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A generic force field for simulating native protein structures using dissipative particle dynamics.

Rakesh Vaiwala1, K Ganapathy Ayappa1,2

  • 1Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India. ayappa@iisc.ac.in.

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|October 15, 2021
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Summary

A new coarse-grained force field for Dissipative Particle Dynamics (DPD) simulations accurately models native protein structures. This method enables efficient in silico studies of proteins and polypeptides, including membrane-bound ones.

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Area of Science:

  • Computational Biology
  • Biophysics
  • Molecular Dynamics

Background:

  • Accurate modeling of protein structures is crucial for understanding biological functions.
  • Existing coarse-grained models often struggle to capture the stability and dynamics of native protein conformations.

Purpose of the Study:

  • To develop and validate a coarse-grained force field within the Dissipative Particle Dynamics (DPD) framework for simulating native protein structures.
  • To enable efficient in silico investigations of protein folding and interactions.

Main Methods:

  • Developed a coarse-grained force field by mapping bonded interactions from atomistic simulations.
  • Introduced a dual-basin potential for backbone angle stabilization and a dihedral potential for protein folding.
  • Validated the force field using model peptides, SARS-CoV-2 fusion peptide, lysozyme, and cytolysin A.

Main Results:

  • The force field successfully stabilized various protein secondary structures (α-helices, β-sheets).
  • Compact native states were confirmed by radius of gyration and RMSD histograms.
  • Ramachandran-like energy landscapes accurately depicted α-helix and β-strand conformational spaces.
  • Residue-residue native contacts were well reproduced.

Conclusions:

  • The developed DPD force field is generic and effective for simulating native protein structures.
  • It shows potential for efficient in silico studies of membrane-bound proteins and polypeptides.