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The Impact of Native State Switching on Protein Sequence Evolution.

Avital Sharir-Ivry1, Yu Xia1

  • 1Department of Bioengineering, McGill University, Montreal, QC, Canada.

Molecular Biology and Evolution
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Protein conformational switches evolve slower than single-state proteins due to evolutionary constraints. This study reveals how maintaining multiple structures impacts protein sequence evolution.

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Area of Science:

  • Structural Biology
  • Evolutionary Biology
  • Biochemistry

Background:

  • Protein 3D structure dictates sequence evolution for single-state proteins.
  • The evolutionary impact of proteins adopting multiple native structures (conformational switches) is less understood.

Purpose of the Study:

  • To investigate how protein structure influences sequence evolution in conformational switches.
  • To compare evolutionary rates of conformational switches versus single-state proteins.

Main Methods:

  • Proteome-wide analysis in Saccharomyces cerevisiae.
  • Pooled analysis of residue burial and packing.
  • Comparison of evolutionary rates between different protein types and residue locations.

Main Results:

  • A linear relationship exists between residue evolutionary rate and burial in conformational switches.
  • Conformational switches evolve significantly slower than single-state proteins, independent of burial or packing.
  • Interfacial residues in binding-induced conformational switches evolve slowly, with the bound state being a better evolutionary predictor.

Conclusions:

  • Encoding multiple native structures imposes strong evolutionary constraints on the entire protein.
  • This constraint affects conformational switches more broadly than previously thought.
  • Provides new insights into the protein structure-evolution relationship for dynamic proteins.