Modeling Dps-DNA condensate formation in starved E. coli

In bacteria such as E. coli, survival under stress relies on DNA-binding protein from starved cells (Dps), which protects and reorganizes the nucleoid by forming dynamic protein–DNA condensates. In vitro, purified Dps rapidly forms stable complexes with DNA, a key step in stabilizing these condensates. To uncover the physical mechanisms of condensation, we combined mean-field thermodynamics and molecular simulations. Using a ternary Flory–Huggins free energy for Dps, DNA, and solvent, we constructed phase diagrams identifying binodal regions for condensate formation, which strengthened with higher Dps–DNA attraction and Dps concentration. Complementing this, a 3D biophysical model was constructed that treats DNA as semiflexible polymers and Dps as spherical particles interacting via Lennard-Jones and Weeks-Chandler-Andersen potentials. This model revealed morphological transitions: low Dps concentrations yielded network-like assemblies, while higher concentrations produced compact condensates whose size scaled with DNA abundance. Together, these results link thermodynamic driving forces to microscopic organization, offering a unified picture of Dps–DNA condensation and its role in bacterial nucleoid regulation under starvation stress.