Supplementary Simulation Data for "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein"

Additional simulation data for "Concerted transformation of a hyper-paused transcription complex and its reinforcing protein", submitted as a preprint to BioRxiv (https://doi.org/10.1101/2023.06.26.546588), posted on June 28, 2023.

Content:

'smog2' folder: Contains Structure-Based Models (SBMs) for RfaH bound to the ops-paused elongation complex (opsPEC) in an encounter complex (opsPEC_Enc), complex 1 of RfaH bound to the opsPEC in a recruited complex (opsPEC_Rec), and a custom-built dual-basin SBM that combines topological information for both opsPEC_Enc and opsPEC_Rec. SBMs were generated using SMOG2 v2.4.5, whereas the dual-basin SBM was build using custom scripts.

'clusters' folder: Contains representative structures for intermediates I1, I2, I3 and I4 retrieved from 500 simulations of RfaH-opsPEC using a dual-basin SBM topology (top) file and the coordinates (gro file) for the opsPEC_Enc as the initial coordinates of the simulation. It also contains representative structures for intermediates I1, I2, I3 and I4 from control simulations for free RfaH (free_RfaH), starting from the coordinates for the opsPEC_Enc complex.

'traj' folder: Contains representative trajectories (xtc files, 2 out of 500) for the fold-switch of RfaH bound to opsPEC from the Enc to the Rec conformation.