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>&nbsp;</p> <p>Two&nbsp;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&nbsp;</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 &#39;md&#39; 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> &nbsp;</li> </ul> </li> <li><strong>figure-3c-s4b</strong> <ul> <li>You can run color_all.tcl&nbsp;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> &nbsp;</li> </ul> </li> <li><strong>figure-s3a</strong> <ul> <li>tmd1_structures.pse&nbsp;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&nbsp;and tmd1_r170g.npy&nbsp;file<br> &nbsp;</li> </ul> </li> <li><strong>figure-s3e</strong> <ul> <li>PyMOL pse files to visualise the dynamics of NBD1/2 structures<br> &nbsp;</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> &nbsp;</li> </ul> </li> <li><strong>figure-s5c</strong> <ul> <li>PyMOL pse files to visualise the dynamics of NBD1/2 structures<br> &nbsp;</li> </ul> </li> <li><strong>figure-s8d</strong> <ul> <li>Data for MRP1/ABCC1</li> <li>You can run color_all.tcl&nbsp;in VMD to reproduce the network communities in structural context; this is dependent&nbsp;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>