Molecular dynamics simulations for "Allosteric network of dynamic coupling within BAP1-UCH revealed by methyl NMR"

BAP1_md.tgz: BAP1-UCH molecular dynamics simulations were performed using GROMACS 2025. The initial configuration was prepared by extracting residues 3–238 from chain L (and M in case of the UBQ bound structure) of the 8H1T PDB structure. The missing loop was modeled using Modeller. The L49V mutation was introduced in PyMOL. The resulting protein conformations were parametrized with the DES-Amber force field and the TIP4P-D water model. Short-range electrostatic and Lennard–Jones interactions were truncated at 1.0 nm, and long-range electrostatics were computed using the particle mesh Ewald (PME) method. Covalent bonds involving hydrogen atoms were constrained using LINCS. Temperature was maintained with the velocity-rescale thermostat, and pressure with the cell-rescale barostat. Each system was placed in a dodecahedral box (volume: 424.5 nm³ for the APO and 539 nm³ for the HOLO simulations) containing 12,808 water molecules (16,152 for the HOLO case) and 150 mM Na⁺/Cl⁻. Systems were energy-minimized, followed by equilibration at 298 K and 1 atm for 2 ns, with positional restraints applied to the protein. For each system, three independent production simulations of 2.2 μs were performed, reinitializing velocities at the start and discarding the first 100 ns of each trajectory. analysis.tgz: The raw data and analysis scripts for the root mean square fluctuations, KL divergence of rotameric probability density distribution and distances between specifc groups reported in the paper.