compared to initial seed structures.
    • Real protein domains, particularly those in eukaryotes, exhibited statistically significant higher designability than prokaryotic counterparts, supporting the simulation's predictions.

    Conclusions:

    • Protein evolution, driven by structural selection and evolutionary dynamics, leads to increased protein designability.
    • The findings provide fundamental insights into the genesis of modern protein structures and their functional capabilities.
    • The study highlights a key principle governing the diversification and complexity of the proteome.