ArticleNature structural & molecular biology2011
The hidden energetics of ligand binding and activation in a glutamate receptor.
Article in Nature structural & molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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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.
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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.
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Who cites it
69 citing papers in PubMed, 114 citations in OpenAlex.
- Pre-activation and gating pathway of AMPA receptors revealed by full and partial agonists.Nature structural & molecular biology · 2026Article
- Evolutionary and functional differentiation of the glutamate receptor-like family in tea (Camellia sinensis) plants and other plants.Functional & integrative genomics · 2025Article
- Structural basis of GluK2 kainate receptor activation by a partial agonist.Nature structural & molecular biology · 2025Article
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- Allosteric Competition and Inhibition in AMPA Receptors.bioRxiv : the preprint server for biology · 2023Article
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- Genome-Wide Identification, Characterization, and Expression Analysis of Glutamate Receptor-like Gene (Plants (Basel, Switzerland) · 2022Article
- Structure, Function, and Pharmacology of Glutamate Receptor Ion Channels.Pharmacological reviews · 2021Review
- Structural biology and thermodynamics of GluD receptors.Neuropharmacology · 2021Review
- Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation.Scientific reports · 2021Article
- D-Serine Potently Drives Ligand-Binding Domain Closure in the Ionotropic Glutamate Receptor GluD2.Structure (London, England : 1993) · 2020Article
- A Computational Pipeline to Predict Cardiotoxicity: From the Atom to the Rhythm.Circulation research · 2020Article
- Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution.Interface focus · 2019Review
- Activation and desensitization of ionotropic glutamate receptors by selectively triggering pre-existing motions.Neuroscience letters · 2019Review
- Druggability Simulations and X-Ray Crystallography Reveal a Ligand-Binding Site in the GluA3 AMPA Receptor N-Terminal Domain.Structure (London, England : 1993) · 2019Article
- Population Shift Mechanism for Partial Agonism of AMPA Receptor.Biophysical journal · 2019Article
- High Conformational Variability in the GluK2 Kainate Receptor Ligand-Binding Domain.Structure (London, England : 1993) · 2019Article
- Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies.Journal of chemical theory and computation · 2018Article
- Structural Mechanisms of Gating in Ionotropic Glutamate Receptors.Biochemistry · 2018Article
- Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that mediate most excitatory synaptic transmission in the central nervous system. The free energy of neurotransmitter binding to the ligand-binding domains (LBDs) of iGluRs is converted into useful work to drive receptor activation. We have computed the principal thermodynamic contributions from ligand docking and ligand-induced closure of LBDs for nine ligands of GluA2 using all-atom molecular dynamics free energy simulations. We have validated the results by comparison with experimentally measured apparent affinities to the isolated LBD. Features in the free energy landscapes that govern closure of LBDs are key determinants of binding free energies. An analysis of accessible LBD conformations transposed into the context of an intact GluA2 receptor revealed that the relative displacement of specific diagonal subunits in the tetrameric structure may be key to the action of partial agonists.
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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.