README.md

Integrative structure of the Nef-CD4(CD)-AP2(Δμ2-CTD) complex

These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the solution structure of the Nef-CD4-AP2 complex using 90 DSSO chemical cross-links and the X-ray structure of the crystal structure, a comparative model of the β2 subunit 24-89 region built based on the AP2 structure.

First, MODELLER is used to generate comparative model of the β2 subunit 24-89 region. Then, IMP is used to model these components using crystal structure and the DSSO crosslinks to obtain the solution structure of the Nef-CD4(CD)-AP2(Δμ2-CTD) complex.

The modeling protocol will work with a default build of IMP, but for most effective sampling, IMP should be built with MPI so that replica exchange can be used.

List of files and directories:

• data contains all relevant data, input structures that were generated by MODELLER or deposited in PDB, etc.

  • mod_extended_AP2beta2.py MODELLER script to add the β2 subunit 24-89 region built based on the AP2 structure using MODELLER

• scripts

  • mod_Nef_AP2_newhelix.py the main IMP/PMI script modeling with 3 crystal interfaces

• scripts/analysis The best 500 models from the modeling are accumulated in this directory, and updated as the calculation proceeds.

• scripts/figures The structures of the lowest temperature replica will be written here as RMF files.

• outputs For reference, the models described in the Nup84 publication are deposited in this directory. For each of the two clusters discovered in the study, the cluster representative (the best scoring individual model in the cluster) is available in RMF format, together with the top five best scoring models in PDB format. An accompanying stat file contains useful statistics on the simulation, such as whether each of the crosslinks was satisfied. The localization densities, as shown in Figure 6 on the publication are also available, as Chimera session files.

Running the MODELLER scripts:

• cd data/
• (python mod_extended_AP2beta2.py > mod_extended_AP2beta2.log)

Running the IMP/PMI scripts for the Nef-CD4(CD)-AP2(Δμ2-CTD) complex:

• cd scripts
• python mod_Nef_AP2_newhelix.py &> mod_Nef_AP2_newhelix.out (on a single processor; prepend mpirun -np 4 or similar if you built IMP with MPI support)
• You can add the --test option to the command line to quickly test the script; this simply runs the sampling for fewer steps (should complete in an hour or two).

Next, analyze resulting models (this script can also be used to combine results from multiple independent runs):

• cd scripts/analysis
• python run_analysis.py ../
• (If you used the --test option above, use it here too.)

Information

Author(s): Ignacia Echeverria

Date: May 5th, 2020

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Last known good IMP version:

Testable: Yes.

Parallelizeable: Yes

Publications:

• Kwon, Y., Kaake, R.M., Echeverria, I. et al. Structural basis of CD4 downregulation by HIV-1 Nef. Nat Struct Mol Biol (2020). (https://doi.org/10.1038/s41594-020-0463-z).