Section 23.2.3. Metals

A number of metals are relatively abundant and available in living systems (Table 23.2.3.1) (Glusker, 1991). The most common ions include sodium, potassium, magnesium and calcium. Along with these ions, a large variety of trace metals are also found coordinated to proteins. The structures of protein complexes with some of these trace ions, including iron, zinc and copper, have been studied extensively for some time (Glusker, 1991). More recently, the structures of protein complexes with more unusual ions, such as nickel, vanadium and tungsten, have been determined (Volbeda et al., 1996).

Specificity in the interactions between proteins and metal ions is conferred through each ion's preference for the coordinating atoms and the geometry of the binding site. All four of the more common metals, i.e. sodium, potassium, magnesium and calcium, are classified as `hard' metals, referring to the polarizability of the electron cloud of the ion. The nucleus of a hard metal has a relatively tight hold on the surrounding electrons. These ions lack easily excitable unshared electrons and have a low polarizability. The interactions between these metals and their ligands tend to have the character of ionic interactions rather than the more covalent nature preferred by the `soft' metals. In general, the hard metals prefer to coordinate with hard acids, such as the oxygen atoms of hydroxyls, carbonyls and carboxyls.

The soft metals have a high polarizability, large ionic radius and several unshared valence electrons. They generally prefer to coordinate with soft acids, such as the thiol and thiol ether groups of cysteine and methionine. The loosely held valence electrons of soft metals tend to favour partially covalent π-bonding with their coordinated ligands. These outer-shell electrons can be donated to the empty outer orbitals of the ligand atom. The partially covalent nature of these bonds yields more stable complexes than the ionic complexes of the hard metals. This partial covalent bond also polarizes the ligand coordinated to the metal and can thus activate adjacent atoms to nucleophilic attack.

A large number of the transition metals, including zinc and iron, form ions that have intermediate polarizability with regard to hard and soft metals. These ions mainly prefer nitrogen ligands like the imidazole side chain of histidine or the central nitrogens of the haem cofactor.

The geometry of the metal-binding site in a protein depends on a combination of the radial size of the ion as well as the polarizability of the metal. The number of coordinating ligands around the metal is primarily correlated with the relative size of the ion, where as many anions as possible are packed around the cationic metal without leaving any cavities (Orgel, 1966). This leads to a relatively simple correlation between the ratio of the radii of the cation and the anion (r_cation/r_anion) with the coordination number. Beyond this simple geometric constraint, the coordination number is also influenced by the repulsion between the closely packed anion ligands. This repulsion can be tempered by the distortions in the cation's electron cloud, leading to a dependency between the coordination number and the polarizability of the metal ion. Table 23.2.3.1 gives the most common coordination numbers and geometries for the listed metal ions. For a more comprehensive description of possible coordination geometries, see Glusker (1991).

A short example of the diversity of metal functions in protein complexes is found in a comparison between the calcium-binding proteins calmodulin and staphyloccocal nuclease. Calmodulin functions in signal transduction by binding to a wide variety of proteins in a calcium-dependent manner. In the absence of calcium, calmodulin adopts a conformation where two loosely folded domains are connected by a flexible α-helix analogous to two balls tied together by a string. In the presence of Ca²⁺, each of the two domains of calmodulin binds to a single metal ion. The binding of Ca²⁺ to the two calmodulin domains induces a large conformational change in the protein, which confers a high affinity for peptide ligands. Crystallographic studies show that the two calcium-bound domains form a clamp that closes on the target peptide ligand (Meador et al., 1995). Thus, in this case, the metal ion plays an indirect role as a structural element in the protein function.

In the case of staphylococcal nuclease, calcium binding appears to play a more direct role in the catalytic function of the protein. A Ca²⁺ ion binds at the active site and coordinates with protein side chains, water molecules and the substrate phosphate group. The addition of calcium affects the nuclease reaction both in the binding of the substrate and directly in the catalytic step. Although calcium increases the K_m of the nucleic acid substrate, this effect can be reproduced with a large number of other metal ions (Tucker et al., 1979). The effect on catalysis, however, is specific to Ca²⁺ ions. In a proposed mechanism, Ca²⁺ directly contributes to catalysis by activating a water-derived hydroxide ion for nucleophilic attack on the phosphorus atom of the nucleic acid backbone (Cotton et al., 1979).