Metal-binding domains

In view of the structural homology, it is likely that the cluster binding subdomadn of Rieske proteins accommodating two metal ions has evolved from an archadc mononuclear metal binding domain. A simi-... 

Figure 7.32 Apo form of metal binding domain 4 of Menkes copper-transporting ATPase described in reference 133 (PDB 1AW0). Visualized using Wavefunction, Inc. Spartan 02 for Windows . See text for visualization details. Printed with permission of Wavefunction, Inc., Irvine, CA. (See color plate.)...

Berg, Jeremy M., Metal-Binding Domains in Nucleic Acid-Binding and... 

O Hara, P.J., Horowitz, H., Eichinger, G., and Young, E.T. (1988) The yeast ADR6 gene encodes homopolymeric amino acid sequences and a potential metal-binding domain. Nucleic Acids Res. 16, 10153-10169. 

Since both proteins bound at pH 7.4, the result suggests that both had isoelectric point (pi) values <7.4. Furthermore, the 78.8-kDa protein bound to the IMAC spot, while the 14.9-kDa protein did not bind. This suggests that the 78.8-kDA protein had a free His imidazole group on its surface, while the 14.9-kDa protein did not have an available metal binding domain. 

Berg,J. M. (1986). Potential metal-binding domains in nucleic acid binding proteins. Science 232, 485-487. 

Class I and/or II MTs have been described in all animals examined. Mammalian MTs have been some of the most extensively studied of the 61 or 62 amino acids, 20 are cysteine residues. Metal ions are bound to the MT exclusively through thiolate bonds involving all 20 cysteines (see Hamer, 1986). They associate with a wide range of metals in vitro, 18 different metals in the case of rat liver MT (Nielson etal., 1985). Divalent and trivalent metals exhibit saturation binding at 7 mole equivalents forming M7-MT, whereas copper (Cu(I)) and silver (Ag(I)) bind as monovalent ions forming M12-MT. The structure of these molecules is such that two metal-binding domains are formed an a-cluster from the carboxy-terminal portion of the protein, contains 11 cysteines which bind either 4 divalent or 6 monovalent ions the (3-cluster, the amino-terminal... 

Let us now put the above principles into practice by considering the assembly of multiple-helical compounds. A simple chemical model for the formation of helicates involves the twisting of molecular threads , as shown in Figure 7-27. The incorporation of metal-binding domains into these threads allows the use of metal ions to control the twisting. 

The trick lies in recognising that the crossing points of the molecular threads correspond to a point at which the two threads are co-ordinated to a single metal ion. This would mean that the two helical structures in Figure 7-27 would be achieved by the incorporation of one- and two metal-binding domains, respectively. The first structure (7.44) arises from interaction with a single metal ion, the second (7.45) from interaction with two metal ions (Fig. 7-28). 

All that remains is to convert the cartoon structures into real molecules Groups such as 2,2 -bipyridine and 1,10-phenanthroline have been popular choices for the metal-bin-ding domains. The principles are actually very simple. If we incorporate a didentate metal-binding domain into the threads, then structure 7.46 simply corresponds to the bin-... 

Figure 7-28. The use of metal ions to control the assembly of double-helical complexes. The twisting of the molecular threads is initiated by the co-ordination of metal-binding domains within the ligand to the metal ions. The assembly of the mononuclear compound 7.46 requires the incorporation of a single metal-binding domain in each molecular thread, whereas compound 7.47 requires two metal-binding domains per thread.

Figure 7-29. The generic features needed in a molecular thread designed to give structures such as 7.47, and an actual example of such a ligand, 7.48. A variety of spacer groups may be incorporated between the metal-binding domains.

Of course, it is quite possible to further extend these assembly processes to give doublehelical complexes with even more bond crossings. For example, a double-helical complex with three bond-crossings should result from the reaction of a molecular thread containing three metal-binding domains with three tetrahedral metal ions (Fig. 7-32). An example of the assembly of such a trinuclear double-helical complex is seen in the formation of 7.52 from the reaction of 7.51 with silver(i) salts (Fig. 7-33). 

Figure 7-32. The interaction of a molecular thread containing three didentate metal-binding domains with tetrahedral metal ions should give a trinuclear double-helical complex.

Figure 7-33. The interaction of the ligand 7.51, which contains three didentate metal-binding domains with copper(i) or silver(i) ions, results in the assembly of a trinuclear double-helical structure, 7.52.

Once again, it is possible to extend these ideas to the formation of complexes containing progressively more metal centres. As an example, consider the ligand 7.57. This contains a total of three didentate 2,2 -bipyridine-like domains. Upon reaction with nickel(n) salts, a trinuclear triple-helical complex, [Ni3(7.57)3]6+ 7.58, is formed, in which each of the six-co-ordinate nickel(n) centres is co-ordinated to a didentate metal-binding domain from each of three ligand threads. 

It should be stressed that the coding for the formation of these topologically complex molecules needs to be carefully controlled in order to obtain the desired structures. To illustrate this, consider ligand 7.59, which contains two didentate metal-binding domains. This might be expected to react with octahedral metal ions to give a triple-helical dinuclear complex. Reaction with iron(n) does indeed give a species of stoichiometry [Fe2(7.59)3]4+ however, the crystal structure reveals that an untwisted complex, 7.60, has been formed. 

Now let us consider what happens if two such molecular threads containing didentate metal-binding domains are twisted into a helical arrangement after co-ordination to a tetrahedral metal centre. Reaction with the difunctional reagent could proceed in several ways. For example, the result could be the formation of a [2+2] macrocyclic complex as a result of the difunctional reagent linking together the two molecular threads (Fig. 7-38). 

Figure 8-34. A new ligand with six unoccupied 2,2 6, 2"-terpyridine metal-binding domains, prepared from the reaction of 8.28 with the complex [Ru(4,4 -Cl2bpy)].

Formation of [6 + 6] double helicates is possible, however, if terdentate metal binding domains are used. A six-coordinate metal ion may thus bind to one domain from each helicand ligand. The simplest example of such a ligand is the attractively named 2,2, 6, 2" 6",2" 6", 2"" 6"",2 ""-sexipyridine (10.120). In the presence of a wide variety of metal ions such as Cd2+, Fe2+, Co2+, Ni2+ and Cu2+ a double helical 2 2 complex is formed. The X-ray molecular structure of the cadmium compound is shown in Figure 10.78.85... 

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