Cargando…

Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations

[Image: see text] The epidermal growth factor receptor (EGFR) is a dimeric membrane protein that regulates key aspects of cellular function. Activation of the EGFR is linked to changes in the conformation of the transmembrane (TM) domain, brought about by changes in interactions of the TM helices of...

Descripción completa

Detalles Bibliográficos
Autores principales:	Lelimousin, Mickaël, Limongelli, Vittorio, Sansom, Mark S. P.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	American Chemical Society 2016
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010359/ https://www.ncbi.nlm.nih.gov/pubmed/27459426 http://dx.doi.org/10.1021/jacs.6b05602

Ejemplares similares

Highly Coarse-Grained Representations of Transmembrane Proteins
por: Madsen, Jesper J., et al.
Publicado: (2017)

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

Flow of the coarse grained free energy for crossover phenomena
por: Bornholdt, S., et al.
Publicado: (1996)

Coarse Grained Models Reveal Essential Contributions of Topological Constraints to the Conformational Free Energy of RNA Bulges
por: Mustoe, Anthony M., et al.
Publicado: (2014)

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models
por: Genheden, Samuel
Publicado: (2017)

Protein–ligand binding with the coarse-grained Martini model
por: Souza, Paulo C. T., et al.
Publicado: (2020)

Elucidating activation and deactivation dynamics of VEGFR-2 transmembrane domain with coarse-grained molecular dynamics simulations
por: Go, Yeon Ju, et al.
Publicado: (2023)

Fast Calculation of Protein–Protein Binding Free Energies Using Umbrella Sampling with a Coarse-Grained Model
por: Patel, Jagdish Suresh, et al.
Publicado: (2017)

Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems
por: Spijker, Peter, et al.
Publicado: (2010)

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

A highly accurate metadynamics-based Dissociation Free Energy method to calculate protein–protein and protein–ligand binding potencies
por: Wang, Jing, et al.
Publicado: (2022)

Free Energy Landscape of Lipid Interactions with Regulatory Binding Sites on the Transmembrane Domain of the EGF Receptor
por: Hedger, George, et al.
Publicado: (2016)

Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations
por: Bell, David R., et al.
Publicado: (2017)

Multiscale Coarse-Graining of the Protein Energy Landscape
por: Hills, Ronald D., et al.
Publicado: (2010)

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

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

The automated optimisation of a coarse-grained force field using free energy data
por: Caceres-Delpiano, Javier, et al.
Publicado: (2021)

Exploring Conformational Dynamics of the Extracellular Venus flytrap Domain of the GABA(B) Receptor: A Path-Metadynamics Study
por: Evenseth, Linn S. M., et al.
Publicado: (2020)

Coarse Grained Molecular Dynamic Simulations for the Study of TNF Receptor Family Members' Transmembrane Organization
por: Sica, Mauricio P., et al.
Publicado: (2021)

Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations
por: Moradi, Mahmoud, et al.
Publicado: (2013)

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

Calculation of therapeutic antibody viscosity with coarse-grained models, hydrodynamic calculations and machine learning-based parameters
por: Lai, Pin-Kuang, et al.
Publicado: (2021)

“Martinizing” the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins
por: Ricci, Clarisse G., et al.
Publicado: (2017)

Transmembrane Recognition of the Semaphorin Co-Receptors Neuropilin 1 and Plexin A1: Coarse-Grained Simulations
por: Aci-Sèche, Samia, et al.
Publicado: (2014)

Rapid discovery of stable materials by coordinate-free coarse graining
por: Goodall, Rhys E. A., et al.
Publicado: (2022)

Martini 3 Coarse-Grained Force Field for Carbohydrates
por: Grünewald, Fabian, et al.
Publicado: (2022)

Coarse-Grained Modeling of EUV Patterning Process Reflecting Photochemical Reactions and Chain Conformations
por: Kim, Tae-Yi, et al.
Publicado: (2023)

Exploring a coarse-grained distributive strategy for finite-difference Poisson–Boltzmann calculations
por: Hsieh, Meng-Juei, et al.
Publicado: (2010)

How to Determine Accurate Conformational Ensembles by Metadynamics Metainference: A Chignolin Study Case
por: Paissoni, Cristina, et al.
Publicado: (2021)

Interfacial activation of M37 lipase: A multi-scale simulation study
por: Willems, Nathalie, et al.
Publicado: (2017)

Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems
por: Srivastava, Anand, et al.
Publicado: (2014)

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

Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data
por: Devaurs, Didier, et al.
Publicado: (2017)

Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA
por: Assenza, Salvatore, et al.
Publicado: (2022)

Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines
por: Shi, Danfeng, et al.
Publicado: (2022)

Energy renormalization for coarse-graining polymers having different segmental structures
por: Xia, Wenjie, et al.
Publicado: (2019)

A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry
por: Sharma, Satyan, et al.
Publicado: (2015)

Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation
por: Okuda, Aya, et al.
Publicado: (2021)

Coarse-Grained Simulations Suggest the Epsin N-Terminal Homology Domain Can Sense Membrane Curvature without Its Terminal Amphipathic Helix
por: Belessiotis-Richards, Alexis, et al.
Publicado: (2020)

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)

Cannot write session to /tmp/vufind_sessions/sess_srg4r099ge2u5eqncdh4t26hpk