MD simulations data for: Role of the αC-β4 loop in protein kinase structure and dynamics
Data files
Mar 25, 2025 version files 10.94 MB
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data_availability_submitted.zip
10.94 MB
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README.md
2.03 KB
Abstract
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 dynamics of K105. The LSP analysis suggests disruption of communication between the N- and C-lobes in the F100A mutant, which would be consistent with the structural changes predicted by the NMR spectroscopy.
We use AMBER to perform all-atom Molecular Dynamics (MD) Simulations
Description of the zip folder
- Once the folder is unzipped, it creates a data-availability folder
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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 hydrogen, then protein and ligand restraint, followed by only protein restraint and lastly with no restraint):
step2.0_min.mdin, step2.1_min.mdin, step2.2_min.mdin, step2.3_min.mdin and step2.4_min.mdinii). multiple and slowly heating from 0K to 300K:
heat1.in, heat2.in, heat3.in, heat4.in, heat5.in, heat6.iniii). equilibration:
equil.iniv). production simulation of 20 ns:
prod.in - Once the input files are ready, then we use running-script to run the MD simulation using AMBER in GPU, which contains all the descriptions of steps used for running the MD simulation strating from minimization, heating, equilibration to production by taking solvated parameter files (complex_solv.prmtop) and coordinates files (complex_solv.inpcrd) from each system.
- After MD is performed, we will enter into the analysis from the folder analysis; it contains two files:
distance.in: how to measure different distances between each atom of particular residues
pca.in: to perform principal component analysis