Published June 12, 2024 | Version v1

The ribosome lowers the entropic penalty of protein folding

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

This work was supported by a Wellcome Trust Investigator Award (to J.C., 206409/Z/17/Z) and by the Francis Crick Institute through provision of access to the MRC Biomedical NMR Centre. The Francis Crick Institute receives its core funding from Cancer Research UK (FC001029), the UK Medical Research Council (FC001029) and the Wellcome Trust (FC001029). This project made use of time on HPC resources on Archer2 (ARCHER2 UK National Supercomputing service, https://www.archer2.ac.uk) granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/R029407/1 and EP/X035603/1). We also acknowledge the EuroHPC Joint Undertaking for awarding this project access to the EuroHPC supercomputer LUMI, hosted by CSC (Finland) and the LUMI consortium through a EuroHPC Regular Access call and the Baskerville Tier 2 HPC service (https://www.baskerville.ac.uk/). Baskerville was funded by the EPSRC and UKRI through the World Class Labs scheme (EP/T022221/1) and the Digital Research Infrastructure programme (EP/W032244/1) and is operated by Advanced Research Computing at the University of Birmingham. We additionally acknowledge the use of the UCL Myriad and Kathleen High Performance Computing Facility (Myriad@UCL and Kathleen@UCL), and associated support services, in the completion of this work.

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Additional details

Funding

Wellcome Trust
Integrative Structural Biology of Protein Folding on the Ribosome 206409/Z/17/Z