ArticlePLoS computational biology2011
Decrypting the sequence of structural events during the gating transition of pentameric ligand-gated ion channels based on an interpolated elastic network model.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed, 46 citations in OpenAlex.
- General anesthetic modulation of a pentameric ligand-gated ion channel explored with simulations.Biophysical journal · 2026Article
- Modeling and Simulation of the NMDA Receptor at Coarse-Grained and Atomistic Levels.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Predicting allosteric sites using fast conformational sampling as guided by coarse-grained normal modes.The Journal of chemical physics · 2023Article
- Exploring the Conformational Impact of Glycine Receptor TM1-2 Mutations Through Coarse-Grained Analysis and Atomistic Simulations.Frontiers in molecular biosciences · 2022Article
- Molecular mechanisms underlying menthol binding and activation of TRPM8 ion channel.Nature communications · 2020Article
- Computational Ways to Enhance Protein Inhibitor Design.Frontiers in molecular biosciences · 2020Article
- Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution.Interface focus · 2019Review
- Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- The conformational wave in capsaicin activation of transient receptor potential vanilloid 1 ion channel.Nature communications · 2018Article
- The nicotinic acetylcholine receptor: a typical 'allosteric machine'.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- Investigating the structural dynamics of the PIEZO1 channel activation and inactivation by coarse-grained modeling.Proteins · 2017Article
- Probing the Structural Dynamics of the NMDA Receptor Activation by Coarse-Grained Modeling.Biophysical journal · 2017Article
- Understand spiciness: mechanism of TRPV1 channel activation by capsaicin.Protein & cell · 2017Review
- An Electrostatic Funnel in the GABA-Binding Pathway.PLoS computational biology · 2016Article
- Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions.Biophysical journal · 2015Review
- Structural mechanism underlying capsaicin binding and activation of the TRPV1 ion channel.Nature chemical biology · 2015Article
- A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation.The Journal of general physiology · 2015Article
- Pentameric Ligand-gated Ion Channels : Insights from Computation.Molecular simulation · 2014Article
- Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.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
2 authors at 1 institution in 1 country.
Funding
Abstract
Despite many experimental and computational studies of the gating transition of pentameric ligand-gated ion channels (pLGICs), the structural basis of how ligand binding couples to channel gating remains unknown. By using a newly developed interpolated elastic network model (iENM), we have attempted to compute a likely transition pathway from the closed- to the open-channel conformation of pLGICs as captured by the crystal structures of two prokaryotic pLGICs. The iENM pathway predicts a sequence of structural events that begins at the ligand-binding loops and is followed by the displacements of two key loops (loop 2 and loop 7) at the interface between the extracellular and transmembrane domain, the tilting/bending of the pore-lining M2 helix, and subsequent movements of M4, M3 and M1 helices in the transmembrane domain. The predicted order of structural events is in broad agreement with the Φ-value analysis of α subunit of nicotinic acetylcholine receptor mutants, which supports a conserved core mechanism for ligand-gated channel opening in pLGICs. Further perturbation analysis has supported the critical role of certain intra-subunit and inter-subunit interactions in dictating the above sequence of events.
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.