In silico data for: Folding correctors can restore CFTR post-translational folding landscape by allosteric domain-domain coupling

Directory layout and description for deposited data, scripts, and results associated with

Folding correctors can restore CFTR post-translational folding landscape by allosteric domain-domain coupling

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

Two files are provided:

1. soya_md_trajectories.tar - This file contains the trajectories merged from the last part (450-500 ns) of the parallel simulations: md_450000_500000.xtc
2. soya_insilico_data.zip - This file contains all other deposited files including input data, scripts, results files.
   The content of this file can be found below:

README.md - the content of this description

homo - Homology modeling

• run*.py, myloopmodel.py, and mymodel.py files are separated for technical reasons, for running model-building in parallel mode
• cftr-loop - Demonstrates the removal of the RI and seeling the break with loopmodeling
• mrp1 - 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
• mrp6 - 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.

md - Moldecular dynamics

• The md_system_info.xlsx file contains the basic properties of simulation boxes
• MD parameter files: step6*.mdp for minimization and equilibration; step7_production.mdp for production run
• wordom.dat is the wordom configuration file
• cmap_mda.mp.py is a script for contact map calculation
• cftr-*, mrp1-*
  • the simulation system generated by CHARMM-GUI: step5_charmm2gmx.pdb
  • the output gro file of parallel simulations (the last state of the sysmtems): md_[1-6].gro
  • ! 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
  • the merged trajectory contains only the SOLU; the corresponding structure file: prot.pdb
  • index.ndx

figures

• figure-3a
  • pdb files are the output of gmx rmsf
  • pse file is saved visualization of the pdb files for PyMOL
     
• figure-3c-s4b
  • 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
  • Network community members (residues) are listed in the Word files
  • dri in file names and in scripts refers to 6ss
     
• figure-s3a
  • tmd1_structures.pse contains the structures for PyMOL
  • Please see the Source Data file for plotting RMSF
  • Contact map data are in the tmd1_wt.npy and tmd1_r170g.npy file
     
• figure-s3e
  • PyMOL pse files to visualise the dynamics of NBD1/2 structures
     
• figure-s4a
  • Contains the calculated betweenness.txt files
  • betweenness_plots.py for plotting
  • wt_prot.pdb: required for plotting with resi thick-labels
     
• figure-s5c
  • PyMOL pse files to visualise the dynamics of NBD1/2 structures
     
• figure-s8d
  • Data for MRP1/ABCC1
  • 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
  • Network community members (residues) are listed in the Word files