ArticleBiophysical journal2012
Crowding effects on the formation and maintenance of nuclear bodies: insights from molecular-dynamics simulations of simple spherical model particles.
Article in Biophysical journal, 2012. 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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Who cites it
20 citing papers in PubMed.
- RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding.Chemical reviews · 2024Review
- Kinetic trapping organizes actin filaments within liquid-like protein droplets.Nature communications · 2024Article
- Article
- Surfactancy in a tadpole model of proteins.Journal of the Royal Society, Interface · 2022Article
- Emerging Roles of Repetitive and Repeat-Containing RNA in Nuclear and Chromatin Organization and Gene Expression.Frontiers in cell and developmental biology · 2021Review
- Application of quantitative cell imaging using label-free optical diffraction tomography.Biophysics and physicobiology · 2021Article
- Weak interactions in higher-order chromatin organization.Nucleic acids research · 2020Review
- Dynamic Crowding Regulates Transcription.Biophysical journal · 2020Article
- Physicochemical Properties of Nucleoli in Live Cells Analyzed by Label-Free Optical Diffraction Tomography.Cells · 2019Article
- Roles for Non-coding RNAs in Spatial Genome Organization.Frontiers in cell and developmental biology · 2019Review
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- Specific genomic cues regulate Cajal body assembly.RNA biology · 2017Review
- Protein folding, binding, and droplet formation in cell-like conditions.Current opinion in structural biology · 2017Review
- Cajal body function in genome organization and transcriptome diversity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2016Review
- Nuclear bodies: Built to boost.The Journal of cell biology · 2016Article
- Cajal bodies are linked to genome conformation.Nature communications · 2016Article
- EAST Organizes Drosophila Insulator Proteins in the Interchromosomal Nuclear Compartment and Modulates CP190 Binding to Chromatin.PloS one · 2015Article
- The Role of Crowding Forces in Juxtaposing β-Globin Gene Domain Remote Regulatory Elements in Mouse Erythroid Cells.PloS one · 2015Article
- PML nuclear bodies: assembly and oxidative stress-sensitive sumoylation.Nucleus (Austin, Tex.) · 2014Review
- Regulation of the tumor suppressor PML by sequential post-translational modifications.Frontiers in oncology · 2012Article
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2 authors.
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Abstract
The physics of structure formation and maintenance of nuclear bodies (NBs), such as nucleoli, Cajal bodies, promyelocytic leukemia bodies, and speckles, in a crowded nuclear environment remains largely unknown. We investigate the role of macromolecular crowding in the formation and maintenance of NBs using computer simulations of a simple spherical model, called Lennard-Jones (LJ) particles. LJ particles form a one-phase, dilute fluid when the intermolecular interaction is weaker than a critical value, above which they phase separate and form a condensed domain. We find that when volume-exclusive crowders exist in significant concentrations, domain formation is induced even for weaker intermolecular interactions, and the effect is more pronounced with increasing crowder concentration. Simulation results show that a previous experimental finding that promyelocytic leukemia bodies disappear in the less-crowded condition and reassemble in the normal crowded condition can be interpreted as a consequence of the increased intermolecular interactions between NB proteins due to crowding. Based on further analysis of the simulation results, we discuss the acceleration of macromolecular associations that occur within NBs, and the delay of diffusive transport of macromolecules within and out of NBs when the crowder concentration increases. This study suggests that in a polydisperse nuclear environment that is enriched with a variety of macromolecules, macromolecular crowding not only plays an important role in the formation and maintenance of NBs, but also may perform some regulatory functions in response to alterations in the crowding conditions.
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