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72 results for “G Protein Coupled Receptor”
G-Protein Coupled Receptor-Ligand Dissociation Rates and Mechanisms from tauRAMD Simulations
<p>Data and Python scripts used for generation and analysis of RAMD dissociation trajectories for several GPCR complexes (including example showing generation of the Protein-Ligand Interaction Fingerprints, IFP, for several representative RAMD trajectories),</p> <p>reported in the manuscript</p> <p>"G-Protein Coupled Receptor-Ligand Dissociation Rates and Mechanisms from tRAMD Simulations" "G-Protein Coupled Receptor-Ligand Dissociation Rates and Mechanisms from tauRAMD Simulations"</p> <p>by Daria B. Kokh, Rebecca C. Wade</p> <p>submitted to the Journal of Chemical Theory and Computation</p> <p> </p> <p>1. <strong>README.txt </strong>- instruction for script usage</p> <p>2. <strong>PDBs.zip</strong> - PDB structures of complexes in water box used in the analysis, ligand PDB and mol2 structures</p> <p>3. <strong>tauRAMD_v2.py </strong>- Python sctipt for estimation relative residence times from Gromacs-RAMD output </p> <p>4. <strong>IFP_preprocess_Gromacs.py</strong> and <strong>IFP_SL-B2AR-WB-EX.py - </strong>Python scripts for preprocessing of RAMD trajectories and generation of IFPs</p> <p>5. <strong>Scripts.zip</strong> - additional python functions </p> <p>6. <strong>IXO-CHL.zip, IXO-ALO-CHL.zip, ACh-CHL.zip, b2AR.zip</strong> - Protein-Ligand Interaction Fingerprints (PL IFPs) generated from RAMD trajectories for <em>mAChR M2 with iperoxo</em>, <em>mAChR M2 </em><em> with iperoxo and PAM, mAChR M2 with ACh, and </em>β<em>2AR with alprenolol </em><em>.</em> </p> <p>7. <strong>Topology.zip</strong> - Gromacs topology, index.ndx, and coordinate gro files for all four systems</p> <p>8. <strong>Example_b2AR-alprenolol.zip </strong>- a set of data for a test example showing how IFP can be generated from RAMD trajectories (including several representative trajectories)</p> <p>9. <strong>Example_b2AR-alprenolol.tar </strong>- almost the same set of data as above (compressed in Windows) but for Linux users. The only difference between tar and zip archive: a short equilibration trajectory that is missing in the zip set but is included in the tar archive.</p> <p>10.<strong> Gromacs-IFP-GPCR.ipynb</strong> - Jupyter Notebook for analysis of trajectories using generated IFP data</p> <p>11. <strong>Auxi-Plots-GPCR.ipynb - </strong>Jupyter Notebook for generation additional plots from the paper</p> <p>12. <strong>Waters.zip</strong> - number of water molecules in the binding pocket in dissociation trajectories of the <em> </em>β<em>2AR - alprenolol system</em></p> <p>13. <strong>GPCR.yml</strong> - JN environment file</p> <p> </p>
Intermolecular interactions in G protein-coupled receptor allosteric sites at the membrane interface from molecular dynamics simulations and quantum chemical calculations
<p>Allosteric modulators are called to be promising candidates in G protein-coupled receptor (GPCR) drug development by displaying target selectivity and fewer side effects. Among the allosteric sites known to date, extrahelical cavities represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability; the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze the dynamics and interactions in the PAR2, C5aR1, and GCGR receptors unbound and bound to allosteric modulators at the receptor-lipid interface using molecular dynamics simulations in three lipid compositions. In addition, we performed quantum chemical calculations to further explore electrostatic interactions and the strength of atom pairwise contacts in the stabilization of the ligand-receptor complexes. We show that besides classical hydrogen bonds weak polar interactions such as O-HC, O-Br, and S-HC contacts and aromatic interactions contribute to the binding of allosteric modulators at the extrahelical sites in the middle of the membrane. The allosteric cavities are open and detectable in various membrane compositions but not always predicted as druggable. The availability of polar atoms for interactions in such cavities can be assessed by water molecules from the simulations. Although ligand-lipid interactions are weak, the lipid tails play a role in sizing and shaping the large part of the allosteric cavity. </p> <p>You will find the following files:</p> <ul> <li>Input files of the equilibration and production protocols of MD simulations (MD_simulations_inputs.zip)</li> <li>Input files and coordinate files of F-SAPT and NCIPLOT calculations (quantum_chemical_coordiates_inputs.zip)</li> </ul>
Secretin-like class B G protein-coupled receptor (GPCR) mutation data set
<p>Curated set of 2463 quantitative mutation data points covering 13 secretin-like class B G protein-coupled receptors.</p> <p>Annotated according to GPCRdb standards (http://gpcrdb.org/), complemented by GPCRdb Ballesteros-Weinstein numbers assigned using GPCRdb KNIME nodes (https://github.com/3D-e-Chem/knime-gpcrdb).</p> <p>The data set is build from data sets published in:</p> <p>- Siu et al. Nature 2013, 499: 444-449. doi:10.1038/nature12393</p> <p>- Hollenstein, de Graaf et al. Tr Pharmacol Sci 2014, 35: 12-22. doi: 10.1016/j.tips.2013.11.001</p> <p>- Yang, de Graaf et al. J Biol Chem 2016, 291: 12991-3004. doi: 10.1074/jbc.M116.721977</p>
Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1- MD simulations
<p>Topology, parameter and coordinates files of the Molecular dynamics (MD) simulations of OR5K1 3D models from AlphaFold 2 (AF2) and Homology Modeling (HM). We used ACEMD3 (v3.5.1) as a molecular engine, CHARMM36 as force field. Three replicas of 100 ns (dcd files) for both systems are reported. Water molecules, ions, and membrane atoms (POPC: phosphatidylcholine) atoms were removed from the original trajectories before the upload.</p>
