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Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular dynamics

Background:

  • Simulating molecular unfolding under mechanical force requires atomistic detail.
  • Coarse-graining methods are often necessary to match experimental timescales in force spectroscopy.

Purpose of the Study:

  • To apply the adaptive resolution scheme (AdResS) to force probe molecular dynamics (FPMD) simulations.
  • To evaluate AdResS accuracy for molecular unfolding pathways using model systems.
  • To investigate the impact of different coarse-graining methodologies on simulation results.

Main Methods:

  • Force probe molecular dynamics (FPMD) simulations.
  • Adaptive resolution scheme (AdResS) with iterative Boltzmann inversion and ideal gas approximation.
  • Analysis of unfolding pathways, characteristic forces, and hydrogen bond changes.

Main Results:

  • AdResS simulations show excellent agreement with fully atomistic FPMD simulations for both simple and complex unfolding pathways.
  • The average number of native contacts is a reliable order parameter for peptide unfolding.
  • The methodology accurately reproduces force distributions and hydrogen bond dynamics.

Conclusions:

  • AdResS is a robust and accurate method for simulating mechanical unfolding of biomolecules.
  • The approach is suitable for studying systems relevant to experimental force spectroscopy.
  • AdResS offers a computationally efficient way to achieve atomistic-level insights into molecular mechanics.