ArticlePhysical chemistry chemical physics : PCCP2014
Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics.
Article in Physical chemistry chemical physics : PCCP, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 79 citations in OpenAlex.
- Molecular Dynamics and Free Energy Calculations Predict Binding Mode and Affinity Determinants of Specialized Pro-Resolving Mediators at GPR101.ACS omega · 2026Article
- Elucidating the Structure and Activation Mechanisms of GPCRs Using Modern Computational and AI Tools.Cell biochemistry and biophysics · 2026Review
- Visualizing agonist-induced M2 receptor activation regulated by aromatic ring dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Coevolution-Driven Method for Efficiently Simulating Conformational Changes in Proteins Reveals Molecular Details of Ligand Effects in the β2AR Receptor.The journal of physical chemistry. B · 2023Article
- Enhanced sampling without borders: on global biasing functions and how to reweight them.Physical chemistry chemical physics : PCCP · 2022Review
- Development of enhanced conformational sampling methods to probe the activation landscape of GPCRs.Advances in protein chemistry and structural biology · 2022Review
- Mechanistic insight into the impact of a bivalent ligand on the structure and dynamics of a GPCR oligomer.Computational and structural biotechnology journal · 2022Article
- Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives.Advances and applications in bioinformatics and chemistry : AABC · 2022Review
- Anti-TNF Alpha Antibody Humira with pH-dependent Binding Characteristics: A constant-pH Molecular Dynamics, Gaussian Accelerated Molecular Dynamics, and In Vitro Study.Biomolecules · 2021Article
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- Elucidation of Mechanism for Ligand Efficacy at Leukotriene BACS medicinal chemistry letters · 2020Article
- Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments.Journal of chemical information and modeling · 2020Article
- Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods.PeerJ · 2020Article
- Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: insights from accelerated molecular dynamics simulations.Nucleic acids research · 2019Article
- Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water.Frontiers in chemistry · 2019Article
- Using accelerated molecular dynamics simulation to shed light on the mechanism of activation/deactivation upon mutations for CCR5.RSC advances · 2018Article
- Peptidic Macrocycles - Conformational Sampling and Thermodynamic Characterization.Journal of chemical information and modeling · 2018Article
- A molecular dynamics simulation study decodes the Zika virus NS5 methyltransferase bound to SAH and RNA analogue.Scientific reports · 2018Article
- Membrane-embedded substrate recognition by cytochrome P450 3A4.The Journal of biological chemistry · 2018Article
- Identification of a Different Agonist-Binding Site and Activation Mechanism of the Human P2YScientific reports · 2017Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
G-protein coupled receptors (GPCRs) mediate cellular responses to various hormones and neurotransmitters and are important targets for treating a wide spectrum of diseases. They are known to adopt multiple conformational states (e.g., inactive, intermediate and active) during their modulation of various cell signaling pathways. Here, the free energy landscape of GPCRs is explored using accelerated molecular dynamics (aMD) simulations as demonstrated on the M2 muscarinic receptor, a key GPCR that regulates human heart rate and contractile forces of cardiomyocytes. Free energy profiles of important structural motifs that undergo conformational transitions upon GPCR activation and allosteric signaling are analyzed in detail, including the Arg(3.50)-Glu(6.30) ionic lock, the Trp(6.48) toggle switch and the hydrogen interactions between Tyr(5.58)-Tyr(7.53).
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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.