Structural Rewiring of IL-7R Dimerization by an Oncogenic Transmembrane Mutation Can Be Reversed by Rational Design

This dataset contains molecular dynamics (MD) simulation input files supporting the study "Structural Rewiring of IL-7R Dimerization by an Oncogenic Transmembrane Mutation Can Be Reversed by Rational Design" (Wang et al., 2025). Files are provided for three IL-7R transmembrane domain homodimer systems embedded in POPC lipid bilayers: (1) the V253G oncogenic mutant at the G253 dimerization interface (named G253-interface mutant) (2) wild-type IL-7R back-mutated to the G253 interface (named V253-interface wildtype) (3) wild-type IL-7R at the L255 interface modeled with Boltz-2 guided by NMR distance constraints (named L255-interface wildtype) Each zip folder contains two subfolders: unbiased 1-2 μs simulations and thermal stability simulations done with simulated annealing. Note that the L255-interface includes 10 different models (000 – 009), each containing independent repeats. For each system, the dataset includes GROMACS parameter files (.mdp), topology files (.top, .itp), initial coordinate files (.gro), and portable binary run files (.tpr) for production (310 K, 1–2 μs) and temperature-scan (310–350 K, 300 ns) simulations. All simulations were performed with GROMACS 2024 and the CHARMM36m force field. Each zip file contains the following files: sa.mdp or production.mdp: GROMACS parameter file toppar/: a folder containing .itp files system_0ns.gro: the initial configuration used for the simulations after 9 step equilibration topol.top: GROMACS topology file rep-*.tpr: GROMACS run topology files (tpr) for each repeat. Below is a tree graph of the file structure of each zip folder: G253-interface_mutant ├── thermal_stability │ ├── rep-1.tpr │ ├── rep-2.tpr │ ├── rep-3.tpr │ ├── rep-4.tpr │ ├── rep-5.tpr │ ├── sa.mdp │ ├── system_0ns.gro │ ├── topol.top │ └── toppar └── unbiased ├── production.mdp ├── rep-10.tpr ├── rep-1.tpr ├── rep-2.tpr ├── rep-3.tpr ├── rep-4.tpr ├── rep-5.tpr ├── rep-6.tpr ├── rep-7.tpr ├── rep-8.tpr ├── rep-9.tpr ├── system_0ns.gro ├── topol.top └── toppar V253-interface wildtype ├── thermal_stability │ ├── rep-1.tpr │ ├── rep-2.tpr │ ├── rep-3.tpr │ ├── rep-4.tpr │ ├── rep-5.tpr │ ├── sa.mdp │ ├── system_0ns.gro │ ├── topol.top │ └── toppar └── unbiased ├── production.mdp ├── rep-10.tpr ├── rep-1.tpr ├── rep-2.tpr ├── rep-3.tpr ├── rep-4.tpr ├── rep-5.tpr ├── rep-6.tpr ├── rep-7.tpr ├── rep-8.tpr ├── rep-9.tpr ├── system_0ns.gro ├── topol.top └── toppar L255-interface wildtype ├── thermal_stability │ ├── 000 │ │ ├── rep-1.tpr │ │ ├── rep-2.tpr │ │ ├── rep-3.tpr │ │ ├── system_0ns.gro │ │ └── topol.top │ . │ . │ . │ ├── 009 │ │ ├── rep-1.tpr │ │ ├── rep-2.tpr │ │ ├── rep-3.tpr │ │ ├── system_0ns.gro │ │ └── topol.top │ ├── sa.mdp │ └── toppar └── unbiased ├── 000 │ ├── rep-1.tpr │ ├── rep-2.tpr │ ├── rep-3.tpr │ ├── system_0ns.gro │ └── topol.top . . . ├── 009 │ ├── rep-1.tpr │ ├── rep-2.tpr │ ├── rep-3.tpr │ ├── system_0ns.gro │ └── topol.top ├── production.mdp └── toppar