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Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

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Published on: October 13, 2022

PSFF-PTM: A Coarse-Grained Force-Field Parameter Patch for Modeling Post-Translational Modification Effects on

Junxi Mu¹, Luhua Lai^1,2,3

¹Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.

Journal of Chemical Theory and Computation

|June 25, 2026

Summary

This summary is machine-generated.

Post-translational modifications (PTMs) critically regulate intrinsically disordered proteins (IDPs) phase separation (PS). We developed new parameters (PSFF-PTM) to accurately model PTM effects on IDP interactions and phase behavior.

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Area of Science:

Biochemistry
Molecular Biology
Computational Biology

Background:

Intrinsically disordered proteins (IDPs) drive biomolecular condensate formation through phase separation (PS).
Post-translational modifications (PTMs) act as crucial regulators of IDP phase separation.
Current coarse-grained molecular dynamics (CGMD) force fields lack parameters for modified residues, limiting molecular understanding.

Purpose of the Study:

To develop novel interaction parameters for common PTMs in IDPs.
To integrate these parameters into existing CGMD frameworks for accurate phase separation simulations.
To elucidate the molecular mechanisms by which PTMs influence IDP phase behavior.

Main Methods:

Developed interaction parameters for five PTMs: pSer, pThr, pTyr, AcLys, and aDMA.
Computed residue-specific potentials of mean force (PMFs) using all-atom umbrella sampling simulations.
Integrated PMF-derived parameters into CALVADOS and Mpipi models via the PSFF-PTM module.

Main Results:

Successfully developed and integrated PSFF-PTM for modeling PTMs in IDP phase separation.
PSFF-PTM accurately captures the impact of PTMs on IDP phase behavior.
Identified novel molecular grammars governing PTM-modulated IDP phase separation beyond charge accumulation.

Conclusions:

PSFF-PTM is a compatible and effective tool for simulating PTM effects on IDP phase separation.
This work provides deeper molecular insights into PTM-mediated regulation of biomolecular condensates.
Advances the understanding of IDP phase separation beyond simple charge-based models.