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A Nonequilibrium Simulation Framework for Reproducing Protein Aggregation in All-Atom Molecular Dynamics Simulations.

Moe Iijima1, Toya Yoshida1, Kentaro Shiraki1

  • 1Institute of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.

The Journal of Physical Chemistry. B
|March 14, 2026
PubMed
Summary
This summary is machine-generated.

Controlling protein denaturation extent allows reproducible molecular dynamics (MD) simulations of protein aggregation. This method accurately predicts stabilizer effects, advancing biopharmaceutical formulation and protein science.

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Area of Science:

  • Protein Science
  • Biophysical Chemistry
  • Computational Biology

Background:

  • Protein aggregation poses significant challenges in protein science and biopharmaceutical formulation.
  • Reproducing protein aggregation using all-atom molecular dynamics (MD) simulations is computationally intensive and difficult.

Purpose of the Study:

  • To develop a method for reproducible protein aggregation simulations using MD.
  • To investigate the influence of denaturation extent on protein aggregation behavior.
  • To computationally evaluate the effects of stabilizers on protein aggregation.

Main Methods:

  • Generating unfolded protein conformational ensembles via high-temperature MD (300-700 K).
  • Employing explicit control over the denaturation extent of initial protein structures.
  • Performing 100 ns MD simulations of hen egg white lysozyme (LYZ) aggregation.

Main Results:

  • Sufficient initial denaturation extent and direct simulation initiation are critical for reproducible aggregation.
  • Simulations successfully reproduced experimental findings on arginine and sodium chloride effects.
  • Arginine suppressed LYZ aggregation at high concentrations (1 M), while NaCl promoted it.

Conclusions:

  • Denaturation-controlled MD provides a practical framework for simulating protein aggregation.
  • This approach enables the computational evaluation of protein aggregation and the effects of stabilizers.
  • The findings advance the understanding of protein aggregation mechanisms and formulation strategies.