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Modeling Protein-Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION.

Nathalie Basdevant¹, Daniel Borgis², Tap Ha-Duong¹

¹Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, UMR8587 CNRS-UEVE-CEA, Université d'Evry-Val-d'Essonne, Bd François Mitterrand, 91025 Evry Cedex, France.

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|November 22, 2015

Summary

We developed SCORPION, a coarse-grained force field for molecular dynamics simulations. This new model accurately simulates protein association, showing successful binding for the barnase/barstar complex in water.

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Area of Science:

Computational Biology
Biophysics
Molecular Dynamics

Background:

Protein association is crucial for biological functions.
Accurate simulation of protein interactions requires efficient computational models.
Existing models may not fully capture solvated protein association dynamics.

Purpose of the Study:

To introduce SCORPION, a novel physics-based coarse-grained force field.
To enable efficient molecular dynamics (MD) simulations of protein association in solution.
To validate the SCORPION force field using protein-protein recognition simulations.

Main Methods:

Developed SCORPION, combining a coarse-grained protein model with a particle-based water model.
Represented amino acids with 1-3 beads, fitted to AMBER force field interactions.
Incorporated an elastic network model for protein internal flexibility.
Included a Polarizable Coarse-Grained Solvent (PCGS) model for accurate electrostatics.
Performed hundreds-of-nanoseconds MD simulations of the barnase/barstar complex.

Main Results:

SCORPION successfully simulated protein-protein recognition for the barnase/barstar complex.
Five out of seven simulations showed native-like binding within 1-500 ns.
Bound complexes remained stable throughout the simulation.
Energetic analysis revealed contributions from both van der Waals and electrostatic interactions.

Conclusions:

SCORPION is an effective tool for studying protein-protein recognition in solvated environments.
The force field accurately captures binding dynamics and stability.
SCORPION facilitates computationally efficient simulations of biomolecular interactions.