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COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins.

Alexander Jussupow1, Divya Bartley1, Lisa J Lapidus2

  • 1Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States.

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|February 5, 2025
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Summary

COCOMO2 is a new computational model for biomolecular interactions. It enhances coarse-grained simulations of protein phase separation and complex formation, including folded proteins and intrinsically disordered peptides.

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Area of Science:

  • Computational biology
  • Biophysics
  • Molecular modeling

Background:

  • Biomolecular interactions drive crucial biological processes like complex formation and phase separation.
  • Coarse-grained computational models are vital tools for simulating these dynamic processes.

Purpose of the Study:

  • To introduce COCOMO2, an advanced residue-based coarse-grained model.
  • To extend the model's capability from intrinsically disordered peptides to folded proteins.
  • To improve predictions of biomolecular phase separation and complex assembly.

Main Methods:

  • Developed COCOMO2, incorporating a surface exposure scaling factor for realistic interaction modeling.
  • Parametrized the model using solubility and phase separation data.
  • Validated against experimental data for improved predictive power.

Main Results:

  • COCOMO2 accurately models interactions involving folded domains without increased computational cost.
  • Enhanced prediction of concentration-dependent phase separation for diverse biomolecular systems.
  • Demonstrated applicability to condensates involving both intrinsically disordered proteins (IDPs) and folded domains.

Conclusions:

  • COCOMO2 expands the scope of coarse-grained simulations for biomolecular interactions.
  • Enables new studies on complex biological assemblies and phase separation.
  • Provides a foundation for multiscale modeling approaches in molecular biology.