Simulation-based Reconstructed Diffusion unveils the effect of aging on protein diffusion in Escherichia coli.

Autor: Mantovanelli L; Department of Biochemistry, University of Groningen, Groningen, the Netherlands., Linnik DS; Department of Biochemistry, University of Groningen, Groningen, the Netherlands., Punter M; Department of Biochemistry, University of Groningen, Groningen, the Netherlands., Kojakhmetov HJ; Dynamical Systems, Geometry and Mathematical Physics Group, University of Groningen, Groningen, the Netherlands., Śmigiel WM; Department of Biochemistry, University of Groningen, Groningen, the Netherlands., Poolman B; Department of Biochemistry, University of Groningen, Groningen, the Netherlands.
Jazyk: angličtina
Zdroj: PLoS computational biology [PLoS Comput Biol] 2023 Sep 11; Vol. 19 (9), pp. e1011093. Date of Electronic Publication: 2023 Sep 11 (Print Publication: 2023).
DOI: 10.1371/journal.pcbi.1011093
Abstrakt: We have developed Simulation-based Reconstructed Diffusion (SbRD) to determine diffusion coefficients corrected for confinement effects and for the bias introduced by two-dimensional models describing a three-dimensional motion. We validate the method on simulated diffusion data in three-dimensional cell-shaped compartments. We use SbRD, combined with a new cell detection method, to determine the diffusion coefficients of a set of native proteins in Escherichia coli. We observe slower diffusion at the cell poles than in the nucleoid region of exponentially growing cells, which is independent of the presence of polysomes. Furthermore, we show that the newly formed pole of dividing cells exhibits a faster diffusion than the old one. We hypothesize that the observed slowdown at the cell poles is caused by the accumulation of aggregated or damaged proteins, and that the effect is asymmetric due to cell aging.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2023 Mantovanelli et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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