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Quantifying Protein-Protein Interactions in Molecular Simulations.

Alfredo Jost Lopez1, Patrick K Quoika1, Max Linke1

  • 1Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany.

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This study demonstrates how dissociation constants (Kd) are determined by second osmotic virial coefficients (B2) and dimer fractions in molecular simulations. New methods for calculating B2 from simulations enable better understanding of molecular interactions and force field parameterization.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Dynamics

Background:

  • Macromolecular interactions are crucial for cellular functions.
  • Dissociation constants (Kd) quantify binding, while second osmotic virial coefficients (B2) measure non-specific interactions and solution properties.
  • B2 is gaining importance for understanding liquid-liquid phase separation in biological systems.

Purpose of the Study:

  • To establish a direct relationship between Kd and B2 in molecular simulations.
  • To develop and validate computational methods for calculating B2.
  • To enable the separation of binding and non-binding interaction contributions.

Main Methods:

  • Derivation of a relationship linking Kd, B2, and dimer fraction.
  • Development of two B2 calculation methods using molecular dynamics or Monte Carlo simulations (BAR and WHAM from insertion/removal energies, or interaction probabilities).
  • Validation using coarse-grained simulations of weakly binding proteins.

Main Results:

  • Kd is shown to be fully determined by B2 and dimer fraction.
  • Two novel methods for calculating B2 from simulations are presented and validated.
  • The methods allow for the quantification and separation of non-specific binding contributions.

Conclusions:

  • The developed methods accurately calculate Kd and B2, aiding in the analysis of molecular interactions.
  • These computational approaches facilitate the re-parameterization and improvement of molecular force fields.
  • The efficiency and accuracy make these methods suitable for high-throughput interactome studies.