Structural studies of metal-binding proteins revealing dynamic behaviour

Abstract: The Mg²⁺ and Mn²⁺ structures of calbindin D_9k have been determined and they reveal a conformational change compared to the structures of apo and (Ca²⁺)2-calbindin D_9k. These findings are unique, since normally calcium and not magnesium is known to induce conformational changes of EF-hand proteins. It has also been shown that calbindin D_9k binds one Mg²⁺ (K_d=1mM) in the regular C-terminal EF-hand close to physiological conditions. The binding of Mg²⁺ decreases the affinity for Ca²⁺, 5-fold and vice versa. Two apo staphylococcal enterotoxin H (SEH) structures and one ZnSEH structure have been determined. The structures reveal that SEH lacks the SEB-like binding to MHC class II. Based upon structural differences for the same protein a novel mechanism for SEH recognition of different TcR Vbeta is suggested. The ZnSEH structure together with the homodimers of SEH formed by the crystal packing in two crystal forms imply the approximate area used for Zn²⁺-dependent binding to MHC class II. A dimeric form of calbindin D_9k has been found. The C-terminal EF-hand of one monomer packs towards the N-terminal EF-hand of the other monomer and vice versa. The dimerisation is primarily caused by the P43M substitution in the linker region between the EF-hands and low pH (= 5.0). The P43M substitution may facilitate 3D domain swapping in two ways; by inducing an extended hydrophobic core in the dimeric form of calbindin D_9k and by stabilizing a partially unfolded form of calbindin D_9k . The structure of staphylococcal enterotoxin A (SEA) with the substitution H187A (SEA_H187A) has been determined. SEA_H187A has previously been shown to give rise to reduced affinity for Zn²⁺ and a 10-fold decrease in Zn²⁺-dependent binding to MHC class II. The structure and aggregation analyses reveal the importance of additional ligands for SEA_H187A to bind Zn²⁺ at low physiological Zn²⁺ concentrations.