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Princeton: Diffusion of Ribosome-sized Particles in E. coli

Writer's picture: Ray SullivanRay Sullivan

Updated: Feb 2




The Shaevitz Lab and the Gitai Lab at Princeton, in collaboration with the Zia Lab at the University of Missouri/Stanford, explored the role of particle size and charge on the localization and dynamics of molecules within the crowded and polydisperse bacterial cytoplasm and provided an alternate perspective on the previously reported anomalous diffusion of molecules in bacterial cells.  They did 3D single-particle tracking using biplane microscopy, developed a colloidal whole-cell computational model, and adapted genetically encoded multimeric nanoparticles (GEMs) from eukaryotic cells to create bacterial nanoparticles (bGEMs) for the experiments. 


- Macromolecular size and charge determine bGEM localization within the bacterial cell, with smaller and more negatively charged particles enriched in the nucleoid region.

- The apparent subdiffusive behavior observed in previous 2D single-particle tracking studies can be attributed to geometric confinement effects rather than anomalous diffusion.

- Combining 3D single-particle tracking experiments and coarse-grained whole-cell modeling enables the exploration of dynamics below the temporal resolution of experiments. It suggests physical mechanisms underlying the experimentally observed phenomena.


Particle size and charge determine bGEM localization within the bacterial cell, driven by entropic and electrostatic interactions, and the apparent anomalous diffusion observed in previous studies can be primarily explained by confinement effects rather than complex cytoplasmic dynamics.  Be sure to check out the very cool videos of the bGEMs moving around the cells. 


Valverde-Mendez D, Sunol AM, Bratton BP, Delarue M, Hofmann JL, Sheehan JP, Gitai Z, Holt LJ, Shaevitz JW, Zia RN. Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells. Proc Natl Acad Sci U S A. 2025 Jan 28;122(4):e2406340121. doi: 10.1073/pnas.2406340121. Epub 2025 Jan 24. PMID: 39854229.  https://www.pnas.org/doi/10.1073/pnas.2406340121

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