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.

*** p38-MKK6**

> no_restraints: independent unbiased simulations
> A-loop_close_to_ATP: simulations started from a conformation originating from the restrained simulations of p38_-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.

*** p38-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