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Folding Rate Optimization Promotes Frustrated Interactions in Entangled Protein Structures.

Federico Norbiato1, Flavio Seno1,2, Antonio Trovato1,2

  • 1Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy.

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Protein folding can be hindered by complex topological structures like knots. Energetic frustration in protein sequences helps avoid these topological traps, enabling faster folding.

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Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Proteins can adopt complex topological structures, including knots and lassos.
  • The rapid folding of these topologically complex proteins remains a significant question in structural biology.
  • A recent hypothesis suggests energetic frustration may prevent topological frustration.

Purpose of the Study:

  • To investigate the role of energetic frustration in protein folding with topological complexity.
  • To test the hypothesis that energetic frustration aids in avoiding topological traps during protein folding.

Main Methods:

  • Utilized a simplified lattice model to simulate protein folding.
  • Compared folding dynamics of entangled and non-entangled protein structures.
  • Introduced evolutionary pressure by optimizing folding time.

Main Results:

  • Folding time was longer for random sequences folding into entangled structures.
  • Optimized sequences for entangled structures exhibited frustrated interactions at loop closures.
  • This frustration was less pronounced in non-entangled control structures.

Conclusions:

  • Evolutionary pressure favors sequences with energetic frustration to mitigate topological challenges.
  • Findings support the hypothesis that energetic frustration is a mechanism to avoid kinetic traps in protein folding.
  • Results align with experimental observations on protein folding and topological constraints.