MD simulations data for: Role of the αC-β4 loop in protein kinase structure and dynamics

Although the aC-b4 loop is a stable feature of all protein kinases, the importance of this motif as a conserved element of secondary structure, as well as its links to the hydrophobic architecture of the kinase core, has been underappreciated. We first review the motif and then describe how it is linked to the hydrophobic spine architecture of the kinase core, which we first discovered using a computational tool, Local Spatial Pattern (LSP) alignment. Based on NMR predictions that a mutation in this motif abolishes the synergistic high-affinity binding of ATP and a pseudo substrate inhibitor, we used LSP to interrogate the F100A mutant. This comparison highlights the importance of the aC-b4 loop and key residues at the interface between the N- and C-lobes. In addition, we delved more deeply into the structure of the apo C-subunit, which lacks ATP. While apo C-subunit showed no significant changes in backbone dynamics of the aC-b4 loop, we found significant differences in the side chain ..., , , # MD simulations data for: Role of the αC-β4 loop in protein kinase structure and dynamics

We use AMBER to perform all-atom Molecular Dynamics (MD) Simulations

## Description of the zip folder

1. Once the folder is unzipped, it creates a data-availability folder
2. Inside this, there are multiple folders for different systems. Each folder contains its own solvated parameter file (complex_solv.prmtop) and topology files/coordinates files (complex_solv.inpcrd) for running an MD simulation:

### System folders:

```
Apo (without ligand like ATP or PKI);
wt-binary (WT PKA protein with ATP/Mg2+);
wt-ternary (WT PKA protein with ATP/Mg2+/PKI);
F100A-binary (mutant system (F100A) with ATP/Mg2+),
F100A-ternary (mutant system (F100A) with ATP/Mg2+/PKI)
```

Also, it contains an input-parameter folder, which contains all the input files for running the MD simulations, including:

i). Multiple minimization steps: (initially restraining the atoms without hydro...,