Molecular Dynamics Simulation of Bomb m 1 Allergen under High Pressure (600 MPa)

Bomb m 1 is a major allergen whose IgE-binding epitopes are sensitive to environmental perturbations. To decipher the structural basis underlying the pressure‑induced reduction in allergenic potency, we performed all‑atom molecular dynamics simulations using GROMACS 2021.6 with the AMBER14SB_PARMBSC1 force field and TIP3P water model. Two independent 200‑ns production runs were carried out at 298.15 K under atmospheric pressure (0.1 MPa, control) and high pressure (600 MPa), the latter being the condition that experimentally caused the greatest loss of IgE‑binding capacity. Long‑range electrostatics were treated by PME, and bonds to hydrogens were constrained with LINCS. Trajectories were saved every 2 ps for post‑simulation analyses, including root‑mean‑square deviation (RMSD), root‑mean‑square fluctuation (RMSF), solvent‑accessible surface area (SASA), and radius of gyration (Rg). By comparing the conformational ensembles between the two pressure regimes, we aim to identify pressure‑sensitive regions, secondary structure rearrangements, and changes in surface hydrophobicity that may occlude or distort critical epitopes. This computational approach provides atomistic insights into the relationship between high‑pressure processing and allergenicity modulation, supporting the rational design of hypoallergenic food products.