Data and code for Integrative Structure Determination using data from point mutant epistatic miniarray profile (pE-MAP).

pE-Map data

The clustered pE-MAP for the histones and correlation maps are available in the supplementary data of [https://science.sciencemag.org/content/370/6522/eaaz4910.abstract].

The yeast RNAPII pE-MAP is available in the supplementary materials of [https://www.sciencedirect.com/science/article/pii/S0092867413009380].

The bacterial RNAP point mutation data are available in the supplementary materials of [https://www.biorxiv.org/content/10.1101/2020.06.16.155770v1.abstract].

pE-Map restraint

Four files are included in the restraint directory:

• update_pemap_imp.sh
• include/PEMAPRestraint.h
• src/PEMAPRestraint.cpp
• restraint/pyext/src/pemap.py

Use the update_pemap_imp.sh file to copy the pEMAP restraint files into the IMP directory. The update_pemap_imp.sh file needs to be edited to indicate the path your local IMP directory. Additionally, edit the file modules/isd/pyext/swig.i-in to add the following lines:

IMP_SWIG_OBJECT(IMP::isd, PEMAPRestraint, PEMAPRestraints);
%include "IMP/isd/PEMAPRestraint.h"

Make sure to re-compile the code after adding the files.

Modeling of the H3-H4 dimer

Data for simulations (directory modeling_histones/data)

Data used for modeling includes:

1. Script and alignments to generate comparative models.

2. Comparative models of H3 and H4

3. Processed pE-MAP data file containing the pairs of residues to which the pE-MAP distance restraints will be applied. The format of these files is:

protein1 protein2 residue1 residue2 MIC_value distance_in_xray_structure (if known)

4. Python scripts to shuffle and resample the pE-MAP data files

Running the simulations (directory modeling_histones/modeling)

• top_his_comp_models.dat: Topology file containing the representation of the h3-h4 system. Each protein has presented as a rigid body. Histones tails are not considering for modeling.

• mod_pemap_histones.py: PMI modeling scripts for running the production simulations. The search for good-scoring models relied on Replica Exchange Gibbs sampling, based on the Metropolis Monte Carlo (MC) algorithm. We recommend producing at least 2,500,000 models from 50 independent runs, each starting from a different initial conformation of H3-H4 dimer to have proper statistics.

Analysis of simulations (directory modeling_histones/analysis)

The analysis uses the PMI_analysis module in: https://github.com/salilab/PMI_analysis

1. run_analysis_trajectories.py:

2. run_extract_models.py: Get the rmf3 files for a random sampled of 30,000 structures in the ensemble. These structures are split into two sets (sample_A, sample_B)

3. run_clustering.sh:

Modeling of RNAP II

Modeling of Bacterial RNAP II

Other files

Information

Author(s): Ignacia Echeverria, Hannes Braberg

Date: November 24th, 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: Braberg, H., Echeverria, I., Bohn, S., Cimermancic, P., Shiver, A., Alexander, R., Xu, J., Shales, M., Dronamraju, R., Jiang, S. and Dwivedi, G., Bogdanoff D., Chaung K. K., Hüttenhain R., Wang S., Mavor D., Pellarin R., Schneidman D., Bader J. S., Fraser J. S., Morris J., Haber J. E., Strahl B. D., Gross C. A., Dai J., Boeke J. D., Sali A., Krogan N. J. 2020. Genetic interaction mapping informs integrative structure determination of protein complexes. Science, 370(6522). [https://science.sciencemag.org/content/370/6522/eaaz4910.abstract]