ArticleThe journal of physical chemistry. B2017
Energetics of Glutamate Binding to an Ionotropic Glutamate Receptor.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 25 citations in OpenAlex.
- Atomistic characterization of the maturation mechanisms in the HIV-1 capsid domain.Nature communications · 2026Article
- The molecular mechanisms of visual chromophore release from cellular retinaldehyde-binding protein.Structure (London, England : 1993) · 2025Article
- A conifer metabolite corrects episodic ataxia type 1 by voltage sensor-mediated ligand activation of Kv1.1.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators.Journal of chemical information and modeling · 2024Article
- Sustained-release behavior and the antitumor effect of charge-convertible poly(amino acid)s drug-loaded nanoparticles.Drug delivery and translational research · 2023Article
- Phosphorylation at Ser65 modulates ubiquitin conformational dynamics.Structure (London, England : 1993) · 2023Article
- Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution.Journal of chemical theory and computation · 2022Article
- Structure, Function, and Pharmacology of Glutamate Receptor Ion Channels.Pharmacological reviews · 2021Review
- A multiscale coarse-grained model of the SARS-CoV-2 virion.Biophysical journal · 2021Article
- Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IPScience advances · 2020Article
- 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
- Glutamate and Glycine Binding to the NMDA Receptor.Structure (London, England : 1993) · 2018Article
Corrections and comments
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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 are responsible for the majority of excitatory transmission at the synaptic cleft. Mechanically speaking, agonist binding to the ligand binding domain (LBD) activates the receptor by triggering a conformational change that is transmitted to the transmembrane region, opening the ion channel pore. We use fully atomistic molecular dynamics simulations to investigate the binding process in the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor, an iGluR subtype. The string method with swarms of trajectories was applied to calculate the possible pathways glutamate traverses during ligand binding. Residues peripheral to the binding cleft are found to metastably bind the ligand prior to ligand entry into the binding pocket. Umbrella sampling simulations were performed to compute the free energy barriers along the binding pathways. The calculated free energy profiles demonstrate that metastable interactions contribute substantially to the energetics of ligand binding and form local minima in the overall free energy landscape. Protein-ligand interactions at sites outside of the orthosteric agonist-binding site may serve to lower the transition barriers of the binding process.
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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.