ArticleNucleic acids research2014
Quantitative influence of macromolecular crowding on gene regulation kinetics.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 57 citations in OpenAlex.
- Space-Confined Hydrogel Particle-Based Biosensor for Early Warning of Aflatoxin B1 via Rapid Label-Free Fluorescence Detection of theAnalytical chemistry · 2025Article
- Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions.Chemical reviews · 2024Review
- Mechanisms and Effects of Substrate Channelling in Enzymatic Cascades.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Macromolecular crowding effects on the kinetics of opposing reactions catalyzed by alcohol dehydrogenase.Biochemistry and biophysics reports · 2021Article
- Transcription and Translation in Cytomimetic Protocells Perform Most Efficiently at Distinct Macromolecular Crowding Conditions.ACS synthetic biology · 2020Article
- Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu.Biophysical journal · 2020Article
- Multi-modality in gene regulatory networks with slow promoter kinetics.PLoS computational biology · 2019Article
- Thermal stability and conformation of DNA and proteins under the confined condition in the matrix of hydrogels.Molecular biology reports · 2018Article
- Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins.Scientific reports · 2018Article
- DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid.Biophysical journal · 2017Article
- Screening of Proximal and Interacting Proteins in Rice Protoplasts by Proximity-Dependent Biotinylation.Frontiers in plant science · 2017Article
- The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study.PloS one · 2016Article
- Single-molecule motions and interactions in live cells reveal target search dynamics in mismatch repair.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Protein Neighbors and Proximity Proteomics.Molecular & cellular proteomics : MCP · 2015Review
- Searching target sites on DNA by proteins: Role of DNA dynamics under confinement.Nucleic acids research · 2015Article
- Real sequence effects on the search dynamics of transcription factors on DNA.Scientific reports · 2015Article
- What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition?Nucleic acids research · 2015Article
- Multi-stable dynamics of the non-adiabatic repressilator.Journal of the Royal Society, Interface · 2015Article
- Making microenvironments: A look into incorporating macromolecular crowding into in vitro experiments, to generate biomimetic microenvironments which are capable of directing cell function for tissue engineering applications.Journal of tissue engineeringArticle
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce macromolecular crowding quantitatively into the model for kinetics of gene regulation in Escherichia coli. We analyse and compute the specific-site searching time for 180 known transcription factors (TFs) regulating 1300 operons. The time is between 160 s (e.g. for SoxS Mw = 12.91 kDa) and 1550 s (e.g. for PepA6 of Mw = 329.28 kDa). Diffusion coefficients for one-dimensional sliding are between for large proteins up to for small monomers or dimers. Three-dimensional diffusion coefficients in the cytoplasm are 2 orders of magnitude larger than 1D sliding coefficients, nevertheless the sliding enhances the binding rates of TF to specific sites by 1-2 orders of magnitude. The latter effect is due to ubiquitous non-specific binding. We compare the model to experimental data for LacI repressor and find that non-specific binding of the protein to DNA is activation- and not diffusion-limited. We show that the target location rate by LacI repressor is optimized with respect to microscopic rate constant for association to non-specific sites on DNA. We analyse the effect of oligomerization of TFs and DNA looping effects on searching kinetics. We show that optimal searching strategy depends on TF abundance.
Indexed as
Identifiers
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.