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Pearl-Necklace-Like Local Ordering Drives Polypeptide Collapse.

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Protein collapse in water involves a race between hydration and internal forces. Polyglycine chains form intermediate clusters before collapsing, revealing unique dynamics distinct from synthetic polymers.

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Area of Science:

  • Biophysics
  • Polymer Physics
  • Protein Folding Dynamics

Background:

  • Protein folding is crucial for biological function.
  • Understanding the physical mechanisms of protein collapse is essential.
  • Polypeptide backbone dynamics influence folding pathways.

Purpose of the Study:

  • To investigate the nonequilibrium pathways of protein collapse in aqueous solutions.
  • To elucidate the role of hydration and intrapeptide interactions in protein collapse.
  • To characterize the dynamics of polyglycine chain collapse.

Main Methods:

  • Utilizing polyglycine as a model system for protein collapse studies.
  • Analyzing the collapse process through the lens of nonequilibrium statistical mechanics.
  • Quantifying intermediate structures and coarsening dynamics via contact probability analysis.

Main Results:

  • Polyglycine collapse is governed by the interplay of hydration and intrapeptide van der Waals interactions.
  • Collapse proceeds via a nonequilibrium pathway involving pearl-necklace-like intermediate clusters.
  • A linear growth of the time-dependent length scale was observed during coarsening.
  • A dynamical critical exponent (z ≈ 0.5) significantly lower than that of nonbiological polymers was determined.

Conclusions:

  • The observed collapse dynamics are distinct from synthetic polymers due to rapid intrachain hydrogen bond formation and local ordering.
  • These findings offer insights into the rapid folding mechanisms observed in biological proteins.
  • The study provides a framework for understanding nonequilibrium processes in biopolymer self-assembly.