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Related Experiment Video

Updated: Sep 5, 2025

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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Transferable and Polarizable Coarse Grained Model for Proteins─ProMPT.

Abhilash Sahoo1, Pei-Yin Lee2, Silvina Matysiak3

  • 1Biophysics Program, University of Maryland, College Park, Maryland 20742, United States.

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Summary

This study introduces a new transferable coarse-grained (CG) force field for accurate protein simulations. It enables efficient exploration of large conformational spaces and captures protein structural transitions with an explicit environment representation.

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Area of Science:

  • Computational Chemistry
  • Biophysics
  • Molecular Modeling

Background:

  • Classical molecular dynamics (MD) simulations at atomic resolution (fine-grained, FG) face computational limitations for large biomolecular systems.
  • Existing coarse-grained (CG) force fields often lack transferability or fail to capture protein secondary/tertiary structure formation.
  • Protein systems possess vast conformational spaces, challenging FG MD simulations' ability to explore dynamics.

Purpose of the Study:

  • To develop a novel transferable coarse-grained (CG) force field for accurate protein simulations.
  • To enable efficient exploration of large protein conformational spaces.
  • To capture protein structural transitions with an explicit environmental representation.

Main Methods:

  • Developed a CG force field using pseudoatoms representing chemical groups for modular biomolecular system construction.
  • Incorporated electronic polarization responsive to environmental fluctuations, coupled to protein structural transitions.
  • Parametrized nonbonded interactions using physics-based features (solvation/partitioning free energies) and bonded potentials from protein structure databases.

Main Results:

  • Validated the CG model through simulations of diverse aqueous protein systems (Trp-cage, Trpzip4, villin, WW-domain, β-α-β).
  • Demonstrated the force field's ability to preserve transferability across various environments and conditions.
  • Successfully applied the force field to study the aqueous aggregation of Aβ 16-22 peptides.

Conclusions:

  • The developed transferable CG force field offers an accurate and efficient alternative to FG MD for protein simulations.
  • This CG model facilitates the study of complex biomolecular processes, including protein folding and aggregation.
  • The explicit environment representation and polarization coupling enhance the simulation of protein dynamics and interactions.