Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells

The bacterial cytoplasm is a heterogenous dynamic environment, with many physical factors that impact biological function. In this work, we present a physics-based whole-cell model of Escherichia coli that represents confinement, macromolecular crowding, size polydispersity, electrostatic intermolecular interactions, and the presence of the nucleoid at the center of the cell to parse the impacts of each of these attributes on macromolecular motion and localization. We show that entropic exclusion and demixing lead to increased localization of large molecules to the region outside the nucleoid and small molecules to inside. Electrostatic interactions of molecules with DNA and ribosomes drive further charge-based segregation of positive molecules to the cell periphery. We predict that dynamics are diffusive at short time scales, but that geometrical confinement can lead to apparent subdiffusivity at experimental time lags. Our model predictions are in excellent agreement with 3D single-particle tracking (SPT) experiments of bacterial Genetically Encoded Multimeric nanoparticles (bGEMs). Thus, colloidal-scale simulation of the cytoplasm is a promising framework to complement SPT experiments by allowing one to probe physical details at greater spatial and temporal resolutions.