Analysis of Superoxide Dismutase Reaction Mechanism of Lysozyme Containing Amino Acid Schiff Base Copper(II) Complexes Using Molecular Dynamics Calculations

Artificial metalloproteins are attracting attention as new materials with metal properties. However, it is difficult to investigate how these properties are generated in vitro. Rigorous computational simulations can therefore be used to check the progression of reactions over time. Since metals exhibit a variety of bonding modes, bond orders and flexible coordination structures, they cannot be well represented by crystal structure nor MD simulations based on classical equations of motion. Therefore, either accurate metal parameterization or QM/MM MD simulations are the best choices for simulating artificial metalloproteins considering flexibility of peptide moieties. The calculations yielded a structure that is very close to the results obtained by protein crystallography. This suggests that the metal complex itself is involved in various functions, rather than changes in the protein caused by the introduction of the metal.