CDK4 directs stem cells towards adipogenesis by rewiring glucose metabolism via the TCA cycle

This dataset contains the atomistic molecular dynamics simulation files and processed trajectories used to compare wild-type human cyclin-dependent kinase 4 (CDK4) with the CDK4-M207T variant in the manuscript “CDK4 directs stem cells towards adipogenesis by rewiring glucose metabolism via the TCA cycle.” The dataset is distributed as two archives: CDK4_production_files.tar.gz Contains the GROMACS production input and output files for wild-type CDK4 and CDK4-M207T. Each system contains ten independent simulation replicates, numbered 0–9. The archive contains: prod.mdp: production simulation parameters. prod[0-9].tpr: GROMACS run-input files containing the simulation parameters, topology, and starting coordinates for each replicate. prod[0-9].gro: final coordinates from each production simulation. prod[0-9].cpt: final checkpoint files that permit continuation of the simulations. prod[0-9].edr: GROMACS energy files. prod[0-9].log: production-run log files. system_HMR.top: simulation topology after hydrogen mass repartitioning. index.ndx: GROMACS index groups used during simulation and trajectory processing. t0.pdb: initial structure of the simulated system. The raw production trajectories, prod[0-9].xtc, are not included because processed trajectories are provided separately. CDK4_processed_trajectories.tar Contains the processed protein trajectories and their corresponding reference structures for wild-type CDK4 and CDK4-M207T. Files follow these naming conventions: CDK4_WT_rep[00-09]_protein.xtc: processed wild-type CDK4 trajectories. CDK4_WT_rep[00-09]_reference.pdb: corresponding wild-type reference structures extracted at the beginning of each trajectory. CDK4_M207T_rep[00-09]_protein.xtc: processed CDK4-M207T trajectories. CDK4_M207T_rep[00-09]_reference.pdb: corresponding mutant reference structures extracted at the beginning of each trajectory. The replicate number maps directly to the production-run number. For example, rep00 corresponds to prod0, and rep09 corresponds to prod9. The processed trajectories were generated using gmx trjconv. Periodic-boundary discontinuities were removed using -pbc nojump, CDK4 was centered, and frames were retained at 100-ps intervals. The processed trajectories contain CDK4 only and exclude solvent and ions.