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Finding multiple reaction pathways of ligand unbinding.

Jakub Rydzewski1, Omar Valsson2

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This study introduces a novel enhanced sampling method to discover diverse ligand unbinding pathways in proteins. The approach overcomes energy barriers and identifies new pathways without initial state guesses, aiding rare event simulations.

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Area of Science:

  • Computational Chemistry
  • Biophysics
  • Molecular Dynamics

Background:

  • Rare event simulations in large systems are challenging.
  • Inaccurate reaction pathways hinder sampling of energy barriers.

Purpose of the Study:

  • Develop a general enhanced sampling method for diverse ligand unbinding pathways.
  • Overcome limitations of traditional methods in exploring complex energy landscapes.

Main Methods:

  • Nonconvex optimization of a ligand-protein interaction loss function.
  • Adaptive bias potential to overcome large energy barriers.
  • Pathway construction along transient tunnels without initial state information.

Main Results:

  • Successfully identified multiple diverse ligand unbinding pathways.
  • Discovered a previously unknown reaction pathway for T4 lysozyme L99A mutant.
  • Demonstrated the ability to capture unbinding mechanism heterogeneity using bias potential and tunnel widths.

Conclusions:

  • The enhanced sampling method effectively finds rare event pathways.
  • Applicable to studying ligand binding and unbinding mechanisms in proteins.
  • Provides insights into the heterogeneity of molecular interactions.