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Stochastic Monte Carlo Model for Simulating the Dynamic Liquid-Liquid Phase Separation in Bacterial Cells
Jingpeng Zhang1,2, Yanyi Huang1,3,4,5, Fan Bai1,2
1Biomedical Pioneering Innovation Center, Peking University, Beijing 100871, China.
The Journal of Physical Chemistry. B
|May 2, 2023
Summary
This study models liquid-liquid phase separation (LLPS) in bacteria, revealing how protein condensate size and number change dynamically. The findings offer insights into bacterial cell processes driven by LLPS.
Area of Science:
- Biophysics
- Cell Biology
- Computational Biology
Background:
- Biological processes are increasingly linked to biomolecule condensates formed via liquid-liquid phase separation (LLPS).
- Quantitative, time-dependent simulations of LLPS in live cells remain limited, hindering a deep understanding of these dynamic events.
Purpose of the Study:
- To develop a quantitative model simulating the dynamic progression of LLPS during bacterial aggresome formation.
- To investigate the factors influencing the kinetics and equilibrium of LLPS in bacterial systems.
Main Methods:
- A stochastic Monte Carlo model was developed to simulate the time-dependent LLPS process.
- The model incorporated diffusion, collision, and nucleation energy barriers to mimic condensate dynamics.
Main Results:
- Simulations showed condensate size distribution shifting from exponential-like to bimodal, with condensate numbers peaking then declining.
- Condensation speed depends on collision energy and initial protein density; equilibrium numbers are linked to dissociation energy.
- LLPS dynamics were largely insensitive to physiological temperature fluctuations, but nucleation barriers slowed condensation.
Conclusions:
- The model successfully recapitulates the two-step LLPS process (formation and merging of condensates) observed in experiments.
- This simulation provides a framework for understanding LLPS dynamics in bacterial cells and guides future experimental designs.
