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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
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Related Experiment Video

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Microfluidic Mixers for Studying Protein Folding
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Protein folding as a jamming transition.

Alex T Grigas1,2, Zhuoyi Liu3,2, Jack A Logan3

  • 1Graduate Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520, USA.

PRX Life
|November 3, 2025
PubMed
Summary
This summary is machine-generated.

Protein cores achieve a stable, densely packed structure through a jamming-like transition, similar to granular materials. This study reveals universal principles governing protein core packing and stability across different models.

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Area of Science:

  • Biophysics
  • Soft Matter Physics
  • Computational Biology

Background:

  • Proteins fold into specific conformations with densely packed cores crucial for stability.
  • The uniform average packing fraction (⟨ ϕ ⟩ ≈ 0.55) of protein cores across diverse folds lacks a quantitative explanation.
  • The physics of jamming in particulate systems offers a potential framework to understand protein core packing.

Purpose of the Study:

  • To extend the jamming framework to explain protein core packing in collapsed polymers and all-atom protein models.
  • To investigate the relationship between hydrophobic interactions, thermal fluctuations, and core packing fraction.
  • To analyze the scaling behavior of physical properties during jamming-like transitions in protein cores.

Main Methods:

  • Simulations of a spherical bead-spring polymer model with varying hydrophobic interactions and constraints.
  • Development and application of an all-atom protein model to study core packing.
  • Analysis of potential energy, excess contact number, and vibrational density of states during jamming transitions.

Main Results:

  • A jamming-like transition occurs in polymer models when the packing fraction exceeds a critical value (ϕ c), exhibiting similar power-law scaling to particulate systems.
  • All-atom protein models show a jamming-like transition above ϕ c ~ 0.55, albeit with anomalous scaling.
  • The all-atom model maintains native protein structure during jamming and facilitates refolding from partially unfolded states.

Conclusions:

  • The jamming framework successfully describes protein core packing, revealing universal principles.
  • Protein core packing exhibits a transition analogous to jamming in granular materials.
  • The developed all-atom model accurately captures protein folding and stability near the jamming transition.