Molecular Dynamics Simulation Coordinates for SMARCB1 Missense Variants: Initial and Final Configurations

This dataset contains the molecular dynamics (MD) simulation coordinates associated with Figure 4 of Cooper et al., "SMARCB1 missense mutants disrupt SWI/SNF complex stability and remodeling activity." To investigate how specific missense mutations alter the structural behavior of SMARCB1, we performed all-atom MD simulations across wild-type (WT), a population variant control (S299L), and two disease-relevant variants (W281P and I315R). Simulations were performed using the AlphaFold2 structure of SMARCB1 (UniProt Q12824) as the starting conformation. Missense mutations were introduced using PyMOL v2.5.4 prior to system preparation. The structure was prepared using pdb4amber and parameterized with the Amber ff19SB force field, solvated in a cubic TIP3P water box with a 15.0 Å buffer, and neutralized with sodium ions. Energy minimization was performed in two sequential stages (restrained then unrestrained, 10,000 steps each), followed by NVT heating equilibration (10 ns, 0–310 K, Langevin thermostat) and NPT equilibration (5 ns, 310 K, 1 atm). Production MD was performed in the NPT ensemble for 200 ns at 310 K and 1 atm using pmemd.cuda on NVIDIA GPUs, with coordinates saved every 100 ps. All simulations were conducted using AmberTools v25 and Amber24. Simulations were conducted across 12 independent biological replicates (Rep4–Rep15) for each variant. This repository provides the initial and final atomic configurations (protein-only, solvent-stripped) for each replicate and variant in standard PDB format, extracted from production trajectories using cpptraj. These coordinates allow readers to inspect the starting conformation and equilibrated final state of each simulation and assess mutation-induced structural changes. Full analysis scripts are available at https://doi.org/10.5281/zenodo.18716542.