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FibrilGen: A Python Package for Atomistic Modeling of Peptide β-Sheet Nanostructures.

Chao-Yu Yang1, Aline F Miller2, Alberto Saiani3

  • 1Department of Materials, Manchester Institute of Biotechnology, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom.

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FibrilGen is a new Python package for designing peptide nanomaterials. It computationally models various cross-β structures, aiding in the design and simulation of novel self-assembling peptide nanostructures.

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Area of Science:

  • Biomaterials Science
  • Computational Chemistry
  • Nanotechnology

Background:

  • Rational design of peptide-based nanomaterials requires accurate modeling of self-assembly.
  • Predicting diverse nanostructures from peptide sequences is computationally challenging.

Purpose of the Study:

  • To introduce FibrilGen, a Python package for atomistic modeling of cross-β peptide nanostructures.
  • To provide a tool for generating, analyzing, and simulating peptide fibril morphologies.

Main Methods:

  • FibrilGen initializes peptide packing and fibril morphology using geometric parameters.
  • A refinement step ensures compact assembly of peptide structures.
  • The package facilitates geometric analysis and simulation trajectory assessment.

Main Results:

  • FibrilGen successfully generated diverse cross-β nanostructures with varying morphologies.
  • Modeled structures showed good agreement with experimental data (cryo-EM, ssNMR).
  • Simulated structures demonstrated conformational stability in molecular dynamics.

Conclusions:

  • FibrilGen enables the construction of atomistic supramolecular peptide structures.
  • The package aids in visualizing, simulating, and assessing peptide nanostructures.
  • FibrilGen supports the rational design of peptide-based nanomaterials.