Senotoxins target senescence via lipid binding specificity, ion imbalance and lipidome remodelling

OVERVIEW This dataset contains molecular dynamics (MD) simulation data supporting Figure 10 of the manuscript. The simulations investigate the membrane-docking helix interactions of the StnIG (TVS1G) octameric pore-forming toxin with three different membrane systems: Proliferating - Symmetric membrane with proliferating cell lipid composition Senescent - Symmetric membrane with senescent cell lipid composition Asymmetric - Asymmetric membrane with PE/PS restricted to inner leaflet SIMULATION DETAILS System Information: Protein: StnIG octamer based on FraC crystal structure (PDB: 4TSY) Replicates: n = 5 independent simulations per system (R1-R5) Duration: 500 ns per replicate Total sampling: 2.5 μs per system (7.5 μs total) Force field: CHARMM36m Temperature: 303.15 K Ion concentration: 150 mM KCl MD engine: GROMACS 2022.4 Key Residues Analyzed: GLN130, TYR133, GLU134, TYR137, TYR138 (α2 helix membrane-docking residues) DATASET CONTENTS Trajectories_Last_10ns/ - Last 10 ns trajectory segments used for Figure 10g RMSF analysis. Each system contains trajectory (.xtc), topology (.psf), and structure (.pdb) files. Analysis_Data/ - Processed contact analysis and RMSF data including all protein-lipid contacts and phosphate RMSF values. Analysis_Scripts/ - Python scripts to reproduce Figures 10B, 10C, 10E, 10F, and 10G. CHARMM-GUI_Input_Files/ - Original CHARMM-GUI system setup files for all three membrane systems. Full documentation including usage examples and detailed file descriptions is provided in the README.md file within the dataset.