This dataset contains files supporting the analyses presented in "Mechanism and energetics of JDP induced Hsp70’s conformational transition towards catalytically active state."
It includes:
(1) Contact analysis of unbiased MD trajectories for DnaK and the DnaK-J-domain complex, including contact frequencies and analysis scripts;
(2) Dynamic network analysis results for the DnaK-J-domain complex detailing network topology and individual trajectory analyses;
(3) Free energy profiles from umbrella sampling simulations, characterizing NBD-SBD distance, DnaK-JD distance, and T199-γ-phosphate distance;
(4) Torsion angle values for the NBD;
(5) Reduced-frame trajectories of the unbiased simulations;
(6) Full-system PDB structures of DnaK and the DnaK-J-domain complex;
(7) PDB structure of the DnaK-D35A J-domain variant complex;
(8) PDB structures of isolated J-domain simulations, wild type and P34A variant;
(9) PDB structure of the Thr-close state for the compensatory mutant DnaK R167A + J-domain D35N; and
(10) Final structures from each umbrella sampling simulation window for DnaK, DnaK+J-domain, DnaK with disrupted beta-sheet, and DnaK+J-domain with intact beta-sheet.
Deposited files are in pdb, tsv, dat, xtc, format and can be processed with MD software like Gromacs, VMD. Custom software is written in Python and deposited in py or npy format.
(2025)
