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

IF 4.3 2区生物学

PLoS Computational Biology Pub Date : 2023-09-11 eCollection Date: 2023-09-01 DOI:10.1371/journal.pcbi.1011093

Luca Mantovanelli, Dmitrii S Linnik, Michiel Punter, Hildeberto Jardón Kojakhmetov, Wojciech M Śmigiel, Bert Poolman

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Abstract

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.

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基于模拟的重建扩散揭示了老化对大肠杆菌中蛋白质扩散的影响。

我们开发了基于模拟的重建扩散（SbRD），以确定针对约束效应和描述三维运动的二维模型引入的偏差进行校正的扩散系数。我们在三维细胞形隔间的模拟扩散数据上验证了该方法。我们使用SbRD，结合一种新的细胞检测方法，来确定一组天然蛋白质在大肠杆菌中的扩散系数。我们观察到，与指数生长细胞的类核区相比，细胞极的扩散速度较慢，这与多聚体的存在无关。此外，我们发现新形成的分裂细胞极比旧的分裂细胞表现出更快的扩散。我们假设，在细胞极观察到的减速是由聚集或受损蛋白质的积累引起的，并且由于细胞老化，这种影响是不对称的。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

PLoS Computational Biology 生物-生化研究方法

CiteScore

7.10

自引率

4.70%

发文量

820

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