ArticlePloS one2014
A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- A Novel Fractional Brownian Dynamics Method for Simulating the Dynamics of Confined Bottle-Brush Polymers in Viscoelastic Solution.Polymers · 2024Article
- What determines sub-diffusive behavior in crowded protein solutions?Biophysical journal · 2024Article
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- Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins.Molecular cell · 2021Article
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- Subdiffusion of loci and cytoplasmic particles are different in compressedCommunications biology · 2018Article
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.The journal of physical chemistry. B · 2017Article
- Diffusing diffusivity: Rotational diffusion in two and three dimensions.The Journal of chemical physics · 2017Article
- Macromolecular crowding directs the motion of small molecules inside cells.Journal of the Royal Society, Interface · 2017Article
- Cell morphology governs directional control in swimming bacteria.Scientific reports · 2017Article
- Cytoplasmic RNA-Protein Particles Exhibit Non-Gaussian Subdiffusive Behavior.Biophysical journal · 2017Article
- Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces.PLoS computational biology · 2016Article
- Physical Modeling of Dynamic Coupling between Chromosomal Loci.Biophysical journal · 2016Article
- Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.Journal of molecular graphics & modelling · 2015Article
- Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics.Journal of chemical theory and computation · 2015Article
- How much territory can a single E. coli cell control?Frontiers in microbiology · 2015Article
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5 authors.
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Abstract
A new coarse-grained model of the E. coli cytoplasm is developed by describing the proteins of the cytoplasm as flexible units consisting of one or more spheres that follow Brownian dynamics (BD), with hydrodynamic interactions (HI) accounted for by a mean-field approach. Extensive BD simulations were performed to calculate the diffusion coefficients of three different proteins in the cellular environment. The results are in close agreement with experimental or previously simulated values, where available. Control simulations without HI showed that use of HI is essential to obtain accurate diffusion coefficients. Anomalous diffusion inside the crowded cellular medium was investigated with Fractional Brownian motion analysis, and found to be present in this model. By running a series of control simulations in which various forces were removed systematically, it was found that repulsive interactions (volume exclusion) are the main cause for anomalous diffusion, with a secondary contribution from HI.
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