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16 results for “GPCRs”
Generic residue numbering of the GAIN domain of adhesion GPCRs
<p>The dataset corresponding to the publication:</p> <ul> <li>Generic residue numbering of the GAIN domain of adhesion GPCRs <div> <div>Florian Seufert, Guillermo Pérez-Hernández, Gáspár Pándy-Szekeres, Ramon Guixà-González, Tobias Langenhan, David E. Gloriam, Peter W. Hildebrand</div> <div>ReasearchSquare</div> <div><a href="https://doi.org/10.21203/rs.3.rs-4761600/v1" rel="nofollow">https://doi.org/10.21203/rs.3.rs-4761600/v1</a></div> </div> </li> </ul> <p>The archive consists of three files:</p> <ul> <li>gaingrn_data.tgz</li> </ul> <p>Contains the underlying data and object structures for the GAIN-GRN creation process and the python package availabe in <a title="repo" href="https://github.com/FloSeu/GAIN-GRN" target="_blank" rel="noopener">https://github.com/FloSeu/GAIN-GRN</a>. This can be downloaded manually and extracted in the respective GAIN-GRN/ directory or automatically retrieved via a dedicated function</p> <ul> <li>agpcr_gains.tgz</li> </ul> <p>Contains the best (rank 1) PDB model of the ColabFold/AlphaFold2 workflow for each adhesion GPCR GAIN domain, named by its UniProt accession number.</p> <ul> <li>pkd_gains.tgz</li> </ul> <p>Contains the best (rank 1) PDB model of the ColabFold/AlphaFold2 workflow for each polycystic kidney disease (PKD1) / PKD1-like 1 protein (PKD1L1) GAIN domain, named by its UniProt accession number.</p>
Model systems with GPCRs embedded in multicomponent membranes
<p>Files required to run coarse-grained simulations on various lipid membranes with embedded adenosine A_2A and dopamine D_2 receptors. These simulations were performed to study the effect of the presence of polyunsaturated fatty acid on GPCR oligomerization. The detailed description of the aims, methodologies and results of this study are explained in the research paper [1]. The composition and purpose of each simulated system will also be explained in this paper [1].</p> <p>The Martini force field [2,3] was employed in the study, and the simulations were performed with version 4.5.x of the GROMACS package [4].</p> <p>For each system the following (in GROMACS compatible format) is provided:</p> <p>1) Initial structure (*Start.gro)</p> <p>2) Topology file (*.top)</p> <p>3) Index file (*.ndx)</p> <p>In addition, for systems other than those containing only one protein, the final structure is given (*End.gro).</p> <p>Other files required to run the simulations, which are common for all the systems, are also provided:</p> <p>4) Simulation parameter file (.mdp)</p> <p>5) Force field parameters (.itp)</p> <p> </p> <p><strong>References:</strong></p> <p> </p> <p>[1] Guixà-González et al., Membrane omega-3 fatty acids modulate the oligomerisation kinetics of adenosine A2A and dopamine D2 receptors. <em>Scientific Reports</em> <strong>6</strong>, Article number: 19839 (2016) <strong>DOI:</strong>10.1038/srep19839</p> <p>[2] Marrink et al., The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations.<em> Journal of Physical Chemistry B </em><strong>111</strong>, 7812–7824 (2007), <strong>DOI:</strong>10.1021/jp071097f</p> <p>[3] Monticelli et al., The MARTINI Coarse-Grained Force Field: Extension to Proteins. <em>Journal of Chemical Theory and Computation </em><strong>4</strong>, 819–834 (2008), <strong>DOI:</strong>10.1021/ct700324x</p> <p>[4] Pronk et al., GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. <em>Bioinformatics </em><strong>29</strong> 845-854 (2013), <strong>DOI:</strong>10.1093/bioinformatics/btt055</p>
Computational dataset for the manuscript "Tethered agonist exposure in intact adhesion/class B2 GPCRs through intrinsic structural flexibility of the GAIN domain"
<p>This repository provides url links to the MDsrv sessions for the manuscript: <em>Tethered agonist exposure in intact adhesion/class B2 GPCRs through intrinsic structural flexibility of the GAIN domain<strong>.</strong></em> </p> <p><strong>Link 1</strong>: L1 dynamic: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1.ngl </a></p> <p><strong>Link 2</strong>: G1 dynamic: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/G1.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/G1.ngl</a></p> <p><strong>Link 3</strong>: E5 static: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5_crevice.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5_crevice.ngl</a></p> <p><strong>Link 4: </strong>E5 dynamic: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5.ngl</a></p> <p><strong>Link 5: </strong>E5 +3 static: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5+3.