ArticleBioMed research international2013
Molecular dynamics studies on the conformational transitions of adenylate kinase: a computational evidence for the conformational selection mechanism.
Article in BioMed research international, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed, 32 citations in OpenAlex.
- Article
- MDGraphEmb: a toolkit for graph embedding and classification of protein conformational ensembles.Bioinformatics (Oxford, England) · 2025Article
- An accelerated molecular dynamics study for investigating protein pathways using the bond-boost hyperdynamics method.Protein science : a publication of the Protein Society · 2025Article
- Allostery can convert binding free energies into concerted domain motions in enzymes.Nature communications · 2024Article
- Rosetta Energy Analysis of AlphaFold2 models: Point Mutations and Conformational Ensembles.bioRxiv : the preprint server for biology · 2024Article
- Conformational dynamics of adenylate kinase in crystals.Structural dynamics (Melville, N.Y.) · 2024Article
- MDSubSampler: a posteriori sampling of important protein conformations from biomolecular simulations.Bioinformatics (Oxford, England) · 2023Article
- The phosphocarrier protein HPr of the bacterial phosphotransferase system globally regulates energy metabolism by directly interacting with multiple enzymes inThe Journal of biological chemistry · 2017Article
- Substrate Binding Specifically Modulates Domain Arrangements in Adenylate Kinase.Biophysical journal · 2015Article
- Constrained Maximum Likelihood Estimation of Relative Abundances of Protein Conformation in a Heterogeneous Mixture from Small Angle X-Ray Scattering Intensity Measurements.IEEE transactions on signal processing : a publication of the IEEE Signal Processing Society · 2015Article
- Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field.Journal of computer-aided molecular design · 2015Article
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
Escherichia coli adenylate kinase (ADK) is a monomeric phosphotransferase enzyme that catalyzes reversible transfer of phosphoryl group from ATP to AMP with a large-scale domain motion. The detailed mechanism for this conformational transition remains unknown. In the current study, we performed long time-scale molecular dynamics simulations on both open and closed states of ADK. Based on the structural analyses of the simulation trajectories, we detected over 20 times conformational transitions between the open and closed states of ADK and identified two novel conformations as intermediate states in the catalytic processes. With these findings, we proposed a possible mechanism for the large-scale domain motion of Escherichia coli ADK and its catalytic process: (1) the substrate free ADK adopted an open conformation; (2) ATP bound with LID domain closure; (3) AMP bound with NMP domain closure; (4) phosphoryl transfer occurred with ATP, and AMP converted into two ADPs, and no conformational transition was detected in the enzyme; (5) LID domain opened with one ADP released; (6) another ADP released with NMP domain open. As both open and closed states sampled a wide range of conformation transitions, our simulation strongly supported the conformational selection mechanism for Escherichia coli ADK.
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.