ArticleScientific reports2013
A quantitative model of ERK MAP kinase phosphorylation in crowded media.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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
33 citing papers in PubMed, 62 citations in OpenAlex.
- Article
- How does cytoplasmic crowding affect reaction rates?Molecular cell · 2026Review
- ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events.Journal of molecular biology · 2025Article
- Purification of a Fc-Fusion Protein with [Bathophenathroline:metal] Complexes.Antibodies (Basel, Switzerland) · 2025Article
- Effects of Molecular Crowding on the Structural, Dynamic, and Functional Properties of Biological Macromolecules: A General Overview.Sub-cellular biochemistry · 2025Review
- AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis.PLoS computational biology · 2024Article
- Viscosity-dependent control of protein synthesis and degradation.Nature communications · 2024Article
- Article
- Architecture of the MKK6-p38α complex defines the basis of MAPK specificity and activation.Science (New York, N.Y.) · 2023Article
- Optimal density of bacterial cells.PLoS computational biology · 2023Article
- Protein homeostasis from diffusion-dependent control of protein synthesis and degradation.bioRxiv : the preprint server for biology · 2023Article
- Precise timing of ERK phosphorylation/dephosphorylation determines the outcome of trial repetition during long-term memory formation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- On the parameter combinations that matter and on those that do not: data-driven studies of parameter (non)identifiability.PNAS nexus · 2022Article
- Symmetry breaking meets multisite modification.eLife · 2021Article
- Transcription and Translation in Cytomimetic Protocells Perform Most Efficiently at Distinct Macromolecular Crowding Conditions.ACS synthetic biology · 2020Article
- Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway.Molecular systems biology · 2020Article
- Dehydration entropy drives liquid-liquid phase separation by molecular crowding.Communications chemistry · 2020Article
- Inference of Multisite Phosphorylation Rate Constants and Their Modulation by Pathogenic Mutations.Current biology : CB · 2020Article
- Single-cell quantification of the concentrations and dissociation constants of endogenous proteins.The Journal of biological chemistry · 2019Article
- When More Is Less: Dual Phosphorylation Protects Signaling Off State against Overexpression.Biophysical journal · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cytoplasm contains a large number of macromolecules at extremely high densities. How this striking nature of intracellular milieu called macromolecular crowding affects intracellular signaling remains uncharacterized. Here, we examined the effect of macromolecular crowding on ERK MAPK phosphorylation by MEK MAPKK. Addition of polyethylene glycol-6000 (PEG-6000) as a crowder to mimic intracellular environments, elicited a biphasic response to the overall ERK phosphorylation rate. Furthermore, probability of processive phosphorylation (processivity) of tyrosine and threonine residues within the activation loop on ERK increased non-linearly for increasing PEG-6000 concentration. Based on the experimental data, we developed for the first time a mathematical model integrating all of the effects of thermodynamic activity, viscosity, and processivity in crowded media, and found that ERK phosphorylation is transition-state-limited reaction. The mathematical model allows accurate estimation of the effects of macromolecular crowding on a wide range of reaction kinetics, from transition-state-limited to diffusion-limited reactions.
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.