The ribosome lowers the entropic penalty of protein folding
- 1. University College London
Description
This dataset contains concatenated MD trajectories for unfolded, isolated FLN5 A3A3 (iso.pdb and iso_traj.xtc) and the unfolded FLN5+31 A3A3 ribosome-nascent chain complex (RNC, nc.pdb and nc_traj.xtc). A representative structure of the ribosome model used in the simulations is also provided (ribosome_sim.pdb). Numpy array files (ending in .npy) contain the weights obtained for every frame in the ensembles after reweighting with PRE-NMR data. Text files including the trajectory frames (1-indexed, frames_nc.ndx and frames_iso.ndx) corresponding to the weights are also included (a few frames were removed because MTSL/spinlabel rotamers could not be accomdated sterically to allow for PRE calculations at protein labelling sites of interest). Both ensembles consist of ~100,000 frames. The FLN5 A3A3 ensemble was generated from ten independent MD trajectories of 2 microseconds, and FLN5+31 A3A3 consists of ten independent simulations lasting 1.5 microseconds (20 and 15 microseconds total, respectively). Independent simulations were initiated from different starting structures. The *.tar files contain initial coordinate files, MD input files and topologies.
Notes
Files
Files
(4.3 GB)
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Additional details
Funding
- Wellcome Trust
- Integrative Structural Biology of Protein Folding on the Ribosome 206409/Z/17/Z