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185 results for “cftr”
6MSM_CFTR_MD_EQUILIBRATED_MISSING_R_DOMAIN_FRAGMENT_MODELLED
<p>A protein structure based on PDB ID 6MSM with the unidentified fragment filled in based on results from molecular dynamics investigations and comparisons with alphafold.</p> <p>In addition to the molecular dynamics workflow used to simulate it.</p>
In silico data for: Folding correctors can restore CFTR post-translational folding landscape by allosteric domain-domain coupling
<p>Directory layout and description for deposited data, scripts, and results associated with</p> <p><strong>Folding correctors can restore CFTR post-translational folding landscape by allosteric domain-domain coupling</strong></p> <p>Naoto Soya, Haijin Xu, Ariel Roldan, Zhengrong Yang, Haoxin Ye, Fan Jiang, Aiswarya Premchandar, Guido Veit, Susan P.C. Cole, John Kappes, Tamas Hegedus, and Gergely L. Lukacs</p> <p> </p> <p>Two files are provided:</p> <ol> <li><strong>soya_md_trajectories.tar</strong> - This file contains the trajectories merged from the last part (450-500 ns) of the parallel simulations: md_450000_500000.xtc</li> <li><strong>soya_insilico_data.zip</strong> - This file contains all other deposited files including input data, scripts, results files.<br> The content of this file can be found below:</li> </ol> <p><strong>README.md </strong>- the content of this description</p> <p><strong>homo - Homology modeling</strong></p> <ul> <li>run*.py, myloopmodel.py, and mymodel.py files are separated for technical reasons, for running model-building in parallel mode</li> <li><strong>cftr-loop</strong> - Demonstrates the removal of the RI and seeling the break with loopmodeling</li> <li><strong>mrp1</strong> - Scripts and input files for human MRP1 homology modeling; the large unresolved loop in NBD1 was not modeled but sealed for MD; this required renumbering of the ouput</li> <li><strong>mrp6</strong> - Scripts, input, and output files for human MRP1 homology modeling; output: mrp6_human_closed.pdb; the selected CFTR and MRP1 models were the input for MD simulaitons; to see these energy minimized structures, please see the corresponding 'md' directory below.</li> </ul> <p><strong>md - Moldecular dynamics</strong></p> <ul> <li>The <strong>md_system_info.xlsx</strong> file contains the basic properties of simulation boxes</li> <li>MD parameter files: step6*.mdp for minimization and equilibration; step7_production.mdp for production run</li> <li>wordom.dat is the wordom configuration file</li> <li>cmap_mda.mp.py is a script for contact map calculation</li> <li><strong>cftr-*, mrp1-*</strong> <ul> <li>the simulation system generated by CHARMM-GUI: step5_charmm2gmx.pdb</li> <li>the output gro file of parallel simulations (the last state of the sysmtems): md_[1-6].gro</li> <li>! the trajectory merged from the last part (450-500 ns) of the parallel simulations: trajectories md_450000_500000.xtc are in a separte file (soya_md_trajectories.tar) with the same directory structure</li> <li>the merged trajectory contains only the SOLU; the corresponding structure file: prot.pdb</li> <li>index.ndx</li> </ul> </li> </ul> <p><strong>figures</strong></p> <ul> <li><strong>figure-3a</strong> <ul> <li>pdb files are the output of gmx rmsf</li> <li>pse file is saved visualization of the pdb files for PyMOL<br> </li> </ul> </li> <li><strong>figure-3c-s4b</strong> <ul> <li>You can run color_all.tcl in VMD to reproduce the network communities in structural context; this is dependent on the .pdb and .vmd files also deposited in this