Molecular dynamics (MD) simulations of β-conglycinin (7S) and glycinin (11S)

Molecular dynamics (MD) simulations of β-conglycinin (7S) and glycinin (11S), the two primary components of SPI, were conducted using GROMACS 2020 software. The crystal structures of the β-conglycinin and glycinin subunits were obtained from the Protein Data Bank (PDB) under the identifiers 1UIK and 1OD5, respectively. These subunits were parameterized using the GROMACS 53a6 force field and solvated in a cubic box employing the TIP3P water model. The protonation states of the subunits were initially assigned at pH values of 2.5 or 7.0, and periodic boundary conditions were applied. Energy minimization was performed using the steepest descent algorithm, after which the system was equilibrated in the constrained NVT and NPT ensembles for 2000 ps to achieve an equilibrated state. The molecular dynamics simulations were then carried out for 30 ns at temperatures of 298.15 K and 358.15 K, with trajectory data recorded at 30 ps intervals. For further analysis, the root mean square deviation (RMSD), root mean square fluctuation (RMSF), and solvent-accessible surface area (SASA) were computed based on the simulation trajectories