Semi-empirical simulation of Zn/Cd binding site preference in the metal binding domains of mammalian metallothionein

Metallothionein, a two-domain protein, naturally binds seven gram atoms of divalent ions such as Zn and Cd. Four of the metals (M1, M5, M6 and M7) are found in the α-domain and three (M2, M3 and M4) in the β-domain. Previous studies have shown that metals in the β-domain are more readily exchangeable, and the level of avidity is site specific. By semi-empirical MNDO modified neglect of diatomic overlap calculations, we found the tendency of binding energy for Cd to be M3 > M2 > M4 in the β-cluster and M5 > M7 > M1, M6 in the α-cluster. Thus, the replacement of Zn by Cd can be expected to follow the order M4 → M2 → M3 in the β-domain and MS → M7 → M1 or M6 in the α-domain. This is reflected by energy differences computed with a series of simulated structures derived from either X-ray crystallography or NMR coordinates.