directory</li> <li>Network community members (residues) are listed in the Word files</li> <li>dri in file names and in scripts refers to 6ss<br> </li> </ul> </li> <li><strong>figure-s3a</strong> <ul> <li>tmd1_structures.pse contains the structures for PyMOL</li> <li>Please see the Source Data file for plotting RMSF</li> <li>Contact map data are in the tmd1_wt.npy and tmd1_r170g.npy file<br> </li> </ul> </li> <li><strong>figure-s3e</strong> <ul> <li>PyMOL pse files to visualise the dynamics of NBD1/2 structures<br> </li> </ul> </li> <li><strong>figure-s4a</strong> <ul> <li>Contains the calculated betweenness.txt files</li> <li>betweenness_plots.py for plotting</li> <li>wt_prot.pdb: required for plotting with resi thick-labels<br> </li> </ul> </li> <li><strong>figure-s5c</strong> <ul> <li>PyMOL pse files to visualise the dynamics of NBD1/2 structures<br> </li> </ul> </li> <li><strong>figure-s8d</strong> <ul> <li>Data for MRP1/ABCC1</li> <li>You can run color_all.tcl in VMD to reproduce the network communities in structural context; this is dependent on the .pdb and .vmd files also deposited in this directory</li> <li>Network community members (residues) are listed in the Word files</li> </ul> </li> </ul>
Molecular dynamics simulation of CFTR with inhibitor CFTRinh-172
<p>Molecular dynamics simulation trajectory, parameter files for the systems of human CFTR protein with inhibitor CFTRinh-172. CFTRinh-172 was tested with two different poses.</p>
"Global Functional Genomics Reveals GRK5 as a Therapeutic Target for Cystic Fibrosis", CFTR interactomes
<p><em>A tidy selection of published CFTR interactomes (or CFTR-related omics datasets)</em></p> <p>Collects data from the original online sources, converts gene/protein identifiers into a standard tidy format and updates the identifiers. The Uniprot ID is taken as reference and all other identifiers are genereated from them. This causes some datasets to end up with less genes/proteins than reported.</p> <p>Datasets included</p> <ul> <li><strong>Botelho (2021)</strong> - CFTR traffic regulators <ul> <li>Botelho <em>et al</em> (2022), submitted</li> </ul> </li> <li><strong>Pankow (2015)</strong> - CFTR interactome <ul> <li>Pankow <em>et al</em> (2015) deltaF508 CFTR interactome remodelling promotes rescue of cystic fibrosis. <em>Nature</em>. 528, 510--516. <a href="https://doi.org/10.1038/nature15729">https://doi.org/10.1038/nature15729</a></li> </ul> </li> <li><strong>Canato (2018)</strong> - CFTR interactome <ul> <li>Canato <em>et al</em> (2018) Proteomic interaction profiling reveals KIFC1 as a factor involved in early targeting of F508del-CFTR to degradation. <em>Cell Mol Life Sci</em>. 75(24):4495-4509. <a href="https://doi.org/10.1007/s00018-018-2896-7">https://doi.org/10.1007/s00018-018-2896-7</a></li> </ul> </li> <li><strong>Santos (2019)</strong> - CFTR interactome <ul> <li>Santos <em>et al</em> (2019) Folding Status Is Determinant over Traffic-Competence in Defining CFTR Interactors in the Endoplasmic Reticulum. <em>Cells</em>. 8(4):353. <a href="https://doi.org/10.3390/cells8040353">https://doi.org/10.3390/cells8040353</a></li> </ul> </li> <li><strong>Hutt (2018)</strong> - CFTR interactome <ul> <li>Hutt <em>et al</em> (2018) A Proteomic Variant Approach (ProVarA) for Personalized Medicine of Inherited and Somatic Disease. <em>J Mol Biol</em>. 430: 2951-2973. <a href="https://doi.org/10.1016/j.jmb.2018.06.017">https://doi.org/10.1016/j.jmb.2018.06.017</a></li> </ul> </li> <li><strong>Rauniyar (2014)</strong> - CFTR proteome <ul> <li>Rauniyar <em>et al</em> (2014) Quantitative Proteomic Profiling Reveals Differentially Regulated Proteins in Cystic Fibrosis Cells. <em>J Proteome Res</em>. 