Molecular insights on the pre-reactive complex between SHAPE probe and RNA molecules and its role in the SHAPE reaction: a multiscale study

Supporting Information for "Molecular insights on the pre-reactive complex between SHAPE probe and RNA molecules and its role in the SHAPE reaction: a multiscale study" by C. Hognon, A. Ben Abdeljaoued, P. Hardouin, M. Etheve-Quelquejeu, B. Sargueuil, D. Laage, E. Frezza.

We focused on the Bacillus subtilis yitJ S box/SAM-I riboswitch RNA, whose structure is available under PDB ID: 4KQY. The RNA was described using the Amber 99SB-ILDN force field with the BSC0 and χOL3 modifications.

All-atom MD simulations were conducted on both the isolated P3a stem-loop and the full RNA structure using GROMACS. The file start.pdb can be used to open the trajectories as the topology file. The plain MD simulations are available in the folder named AA. Each folder contains three repeats:

rep1 (ld-seed: -405291154 for the full structure and -1633222772 for the isolated stem-loop),

rep2 (ld-seed: -135266566 for the full structure and -1392585889 for the isolated stem-loop),

rep3 (ld-seed: -553742348 for the full structure and -419463185 for the isolated stem-loop).

In the folders 1DUS and 2DUS, we concatenated the simulations for each window and deposited the resulting trajectory for each nucleotide under investigation. 

In 1D US all-atom MD simulations, the collective variable is defined as the distance between the reactive carbon (C*) and the hydroxyl oxygen.

In 2D US all-atom MD simulations, we also included the angle α, defined by atoms C*, C4’, and C2’.

1D US QM-MM Simulations

The 1D US QM-MM simulations were performed using the AMBER software.

Amber Input FilesUmbrella sampling input files for the window at CV = 4 Å are provided as an example.

Trajectory VisualizationTo visualize the trajectories, use the provided topology file.

Topology

start.pdb: PDB file from the last frame of the production run at CV = 4 Å for αᵢ = 30°, used as the topology to open the trajectories.

Trajectories

all_noWAT_*.xtc:  concatenated windows from CV = 4 Å to CV = 1 Å of overall 61 windows of 250 ps each (625 frames per window) without ions and water molecules.

all_noWAT_30.xtc: trajectory for αi at 30°

all_noWAT_60.xtc: trajectory for αi  at 60°

all_noWAT_80.xtc: trajectory for αi at 80°