Cargando…

An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber

Computational strategies aimed at unveiling the thermodynamic and kinetic properties of G Protein-Coupled Receptor (GPCR) activation require extensive molecular dynamics simulations of the receptor embedded in an explicit lipid-water environment. A possible method for efficiently sampling the confor...

Descripción completa

Detalles Bibliográficos
Autores principales:	Meral, Derya, Provasi, Davide, Filizola, Marta
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	AIP Publishing LLC 2018
Materias:	ARTICLES
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6291190/ https://www.ncbi.nlm.nih.gov/pubmed/30553249 http://dx.doi.org/10.1063/1.5060960

Ejemplares similares

A combination of machine learning and infrequent metadynamics to efficiently predict kinetic rates, transition states, and molecular determinants of drug dissociation from G protein-coupled receptors
por: Lamim Ribeiro, João Marcelo, et al.
Publicado: (2020)

Molecular details of dimerization kinetics reveal negligible populations of transient µ-opioid receptor homodimers at physiological concentrations
por: Meral, Derya, et al.
Publicado: (2018)

Metadynamics simulations leveraged by statistical analyses and artificial intelligence-based tools to inform the discovery of G protein-coupled receptor ligands
por: Salas-Estrada, Leslie, et al.
Publicado: (2022)

Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors
por: Johnston, Jennifer M., et al.
Publicado: (2012)

Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis
por: Hu, Xiaohu, et al.
Publicado: (2019)

Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques
por: Provasi, Davide, et al.
Publicado: (2011)

Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity
por: Kapoor, Abhijeet, et al.
Publicado: (2017)

Atomic-Level Characterization of the Methadone-Stabilized Active Conformation of µ-Opioid Receptor
por: Kapoor, Abhijeet, et al.
Publicado: (2020)

Lessons from Free Energy Simulations of δ-Opioid Receptor Homodimers Involving the Fourth Transmembrane Helix
por: Provasi, Davide, et al.
Publicado: (2010)

Structure-Kinetics Relationships of Opioids from Metadynamics and Machine Learning
por: Mahinthichaichan, Paween, et al.
Publicado: (2023)

Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics
por: Bonomi, Massimiliano, et al.
Publicado: (2016)

Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association
por: Provasi, Davide, et al.
Publicado: (2015)

Impact of Lipid Composition and Receptor Conformation on the Spatio-temporal Organization of μ-Opioid Receptors in a Multi-component Plasma Membrane Model
por: Marino, Kristen A., et al.
Publicado: (2016)

Unbinding Kinetics of Muscarinic M3 Receptor Antagonists Explained by Metadynamics Simulations
por: Galvani, Francesca, et al.
Publicado: (2023)

Metadynamics studies of crystal nucleation
por: Giberti, Federico, et al.
Publicado: (2015)

Neural network potentials for accelerated metadynamics of oxygen reduction kinetics at Au–water interfaces
por: Yang, Xin, et al.
Publicado: (2023)

Efficient Maximum Likelihood Estimation of Kinetic Rate Constants from Macroscopic Currents
por: Stepanyuk, Andrey R., et al.
Publicado: (2011)

Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations
por: Moraca, Federica, et al.
Publicado: (2017)

GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems
por: Kumar, Anshuman, et al.
Publicado: (2023)

Approximate maximum likelihood estimation for stochastic chemical kinetics
por: Andreychenko, Aleksandr, et al.
Publicado: (2012)

Probing the Mechanical Properties of DNA Nanostructures with Metadynamics
por: Kaufhold, Will T., et al.
Publicado: (2022)

Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors
por: Shang, Yi, et al.
Publicado: (2016)

Caliber-Persistent Artery
por: Costa, Sabrina Araújo Pinho, et al.
Publicado: (2015)

Gαs slow conformational transition upon GTP binding and a novel Gαs regulator
por: Ahn, Donghoon, et al.
Publicado: (2023)

Structural Insights into the Unexpected Agonism of Tetracyclic Antidepressants at Serotonin Receptors 5-HT1eR and 5-HT1FR
por: Zilberg, Gregory, et al.
Publicado: (2023)

Insights From Molecular Dynamics Simulations of a Number of G-Protein Coupled Receptor Targets for the Treatment of Pain and Opioid Use Disorders
por: Ribeiro, João Marcelo Lamim, et al.
Publicado: (2019)

Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations
por: Leone, Vanessa, et al.
Publicado: (2009)

Exploring canyons in glassy energy landscapes using metadynamics
por: Thirumalaiswamy, Amruthesh, et al.
Publicado: (2022)

Update on retinal vascular caliber
por: Dumitrescu, Alina Gabriela, et al.
Publicado: (2017)

Highlighting the Influence of Thermodynamic Coupling on Kinetic Separations with Microporous Crystalline Materials
por: Krishna, Rajamani
Publicado: (2019)

Solving Equations of Motion by Using Monte Carlo Metropolis: Novel Method Via Random Paths Sampling and the Maximum Caliber Principle
por: González Diaz, Diego, et al.
Publicado: (2020)

Molecular Dynamics and Metadynamics Simulations of the Cellulase Cel48F
por: Vital de Oliveira, Osmair
Publicado: (2014)

Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates
por: Deriu, Marco A., et al.
Publicado: (2016)

Empirical Corrections to the Amber RNA Force Field with Target Metadynamics
por: Gil-Ley, Alejandro, et al.
Publicado: (2016)

Collective Variable for Metadynamics Derived From AlphaFold Output
por: Spiwok, Vojtěch, et al.
Publicado: (2022)

Free-Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitors Using Metadynamics
por: Kulkarni, Mandar, et al.
Publicado: (2023)

Folding intermediate states of the parallel human telomeric G-quadruplex DNA explored using Well-Tempered Metadynamics
por: Rocca, Roberta, et al.
Publicado: (2020)

Making Structural Sense of Dimerization Interfaces of Delta Opioid Receptor Homodimers
por: Johnston, Jennifer M., et al.
Publicado: (2011)

Efficient estimation of the maximum metabolic productivity of batch systems
por: St. John, Peter C., et al.
Publicado: (2017)

Control of axonal caliber by neurofilament transport
Publicado: (1984)

Cannot write session to /tmp/vufind_sessions/sess_4s2adfo3c3fgb612movudakvbp