Data underlying the article: 3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors
<p>This repository contains the datasets and results supporting the conclusions of the manuscript "<strong>3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors</strong>". </p> <p>Publicly available data is not included in this repository. The source code to generate the results gathered here can be found on GitHub (https://github.com/CDDLeiden/3ddpd). </p>
Aminergic G protein-coupled receptor (GPCR) mutation data set
<p>Curated set of 6553 quantitative mutation data points covering 34 aminergic G protein-coupled receptors, annotated according to GPCRdb standards (http://gpcrdb.org/) building from the data set published by Kooistra et al. in BJP 2013, 170, 101.</p>
Chemokine G protein-coupled receptor (GPCR) mutation data set
<p>Curated set of 2004 quantitative mutation data points covering 10 chemokine G protein-coupled receptors, annotated according to GPCRdb standards (http://gpcrdb.org/) building from the data set published by Scholten et al. in BJP 2012, 165, 1617.</p>
Chemokine G protein-coupled receptor (GPCR) mutation data set - revision
<p>Curated set of 2004 quantitative mutation data points covering 10 chemokine G protein-coupled receptors, annotated according to GPCRdb standards (http://gpcrdb.org/) building from the data set published by Scholten et al. in BJP 2012, 165, 1617.</p> <p>Errors in the previous version were corrected and new data points for CCR2 and CCR9 were added.</p>
Single cell imaging of ERK and Akt activation dynamics and heterogeneity induced by G protein-coupled receptors - Scripts & Source data
<p>Source data and scripts to reproduce the figures that are part of the publication "Single cell imaging of ERK and Akt activation dynamics and heterogeneity induced by G protein-coupled receptors".</p> <p>Journal of Cell Science (2022) 135, jcs259685, DOI: 10.1242/jcs.259685</p> <p> </p> <p>An earlier version of this work is published as a preprint: "Heterogeneity and dynamics of ERK and Akt activation by G protein-coupled receptors depend on the activated heterotrimeric G proteins", DOI: <a href="https://doi.org/10.1101/2021.07.27.453948">10.1101/2021.07.27.453948</a></p>
Computational data for Structure of G protein-coupled receptor GPR1 bound to full-length chemerin adipokine reveals a chemokine-like reverse binding mode
<p>MD simulation data for the research article titled "Structure of G protein-coupled receptor GPR1 bound to full-length chemerin adipokine reveals a chemokine-like reverse binding mode".</p>
A pharmacological chaperone stabilizer rescues the expression of the vast majority of pathogenic variants in a G protein-coupled receptor
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The pocketome of G-protein-coupled receptors reveals previously untargeted allosteric sites
<p>Supplementary Data 1: list of all analysed structures together with the docking files</p> <p>Supplementary Data 2: grid files, template and README for visualising the class-specific density maps by using Pymol</p>
Asthma, Inflammation and G Protein-coupled Receptors (GPCR)
ClinicalTrials.gov study NCT00793676. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data for "Molecular mechanism of biased signaling in a prototypical G protein–coupled receptor"
<p>Data and analysis code for "Molecular mechanism of biased signaling in a prototypical G protein–coupled receptor" (Suomivuori <em>et al.</em>, Science 367, 881–887 (2020)). See the included READMEs for more details. Please cite the paper if you use these data.</p>
Molecular basis for the evolved instability of a human G-protein coupled receptor
<p>Membrane proteins are prone to misfolding and degradation. This is particularly true for mammalian forms of the gonadotropin-releasing hormone receptor (GnRHR). Although they function at the plasma membrane, mammalian GnRHRs accumulate within the secretory pathway. Their apparent instability is believed to have evolved through selection for attenuated GnRHR activity. Nevertheless, the molecular basis of this adaptation remains unclear. We show that adaptation coincides with a C-terminal truncation that compromises the translocon-mediated membrane integration of its seventh transmembrane domain (TM7). We also identify a series of polar residues in mammalian GnRHRs that compromise the membrane integration of TM2 and TM6. Reverting a lipid-exposed polar residue in TM6 to an ancestral hydrophobic residue restores expression with no impact on function. Evolutionary trends suggest variations in the polarity of this residue track with reproductive phenotypes. Our findings suggest that the marginal energetics of cotranslational folding can be exploited to tune membrane protein fitness.</p>
Molecular basis for the evolved instability of a human G-protein coupled receptor
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A G-protein-coupled receptor modulates gametogenesis via PKG-mediated signaling cascade in Plasmodium berghei
GEO Series GSE198287. Plasmodium berghei. 4 samples. Type: Expression profiling by high throughput sequencing.
G protein-coupled estrogen receptor stimulates human trophoblast cell invasion via YAP-mediated ANGPTL4 expression
GEO Series GSE183879. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Single cell RNA Sequencing Identifies G-protein Coupled Receptor 87 as a Basal Cell Marker Expressed in Distal Honeycomb Cysts in Idiopathic Pulmonary Fibrosis
GEO Series GSE190889. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
The G-Protein-Coupled Receptor Kinase 2 (GRK2) Orchestrates Hair Follicle Homeostasis
GEO Series GSE261821. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.