Molecular Dynamics Simulations of Protein A–IgG Complexes at pH 7.3 and pH 5.6

This dataset contains the molecular dynamics (MD) input, parameter, and trajectory files for two systems simulating Protein A (ProA) bound to IgG under different pH conditions (7.3 and 5.6). These simulations were performed to investigate how pH-dependent electrostatics influence antibody immobilization and orientation on biosensor platforms, providing predictive insights into experimental observations. Each ProA–IgG complex was simulated for 400 ns using GROMACS 2020.6 with the CHARMM36m force field (July 2021 release), resulting in a cumulative simulation time of ~1 μs across both systems. Systems were solvated with the CHARMM-modified TIP3P water model, neutralized, and set to 0.15 M NaCl ionic strength. Systems Provided (2 total) Protein A–IgG complex at pH 7.3Folder: pH7.3/Contains: proa_igg_pH7.3.pdb – initial docked structure. topol_pH7.3.top – full system topology. .itp and posre.itp files – parameter and restraint files. proa_igg_pH7.3.gro – minimized, solvated, ionized configuration. proa_igg_pH7.3.xtc – MD trajectory (400 ns). charmm36-jul2021.ff/ – complete CHARMM36m force field directory. Protein A–IgG complex at pH 5.6Folder: pH5.6/Contains: proa_igg_pH5.6.pdb – initial docked structure. topol_pH5.6.top – full system topology. .itp and posre.itp files – parameter and restraint files. proa_igg_pH5.6.gro – minimized, solvated, ionized configuration. proa_igg_pH5.6.xtc – MD trajectory (400 ns). charmm36-jul2021.ff/ – complete CHARMM36m force field directory. File Description .pdb – Initial docked structure of the Protein A–IgG complex. .top – System topology referencing all molecular components. .itp – Include files for Protein A, IgG, water, ions, and restraints. .gro – Coordinates of solvated and ionized system after minimization. .xtc – Compressed MD trajectory (400 ns). charmm36-jul2021.ff/ – Force field parameters for reproducibility. All files are provided to allow full reproducibility of the simulations and enable further analysis of pH-dependent Protein A–IgG binding dynamics.