ArticleBiophysical journal2014
Diffusion within the cytoplasm: a mesoscale model of interacting macromolecules.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Intracellular CaBiologia futura · 2025Review
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- Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in liveProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Live-cell imaging reveals the trade-off between target search flexibility and efficiency for Cas9 and Cas12a.Nucleic acids research · 2024Article
- Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in livebioRxiv : the preprint server for biology · 2024Article
- Viscosity Prediction of High-Concentration Antibody Solutions with Atomistic Simulations.Journal of chemical information and modeling · 2023Article
- Protein secretion zones during overexpression of amylase within the Gram-positive cell wall.BMC biology · 2023Article
- Longitudinal diffusion barriers imposed by myofilaments and mitochondria in murine cardiac myocytes.The Journal of general physiology · 2023Article
- Deconstructing Electrostatics of Functionalized Metal Nanoparticles from Molecular Dynamics Simulations.The journal of physical chemistry. B · 2023Article
- Orientationally Averaged Version of the Rotne-Prager-Yamakawa Tensor Provides a Fast but Still Accurate Treatment of Hydrodynamic Interactions in Brownian Dynamics Simulations of Biological Macromolecules.Journal of chemical theory and computation · 2023Article
- Optimal density of bacterial cells.PLoS computational biology · 2023Article
- The influence of astrocytic leaflet motility on ionic signalling and homeostasis at active synapses.Scientific reports · 2023Article
- Pore-like diffusion barriers in murine cardiac myocytes.bioRxiv : the preprint server for biology · 2023Article
- Computational Modeling and Imaging of the Intracellular Oxygen Gradient.International journal of molecular sciences · 2022Article
- The impeded diffusion fraction quantitative imaging assay demonstrated in multi-exponential diffusion phantom and prostate cancer.Magnetic resonance in medicine · 2022Article
- Aggregation behavior of nanoparticles: Revisiting the phase diagram of colloids.Frontiers in molecular biosciences · 2022Review
- Heterogeneity of Subcellular Diffusion in Bacteria Based on Spatial Segregation of Ribosomes and Nucleoids.Microbial physiology · 2022Review
- Transcription-dependent confined diffusion of enzymes within subcellular spaces of the bacterial cytoplasm.BMC biology · 2021Article
- Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria.PLoS computational biology · 2021Article
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2 authors.
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Abstract
Recent experiments carried out in the dense cytoplasm of living cells have highlighted the importance of proteome composition and nonspecific intermolecular interactions in regulating macromolecule diffusion and organization. Despite this, the dependence of diffusion-interaction on physicochemical properties such as the degree of poly-dispersity and the balance between steric repulsion and nonspecific attraction among macromolecules was not systematically addressed. In this work, we study the problem of diffusion-interaction in the bacterial cytoplasm, combining theory and experimental data to build a minimal coarse-grained representation of the cytoplasm, which also includes, for the first time to our knowledge, the nucleoid. With stochastic molecular-dynamics simulations of a virtual cytoplasm we are able to track the single biomolecule motion, sizing from 3 to 80 nm, on submillisecond-long trajectories. We demonstrate that the size dependence of diffusion coefficients, anomalous exponents, and the effective viscosity experienced by biomolecules in the cytoplasm is fine-tuned by the intermolecular interactions. Accounting only for excluded volume in these potentials gives a weaker size-dependence than that expected from experimental data. On the contrary, adding nonspecific attraction in the range of 1-10 thermal energy units produces a stronger variation of the transport properties at growing biopolymer sizes. Normal and anomalous diffusive regimes emerge straightforwardly from the combination of high macromolecular concentration, poly-dispersity, stochasticity, and weak nonspecific interactions. As a result, small biopolymers experience a viscous cytoplasm, while the motion of big ones is jammed because the entanglements produced by the network of interactions and the entropic effects caused by poly-dispersity are stronger.
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