13(11): 4668-4675. <a href="https://doi.org/10.1021/pr500370g">https://doi.org/10.1021/pr500370g</a></li> </ul> </li> <li><strong>Almaça (2013)</strong> - ENaC regulome <ul> <li>Almaça <em>et al</em> (2013) High-content siRNA screen reveals global ENaC regulators and potential cystic fibrosis therapy targets. <em>Cell</em>. 154(6):1390-400. <a href="https://doi.org/10.1016/j.cell.2013.08.045">https://doi.org/10.1016/j.cell.2013.08.045</a></li> </ul> </li> <li><strong>Tomati (2018)</strong> - CFTR regulome <ul> <li>Tomati <em>et al</em> (2018) High-throughput screening identifies FAU protein as a regulator of mutant cystic fibrosis transmembrane conductance regulator channel. <em>J Biol Chem</em>. 293(4):1203-1217. <a href="https://doi.org/10.1074/jbc.m117.816595">https://doi.org/10.1074/jbc.m117.816595</a></li> </ul> </li> <li><strong>Simpson (2012)</strong> - Secretome <ul> <li>Simpson <em>et al</em> (2012) Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway. <em>Nature Cell Biology</em>. 14, 764-774. <a href="https://doi.org/10.1038/ncb2510">https://doi.org/10.1038/ncb2510</a></li> </ul> </li> <li><strong>Wang (2006)</strong> - CFTR interactome <ul> <li>Wang <em>et al</em> (2006) Hsp90 Cochaperone Aha1 Downregulation Rescues Misfolding of CFTR in Cystic Fibrosis. <em>Cell</em>. 127(4):803-815. <a href="https://doi.org/10.1016/j.cell.2006.09.043">https://doi.org/10.1016/j.cell.2006.09.043</a></li> </ul> </li> <li><strong>Reilly (2017)</strong> - CFTR interactome <ul> <li>Reilly <em>et al</em> (2017) Targeting the PI3K/Akt/mTOR signalling pathway in Cystic Fibrosis. <em>Sci Rep</em>. 9;7(1):7642. <a href="https://doi.org/10.1038/s41598-017-06588-z">https://doi.org/10.1038/s41598-017-06588-z</a></li> </ul> </li> <li><strong>Gilchrist (2006)</strong> - Secretome <ul> <li>Gilchrist <em>et al</em> (2006) Quantitative Proteomics Analysis of the Secretory Pathway. <em>Cell</em>. 127(6):1265-1281. <a href="https://doi.org/10.1016/j.cell.2006.10.036">https://doi.org/10.1016/j.cell.2006.10.036</a></li> </ul> </li> <li><strong>Pankow (2019)</strong> - CFTR interactome <ul> <li>Pankow <em>et al</em> (2019) A posttranslational modification code for CFTR maturation is altered in cystic fibrosis. <em>Science Signaling</em>. 12(562):eaan7984. <a href="https://doi.org/10.1126/scisignal.aan7984">https://doi.org/10.1126/scisignal.aan7984</a></li> </ul> </li> <li><strong>Dang (2020)</strong> - CF lung disease modifier genes <ul> <li>Dang <em>et al</em> (2020) Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation. <em>PLoS One</em>. 15(11):e0239189. <a href="https://doi.org/10.1371/journal.pone.0239189">https://doi.org/10.1371/journal.pone.0239189</a></li> </ul> </li> <li><strong>Hodos (2020)</strong> - CF genomic meta-analysis <ul> <li>Hodos <em>et al</em> (2020) Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and deltaF508-CFTR rescue. <em>Sci Rep</em> 10(1):20553. <a href="http://dx.doi.org/10.1038/s41598-020-76347-0">http://dx.doi.org/10.1038/s41598-020-76347-0</a></li> </ul> </li> </ul>
A Study to Evaluate Efficacy of Ivacaftor in Subjects With Cystic Fibrosis Who Have a 3849 + 10KB C→T or D1152H CFTR Mutation
ClinicalTrials.gov study NCT03068312. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Study of VX-809 Alone and in Combination With VX-770 in Cystic Fibrosis (CF) Patients Homozygous or Heterozygous for the F508del-CFTR Mutation
ClinicalTrials.gov study NCT01225211. IPD Sharing: Not stated. Countries: 7. Publications: 4.
