Molecular Dynamics Simulation of an Iron(III) Binding Site on the Fc Domain of IgG1 Relevant for Visible Light-Induced Protein Fragmentation

Molecular dynamics simulations were employed to investigate the interaction between Fe-(III) and an iron-binding site composed of THR259, ASP252, and GLU261 on the Fc domain of an IgG1. The goal was to provide microscopic mechanistic information for the photochemical, iron-dependent site-specific oxidative fragmentation of IgG1 at THR259 reported in our previous paper. The distance between Fe-(III) and residues of interest as well as the binding pocket size was examined for both protonated and deprotonated THR259. The Fe-(III) binding free energy (Delta G) was estimated by using an umbrella sampling approach. The pK(a) shift of the THR259 hydroxyl group caused by the presence of nearby Fe-(III) was estimated based on a thermodynamic cycle. The simulation results show that Fe-(III) resides inside the proposed binding pocket and profoundly changes the pocket configuration. The Delta G values indicate that the pocket possesses a strong binding affinity for Fe-(III). Furthermore, Fe-(III) profoundly lowers the pK(a) value of the THR259 hydroxyl group by 5.4 pK(a) units.