PhoQ

This directory contains the input data, protocols and output model for the modeling of the PhoQ homodimer, using cysteine crosslinking and multi-state Bayesian modeling in IMP.

solution_ensemble: all the 2-state models within the same cluster of similar structures. Each model is made of two structures, labeled by number 1 and 2.

localization_densities: all the calculated localization densities, for given domains, and for the two states.

ucsf_chimera_files: files used to generate the figures in the paper.

modeling: scripts for modeling the system:

• 2Y20_MC_1_FULL 1-state modeling
• 2Y20_MC_2_FULL 2-state modeling
• 2Y20_MC_2_FULL_90_PERCENT_DATA_1 2-state modeling with 90% data jackknifing
• 2Y20_MC_2_FULL_90_PERCENT_DATA_2 2-state modeling with 90% data jackknifing
• 2Y20_MC_2_FULL_95_PERCENT_DATA_1 2-state modeling with 95% data jackknifing
• 2Y20_MC_2_FULL_95_PERCENT_DATA_2 2-state modeling with 95% data jackknifing
• 2Y20_MC_3_FULL 3-state modeling

To run a modeling script, just change into its directory and run it from the command line, e.g.

• cd modeling/2Y20_MC_2_FULL
• ./HK_model_ENSEMBLE_REM.py (on a single processor; prepend mpirun -np 4 or similar if you built IMP with MPI support)

Two output files will be produced: a log file containing statistics, and a trajectory of model structures in RMF format. The latter can be viewed in UCSF Chimera.

Author(s): Max Bonomi, Riccardo Pellarin, Ben Webb

Date: March 18th, 2015

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:

• K. Molnar, M. Bonomi, R. Pellarin, G. Clinthorne, G. Gonzalez, S. Goldberg, M. Goulian, A. Sali, W. DeGrado. Cys-Scanning Disulfide Crosslinking and Bayesian Modeling Probe the Transmembrane Signaling Mechanism of the Histidine Kinase, PhoQ, Structure 22, 1239-1251, 2014.