Impact of Discontinuing Chronic Therapies in People With Cystic Fibrosis on Highly Effective CFTR Modulator Therapy
ClinicalTrials.gov study NCT04378153. IPD Sharing: NO. Countries: 1. Publications: 4.
Study of Ivacaftor in Cystic Fibrosis Subjects 2 Through 5 Years of Age With a CFTR Gating Mutation
ClinicalTrials.gov study NCT01705145. IPD Sharing: Not stated. Countries: 3. Publications: 1.
Exploratory Study to Evaluate QR-010 in Subjects With Cystic Fibrosis ΔF508 CFTR Mutation
ClinicalTrials.gov study NCT02564354. IPD Sharing: Not stated. Countries: 3. Publications: 1.
A Study to Evaluate the Efficacy and Safety of VX-661 in Combination With Ivacaftor in Subjects Aged 12 Years and Older With Cystic Fibrosis, Heterozygous for the F508del-CFTR Mutation
ClinicalTrials.gov study NCT02516410. IPD Sharing: Not stated. Countries: 7. Publications: 1.
A Study to Evaluate the Efficacy and Safety of Lumacaftor in Combination With Ivacaftor in Subjects With CF, Homozygous for the F508del-CFTR Mutation
ClinicalTrials.gov study NCT02514473. IPD Sharing: Not stated. Countries: 9. Publications: 3.
Cystic Fibrosis Related Bone Disease: the Role of CFTR
ClinicalTrials.gov study NCT01549314. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Study of Ivacaftor in Cystic Fibrosis Subjects Aged 12 Years and Older Homozygous for the F508del-CFTR Mutation
ClinicalTrials.gov study NCT00953706. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Study of VX-809 in Cystic Fibrosis Subjects With the ∆F508-CFTR Gene Mutation
ClinicalTrials.gov study NCT00865904. IPD Sharing: Not stated. Countries: 5. Publications: 3.
Safety and Pharmacokinetic Study of N6022 in Subjects With Cystic Fibrosis Homozygous for the F508del-CFTR Mutation
ClinicalTrials.gov study NCT01746784. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Study of Lumacaftor in Combination With Ivacaftor in Subjects 6 Through 11 Years of Age With Cystic Fibrosis, Homozygous for the F508del-CFTR Mutation
ClinicalTrials.gov study NCT01897233. IPD Sharing: Not stated. Countries: 2. Publications: 4.
Effects of Sildenafil on CFTR-dependent Ion Transport Activity
ClinicalTrials.gov study NCT01132482. IPD Sharing: Not stated. Countries: 1. Publications: 6.
A Two-Part Multicenter Prospective Longitudinal Study of CFTR-dependent Disease Profiling in Cystic Fibrosis (PROSPECT)
ClinicalTrials.gov study NCT02477319. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A Study to Evaluate the Safety and Efficacy of Long-term Treatment With TEZ/IVA in CF Participants With an F508del CFTR Mutation
ClinicalTrials.gov study NCT03537651. IPD Sharing: Not stated. Countries: 11. Publications: 3.
Roll-Over Study of Ivacaftor in Cystic Fibrosis Pediatric Subjects With a CF Transmembrane Conductance Regulator Gene (CFTR) Gating Mutation
ClinicalTrials.gov study NCT01946412. IPD Sharing: Not stated. Countries: 3. Publications: 1.
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