OaPAC molecular dynamics trajectories (4 models × 15 μs)

Description: This dataset contains all-atom molecular dynamics (MD) simulation trajectories of OaPAC (photoactivated adenylyl cyclase from Oscillatoria acuminata), comprising four simulation models each run for 15 μs (5 independent 3 μs production runs per model). Simulation models Four models were constructed to investigate the signal transduction mechanism involving the W90–M92 conformational switch: WTdark: Wild-type dark state, based on PDB 4YUS (Ohki et al., 2016) WTlight: W90–M92 unswitched wild-type light state, based on PDB 4YUS 8qfg: W90–M92 switched wild-type light state, based on PDB 8QFG (Chretien et al., 2024) Mutlight: W90–M92 unswitched L111A/L115A double mutant light state, based on PDB 4YUS Homodimeric structures were generated using PyMOL, and missing C-terminal residues (351–366) were complemented using Modeller. ATP and Mg²⁺ were modeled by superposition from the bPAC structure (PDB 5MBK). Atomic charges and coordinates in the photoreceptor region (FMN isoalloxazine ring, Y6, and Q48 side chains) were replaced with values from QM/MM free-energy geometry optimizations (Taguchi et al., 2024). Simulation conditions All simulations were performed using an in-house modified version of Amber20 with a multi-rigid-body treatment of the photoreceptor regions. The AMBER ff14SB force field was used for the protein, GAFF2 for FMN, and polyphosphate parameters from Meagher et al. (2003) for ATP. The system was solvated with TIP3P water (minimum 18.0 Å buffer) and 150 mM NaCl. Production runs were performed in the NVT ensemble at 300 K using Langevin dynamics with a 2 fs time step and 10 Å nonbonded cutoff. Directory structure The archive contains trajectories saved with different atom selections for different analysis purposes: traj_ww/ — full solvated system (protein, cofactors, water, ions) traj_wfmn/ — protein with FMN cofactor (solvent stripped) traj_wcterm/ — protein with C-terminal region (solvent stripped) traj_woligand/ — protein without ligands (for residue contact analysis) Each subdirectory contains the four models (WTlight, WTdark, Mutlight, 8qfg), and each model directory includes an Amber topology file (.prmtop) and a concatenated NetCDF trajectory file (.nc). A README file is provided in each atom-selection directory. File format Trajectories are in Amber NetCDF format and can be loaded with cpptraj, pytraj, MDAnalysis, or MDTraj using the corresponding .prmtop topology file. The archive is compressed with tar + xz.