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Improved coarse-grained model for studying sequence dependent phase separation of disordered proteins.

Roshan Mammen Regy1, Jacob Thompson1, Young C Kim2

  • 1Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA.

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Summary

We improved a coarse-grained model for simulating intrinsically disordered proteins (IDPs) and their liquid-liquid phase separation (LLPS). The new HPS-Urry model uses a different hydropathy scale, improving accuracy for LLPS simulations.

Keywords:
coarse-grained modelhydropathy scalesliquid-liquid phase separationmolecular simulationphysics-based model

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Science

Background:

  • Intrinsically disordered proteins (IDPs) exhibit sequence-specific behavior and undergo liquid-liquid phase separation (LLPS).
  • Previous coarse-grained (CG) models, like the hydropathy scale (HPS) based on the Kapcha and Rossky (KR) scale, struggle to accurately predict LLPS trends, particularly the impact of mutations.

Purpose of the Study:

  • To enhance the HPS CG model for more accurate simulation of IDP sequence-specific behavior and LLPS.
  • To introduce a new hydropathy scale and adjustable parameters to improve the model's predictive power for LLPS phenomena.

Main Methods:

  • Replaced the KR hydropathy scale with the Urry hydropathy scale in the HPS CG model.
  • Introduced two free parameters (Δ and µ) to adjust interaction strengths.
  • Optimized parameter values using experimental radius of gyration data from diverse IDPs.
  • Validated the model's performance using the phase behavior of the FUS low-complexity (LC) sequence.

Main Results:

  • The new HPS-Urry model demonstrates improved accuracy in simulating LLPS trends compared to the previous KR-based model.
  • Optimal parameter (Δ, µ) combinations were identified, though validation with specific sequences like FUS highlights the need for careful parameter selection.
  • The model provides a microscopically detailed view of molecular interactions driving protein LLPS.

Conclusions:

  • The HPS-Urry CG model offers a more reliable tool for simulating protein LLPS and understanding the underlying molecular mechanisms.
  • Accurate simulation of IDP behavior, including LLPS, is crucial for understanding cellular function and disease.
  • Further validation across a broader range of IDPs and LLPS conditions is recommended for comprehensive model application.