Molecular dynamics calculations on peroxidases: The effect of calcium ions on protein structure

Molecular dynamics (MD) calculations were performed on two peroxidases, lignin peroxidase (LiP) and horseradish peroxidase (HRP), in the presence of the two endogenous calcium ions. The resulting averaged structures were compared to the structures obtained in the absence of the calcium ions. The overall protein folding was not affected by the presence or the lack of the calcium ions, while the active site was perturbed. In particular, on the distal side, a sizeable rearrangement of the distal histidine was observed in the absence of the calcium ions. These structural rearrangements are critically discussed with respect. io the enzymatic mechanism.