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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Protein Dynamics

Background:

  • Experiments on disordered chains inform protein folding time scales.
  • Interpretation often relies on simplified one-dimensional (1D) diffusion models.
  • Probing single distances limits understanding of complex chain behavior.

Purpose of the Study:

  • To use all-atom molecular simulations to analyze contact formation and peptide length scaling.
  • To reveal how experimental quenching times depend on explored configurational space.
  • To validate 1D diffusion models against simulation data.

Main Methods:

  • All-atom molecular simulations.
  • Analysis of contact formation time scales.
  • Application of Szabo-Schulten-Schulten theory to 1D diffusion models.

Main Results:

  • Simulations captured contact formation time scales and peptide length scaling.
  • Experimental quenching times showed sensitivity to explored configurational space.
  • A strong consistency was found between full calculations and 1D diffusion models.
  • Reduced diffusion coefficients at small separations were observed.

Conclusions:

  • One-dimensional diffusion models are supported by simulation results for protein folding.
  • Contact formation and Förster resonance energy transfer experiments offer complementary diffusivity insights.
  • Simulations provide a detailed view of chain dynamics and experimental sensitivities.