title: The Unfolding Journey of Superoxide Dismutase 1 Barrels Under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions With Crowders
author: Stepan Timr
description: This data accompanies the article entitled The Unfolding Journey of Superoxide Dismutase 1 Barrels Under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions With Crowders, published in J. Phys. Chem. Lett. (https://doi.org/10.1021/acs.jpclett.0c00699). 01_SOD1bar_unfolding_REST2.zip: The zip archive includes REST2 trajectories for the three systems investigated in the paper: 1:1 packing, 2:1 packing, and the dilute case. The trajectories are saved in the GROMACS XTC file format, separately for each temperature (i=0,...,23). Given the large trajectory sizes, only protein coordinates (SOD1bar + crowders) are reported, and the output frequency is reduced to 100 ps. A starting geometry (in the Gromos87 GRO format) after equilibration of the initial packing is provided for each REST2 simulation (conf_prot.gro). Moreover, for each REST2 simulation, an xarray (http://xarray.pydata.org) dataset, saved in the netCDF file format, is included with computed fraction of native contacts, secondary structure content, and the Calpha RMSD of the barrel core (beta sheets beta1 - beta8) with respect to the crystal structure. 02_SOD1bar_geometries_representative_unfolding.zip: Representative SOD1bar geometries along the unfolding pathway (presented in Figure 3 of the paper). 03_SOD1bar_geometries_loopVII.zip: SOD1bar geometries with varying loop VII conformation which were isolated from dilute REST2 and which are presented in Figure S9 of the paper.