ArticlePLoS computational biology2010
Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 321 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
321 citing papers in PubMed, 1 synthesis or guideline pooled it, 700 citations in OpenAlex.
- Macromolecular Crowding in Cytoplasm and Cellular Organelles.Sub-cellular biochemistry · 2025Pooled it
- Isoelectric point stabilization and protein mass compression are associated with antimicrobial resistance in the genus Acinetobacter.World journal of microbiology & biotechnology · 2026Article
- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
- Molecular crowding effects on protein stability in a bacterial proteome.Scientific reports · 2026Article
- Exploring the effects of excipients on complex coacervation.Journal of colloid and interface science · 2025Article
- PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modeling and machine learning.Acta crystallographica. Section F, Structural biology communications · 2025Article
- Mechanisms and Pathological Significance of Liquid-Liquid Phase Separation in Bacteria.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025Review
- Comparative Analysis of Biochemical and Cellular Assay Conditions and the Need for a Buffer That Mimics Cytoplasmic Environments.Molecules (Basel, Switzerland) · 2025Review
- FINCHES: A Computational Framework for Predicting Intermolecular Interactions in Intrinsically Disordered Proteins.International journal of molecular sciences · 2025Review
- Nonequilibrium polysome dynamics promote chromosome segregation and its coupling to cell growth ineLife · 2025Article
- Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Decoding in-cell respiratory enzyme dynamics by label-free in situ electrochemistry.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- In silico nanoscope to study the interplay of genome organization and transcription regulation.Nucleic acids research · 2025Article
- Nonequilibrium polysome dynamics promote chromosome segregation and its coupling to cell growth inbioRxiv : the preprint server for biology · 2025Article
- 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
- Dynamic energy conversion in protein catalysis: From brownian motion to enzymatic function.Computational and structural biotechnology journal · 2025Review
- Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells.Journal of chemical information and modeling · 2024Review
- Protein translation can fluidize bacterial cytoplasm.PNAS nexus · 2024Article
- Heterogeneous Slowdown of Dynamics in the Condensate of an Intrinsically Disordered Protein.The journal of physical chemistry letters · 2024Article
- Combining systems and synthetic biology for in vivo enzymology.The EMBO journal · 2024Article
261 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A longstanding question in molecular biology is the extent to which the behavior of macromolecules observed in vitro accurately reflects their behavior in vivo. A number of sophisticated experimental techniques now allow the behavior of individual types of macromolecule to be studied directly in vivo; none, however, allow a wide range of molecule types to be observed simultaneously. In order to tackle this issue we have adopted a computational perspective, and, having selected the model prokaryote Escherichia coli as a test system, have assembled an atomically detailed model of its cytoplasmic environment that includes 50 of the most abundant types of macromolecules at experimentally measured concentrations. Brownian dynamics (BD) simulations of the cytoplasm model have been calibrated to reproduce the translational diffusion coefficients of Green Fluorescent Protein (GFP) observed in vivo, and "snapshots" of the simulation trajectories have been used to compute the cytoplasm's effects on the thermodynamics of protein folding, association and aggregation events. The simulation model successfully describes the relative thermodynamic stabilities of proteins measured in E. coli, and shows that effects additional to the commonly cited "crowding" effect must be included in attempts to understand macromolecular behavior in vivo.
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What OpenQuestion holds
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.