ArticleBiophysical journal2011
Effects of macromolecular crowding on genetic networks.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Hydrogel-Based Multi-enzymatic System for Biosynthesis.Advances in biochemical engineering/biotechnology · 2023Review
- J-aggregation of 5, 10, 15, 20-tetraphenyl-21H, 23H-porphinetetrasulfonic acid in a molecular crowding environment simulated using dextran.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2022Article
- Comparative study of SARS-CoV-2 infection in different cell types: Biophysical-computational approach to the role of potential receptors.Computers in biology and medicine · 2022Article
- In vitro cell cycle oscillations exhibit a robust and hysteretic response to changes in cytoplasmic density.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Concentration sensing in crowded environments.Biophysical journal · 2021Article
- Growth factor and macromolecular crowding supplementation in human tenocyte culture.Biomaterials and biosystems · 2021Article
- Development of a robustBiochemical engineering journal · 2021Article
- Silk fibroin as an additive for cell-free protein synthesis.Synthetic and systems biotechnology · 2020Article
- Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu.Biophysical journal · 2020Article
- Disordered chromatin packing regulates phenotypic plasticity.Science advances · 2020Article
- Understanding biochemical processes in the presence of sub-diffusive behavior of biomolecules in solution and living cells.Biophysical reviews · 2019Review
- Transcription factor target site search and gene regulation in a background of unspecific binding sites.Journal of theoretical biology · 2018Article
- Automated cell cycle and cell size measurements for single-cell gene expression studies.BMC research notes · 2018Article
- Macrogenomic engineering via modulation of the scaling of chromatin packing density.Nature biomedical engineering · 2017Article
- The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation.Scientific reports · 2017Article
- The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression.Scientific reports · 2017Article
- Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion.PLoS computational biology · 2016Article
- The function of chromatin modifiers in lineage commitment and cell fate specification.The FEBS journal · 2015Review
- Synthetic Biology: A Bridge between Artificial and Natural Cells.Life (Basel, Switzerland) · 2014Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The intracellular environment is crowded with proteins, DNA, and other macromolecules. Under physiological conditions, macromolecular crowding can alter both molecular diffusion and the equilibria of bimolecular reactions and therefore is likely to have a significant effect on the function of biochemical networks. We propose a simple way to model the effects of macromolecular crowding on biochemical networks via an appropriate scaling of bimolecular association and dissociation rates. We use this approach, in combination with kinetic Monte Carlo simulations, to analyze the effects of crowding on a constitutively expressed gene, a repressed gene, and a model for the bacteriophage λ genetic switch, in the presence and absence of nonspecific binding of transcription factors to genomic DNA. Our results show that the effects of crowding are mainly caused by the shift of association-dissociation equilibria rather than the slowing down of protein diffusion, and that macromolecular crowding can have relevant and counterintuitive effects on biochemical network performance.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.