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Simplified lattice model for polypeptide fibrillar transitions.

Xuhui Xiao1, Ming-Chya Wu2

  • 1Department of Physics, National Taiwan University, Taipei 10617, Taiwan.

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This study models polypeptide fibrillar transitions using a lattice model. It reveals phase diagrams governing protein aggregation, offering insights into nucleation-growth processes.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Materials Science

Background:

  • Polypeptide fibrillar transitions are complex processes crucial for biological function and disease.
  • Understanding these transitions requires robust theoretical models that capture diverse structural states.

Purpose of the Study:

  • To develop and analyze a simplified lattice model for polypeptide fibrillar transitions.
  • To investigate phase transitions among coil, helical, sheet, and fibrillar structures.
  • To elucidate the factors governing transition sequences and temperatures.

Main Methods:

  • Modification of the three-state Potts model on a cubic lattice.
  • Utilizing the transfer matrix method and numerical calculations.
  • Analysis of the partition function to construct phase diagrams.

Main Results:

  • The model exhibits phase transitions controlled by bond coupling energies (ɛh, ɛs, ɛf) and structural entropies (sh, ss, sf).
  • Phase diagrams illustrate transition sequences governed by coupling energies, with transition temperatures depending on energies, entropies, and density (ρ).
  • Fibrillation occurs via abrupt transitions, mimicking nucleation-growth, even for short polypeptide lengths.

Conclusions:

  • The developed lattice model accurately represents polypeptide fibrillar transitions and their rich phase-behavior.
  • The model provides a valuable framework for interpreting protein aggregation experiments.
  • It serves as a reference for future computational modeling of protein self-assembly.