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5+3.ngl</a></p> <p><strong>Link 6: </strong>E5 +6 static: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5+6.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E5+6.ngl</a></p> <p><strong>Link 7: </strong>E2 dynamic: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E2.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/E2.ngl</a></p> <p><strong>Link 8: </strong>L1 Phe+3Lys dynamic: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1Phe+3Lys.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1Phe+3Lys.ngl</a></p> <p><strong>Link 9: </strong>L1 Leu+6Lys dynamic: <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1Leu+6Lys.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1Leu+6Lys.ngl</a></p> <p><strong>Link 10: </strong>L1 dynamic (ribbon representation): <a href="http://proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1Ribbon.ngl">proteinformatics.uni-leipzig.de/html/mdsrv.html?load=file://base/aGPCRs/L1Ribbon.ngl</a></p> <p> </p> <p> </p>
ActTemp+sMSA dataset of "Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties"
<p>PDB models generated with the protocol described in "Biasing AlphaFold2 to predict GPCRs and Kinases with user-defined functional or structural properties"</p>
MD data for "Structural Basis of Efficacy-Driven Ligand Selectivity at GPCRs"
<p>Molecular dynamics (MD) data for "Structural Basis of Efficacy-Driven Ligand Selectivity at GPCRs" published Nature Chemical Biology 2023. See the included readme.txt for more details. Please cite the paper if you use these data.</p>
Identifying GPCRs involved in adipose tissue function using the innovative RNA-seq database FATTLAS
<p>G protein-coupled receptors (GPCRs) modulate the function of adipose tissue (AT) in general and of adipocytes, specifically. Although it is well-established that GPCRs are widely expressed in AT, their repertoire as well as their regulation and function in (patho)physiological conditions (e.g., obesity) is not fully resolved. Here, we established FATTLAS, an interactive public database, for improved access and analysis of RNA-seq data of mouse and human AT. After extracting the GPCRome of non-obese and obese individuals, highly expressed and regulated GPCRs were identified. Exemplarily, we describe four receptors (MRGPRF, GPR146, FZD5, PTGER2) and analyzed their functions in a (pre)adipocyte cell model. Besides all receptors being involved in adipogenesis, MRGPRF is essential for adipocyte viability and regulates cAMP levels, while GPR146 modulates adipocyte lipolysis via constitutive activation of Gi proteins. Taken together, by implementing and using FATTLAS we describe four hitherto unrecognized GPCRs associated with AT function and adipogenesis.</p>
RNA-seq Analysis of GPCRs expressed in mouse inguinal white adipocytes (iWAT), epididymal white adipocytes (eWAT) and brown adipose tissues (BAT) after high fat diet treatment.
GEO Series GSE134914. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses
GEO Series GSE194125. Homo sapiens. 30 samples. Type: Expression profiling by high throughput sequencing.
Differential activation of P-TEFb complexes in the development of cardiomyocyte hypertrophy following activation of distinct GPCRs
GEO Series GSE147402. Rattus norvegicus. 12 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq Analysis of Gs-linked GPCRs expressed in mouse inguinal white adipocytes (iWAT), epididymal white adipocytes (eWAT) and brown adipose tissues (BAT)
GEO Series GSE131861. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Targeting class A GPCRs for hard tissue regeneration [RNA-seq]
GEO Series GSE217371. Homo sapiens. 7 samples. Type: Expression profiling by high throughput sequencing.
Aspergillus nidulans: Control (Wt) vs. GPCRs mutants (ΔgprB and ΔgprD)
GEO Series GSE42553. Aspergillus nidulans. 8 samples. Type: Expression profiling by array.
Endocytosis sculpts distinct cAMP signal transduction by endogenously coexpressed GPCRs
GEO Series GSE290019. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Targeting class A GPCRs for hard tissue regeneration [ATAC-seq]
GEO Series GSE217264. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Targeting class A GPCRs for hard tissue regeneration
GEO Series GSE217437. Homo sapiens. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Expression profiling by array.
Targeting class A GPCRs for hard tissue regeneration [microarray]
GEO Series GSE217436. Homo sapiens. 1 samples. Type: Expression profiling by array.
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