Architecture of the MKK6-p38α complex defines the basis of MAPK specificity and activation

> Molecular Dynamics simulations data. The list of the trajectories in this repository corresponds to the list of the simulations reported in, "Table S6. Summary of the unbiased simulations of the p38-MKK6" All simulations were run with the GROMACS 2021.3 simulation package. When restraints were applied at the interface of the two kinases during simulations, the restraints were applied using PLUMED 2.4.1. Each directory has a "struc_for_trajectories.pdb" file, which is a PDB structure that can be used to load the trajectories of the subdirectories. *** p38α-MKK6 *** > no_restraints: independent unbiased simulations starting from the same conformation but with different initial velocities > A-loop_close_to_ATP: simulations started from a conformation originating from the restrained simulations of p38α-MKK6GRA, where p38_ Y182 was close to MKK6 ATP > adaptive: simulations corresponding to the different epochs that were explored during the adaptive sampling simulations > MD_topology_files: topology files that were used for all the reported simulations > with_restraints: simulations where harmonic restraints on the interface interactions have been applied to stabilise the relative orientation of the monomers in the complex. The plumed file that was used to apply the restraints during the simulation is also included. *** p38α-MKK6WT *** > no_restraints: independent unbiased simulations > MD_topology_files: topology files that were used for all the reported simulations > adaptive: simulations corresponding to the different epochs that were explored during the adaptive sampling simulations > SAXS refined ensembles Ensemble of conformations resulting from the total of the MD simulations run after being refined using an iterative Bayesian/Maximum Entropy (iBME) protocol to obtain a structural ensemble that reflects the states captured in the SAXS data. *** Ensemble obtained through fitting to the MKK6DDGRA + p38αWT + ADP + SAXS curve (Fig. S2) *** fitting_to_ADP: PDB files of the conformations that correspond to this ensemble *** Ensemble obtained through fitting to the MKK6DDGRA + p38αWT + ADP + AMP-PCP SAXS curve (Fig. S2) *** fitting_to_AMP: PDB files of the conformations that correspond to this ensemble

Organizational unit

Gervasio Group

Type

Dataset

DOI

10.26037/yareta:5w7luymjcncd3ipjm3v76bqezm

License

Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International

Keywords

Molecular dynamics trajectories, p38α, ΜΚΚ6, Bayesian/Maximum Entropy, SAXS, MD simulations, Adaptive sampling