ArticleBiophysical journal2015
Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 32 citations in OpenAlex.
- Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell.The journal of physical chemistry. B · 2026Article
- A roadmap for ribosome assembly in human mitochondria.Nature structural & molecular biology · 2024Article
- Multi-Grid Reaction-Diffusion Master Equation: Applications to Morphogen Gradient Modelling.Bulletin of mathematical biology · 2024Article
- Discovering optimal kinetic pathways for self-assembly using automatic differentiation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Emerging Quantitative Biochemical, Structural, and Biophysical Methods for Studying Ribosome and Protein-RNA Complex Assembly.Biomolecules · 2023Review
- Article
- Uncovering a delicate balance between endonuclease RNase III and ribosomal protein S15 in E. coli ribosome assembly.Biochimie · 2021Article
- NERDSS: A Nonequilibrium Simulator for Multibody Self-Assembly at the Cellular Scale.Biophysical journal · 2020Article
- Autonomous synthesis and assembly of a ribosomal subunit on a chip.Science advances · 2020Article
- Ribosome assembly defects subvert initiation Factor3 mediated scrutiny of bona fide start signal.Nucleic acids research · 2019Article
- Multiscale Stochastic Reaction-Diffusion Algorithms Combining Markov Chain Models with Stochastic Partial Differential Equations.Bulletin of mathematical biology · 2019Article
- Essential metabolism for a minimal cell.eLife · 2019Article
- Kinetic Modeling of the Genetic Information Processes in a Minimal Cell.Frontiers in molecular biosciences · 2019Article
- Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations.The journal of physical chemistry. B · 2017Article
- Article
- Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules.The Journal of chemical physics · 2016Article
- Molecular stripping, targets and decoys as modulators of oscillations in the NF-κB/IκBα/DNA genetic network.Journal of the Royal Society, Interface · 2016Article
- Effects of DNA replication on mRNA noise.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
Central to all life is the assembly of the ribosome: a coordinated process involving the hierarchical association of ribosomal proteins to the RNAs forming the small and large ribosomal subunits. The process is further complicated by effects arising from the intracellular heterogeneous environment and the location of ribosomal operons within the cell. We provide a simplified model of ribosome biogenesis in slow-growing Escherichia coli. Kinetic models of in vitro small-subunit reconstitution at the level of individual protein/ribosomal RNA interactions are developed for two temperature regimes. The model at low temperatures predicts the existence of a novel 5'→3'→central assembly pathway, which we investigate further using molecular dynamics. The high-temperature assembly network is incorporated into a model of in vivo ribosome biogenesis in slow-growing E. coli. The model, described in terms of reaction-diffusion master equations, contains 1336 reactions and 251 species that dynamically couple transcription and translation to ribosome assembly. We use the Lattice Microbes software package to simulate the stochastic production of mRNA, proteins, and ribosome intermediates over a full cell cycle of 120 min. The whole-cell model captures the correct growth rate of ribosomes, predicts the localization of early assembly intermediates to the nucleoid region, and reproduces the known assembly timescales for the small subunit with no modifications made to the embedded in vitro assembly network.
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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.