ArticlePLoS computational biology2014
An allosteric signaling pathway of human 3-phosphoglycerate kinase from force distribution analysis.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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
12 citing papers in PubMed.
- Glyceraldehyde-3-phosphate dehydrogenase/1,3-bisphosphoglycerate-NADH as key determinants in controlling human retinal endothelial cellular functions: Insights from glycolytic screening.The Journal of biological chemistry · 2025Article
- PGK1 Is Involved in the HIF-1 Signaling Pathway as a Hub Gene for Ferroptosis After Traumatic Brain Injury.Molecular neurobiology · 2025Article
- Secreted PGK1 and IGFBP2 contribute to the bystander effect of miR-10b gene editing in glioma.Molecular therapy. Nucleic acids · 2023Article
- Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods.Frontiers in molecular biosciences · 2022Article
- Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea.Open biology · 2020Review
- Dynamics of Substrate Processing by PPIP5K2, a Versatile Catalytic Machine.Structure (London, England : 1993) · 2019Article
- One-Way Allosteric Communication between the Two Disulfide Bonds in Tissue Factor.Biophysical journal · 2017Article
- Release of Entropic Spring Reveals Conformational Coupling Mechanism in the ABC Transporter BtuCD-F.Biophysical journal · 2016Article
- Mapping Mechanical Force Propagation through Biomolecular Complexes.Nano letters · 2015Article
- Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces.PLoS computational biology · 2015Article
- Allosteric regulation of focal adhesion kinase by PIP₂ and ATP.Biophysical journal · 2015Article
- Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules.PloS one · 2014Article
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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
3-Phosphogycerate kinase (PGK) is a two domain enzyme, which transfers a phosphate group between its two substrates, 1,3-bisphosphoglycerate bound to the N-domain and ADP bound to the C-domain. Indispensable for the phosphoryl transfer reaction is a large conformational change from an inactive open to an active closed conformation via a hinge motion that should bring substrates into close proximity. The allosteric pathway resulting in the active closed conformation has only been partially uncovered. Using Molecular Dynamics simulations combined with Force Distribution Analysis (FDA), we describe an allosteric pathway, which connects the substrate binding sites to the interdomain hinge region. Glu192 of alpha-helix 7 and Gly394 of loop L14 act as hinge points, at which these two secondary structure elements straighten, thereby moving the substrate-binding domains towards each other. The long-range allosteric pathway regulating hPGK catalytic activity, which is partially validated and can be further tested by mutagenesis, highlights the virtue of monitoring internal forces to reveal signal propagation, even if only minor conformational distortions, such as helix bending, initiate the large functional rearrangement of the macromolecule.
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.