Biological Ligands

We shall in this chapter meet an array of different examples of metal complexes which we can term Metallo biomolecules. Initially, however, it would seem appropriate to identify the basic types of donor atoms and groups that are available, since this aspect clearly governs the capacity for metal ions to form complexes with biomolecules. Overwhelmingly, the donor atoms that are offered by biomolecules are oxygen nitrogen and sulfur. These are available from a number of sources. While some small molecules that form fairly simple complexes occur, the vast majority of molecules involved in metal ion binding are oligomeric or poly- meric, with the two dominant classes being peptides and nucleotide chains (RNA and DNA). Peptides consist of chains of amino acid residues linked through amide groups (-CO-NH-); amino acids (HOOC-CH(R)-NH₂) that form the peptide chain employ both their carboxylate and amine groups in peptide chain formation. The amide groups formed are good donor groups when deprotonated, and the substituent R-groups on the amino acid residues often carry function groups (such as -COOH -NH₂ -OH and -SH) that are also available for coordination. Examples of coordination of simple amino acids and peptides appear in Figure 8.1.

Figure 8.1 R Examples of amino acid and peptide coordination to a metal ion. Deprotonation of carboxylic acid and amide groups is required for efficient coordination; potential donor groups are highlighted in the free ligands.

Nucleotide 'building blocks' of DNA/RNA polymers contain a phosphate ester, a sugar ring and an aromatic nitrogen base, and thus contain a number of potential O- and N-donor groups (Figure 8.2). RNA single chains and DNA duplex chains consist of a backbone of linked phosphate diesters R-O-PO(O)-O-R, that each offer an oxygen anion suitable for complexation or at least ion-pair binding. Moreover, the array of aromatic nitrogen bases that branch from the backbone offer nitrogen donors that have the potential to participate

Figure 8.2

Examples of potential nucleotide coordination to a metal ion. Both oxygen and nitrogen donors (examples circled) have the ability to bind to metal ions.

Figure 8.3

The basic heme framework, and its coordination to a M(II) ion.

in complexation, although they are usually involved in noncovalent bonding important to the polymer structure.

Another key class of molecules that are often involved in complex formation are unsatu- rated macrocycles, usually 15- or 16-membered rings that contain four nitrogen donors. The most common of these is the heme group, which has a framework as shown in Figure 8.3. This coordinates as a di-deprotonated ligand to metal ions, particularly iron (II) producing in that case an overall neutral complex. Additional axial coordinate bonds to groups on a peptide backbone anchor the complex unit to a biopolymer. Some metal-containing biomolecules also incorporate simple anions such as HO, S2 or CN as part of their coordination spheres.

For polymeric chains, the act of coordination almost invariably requires a change in the shape of the chain as a consequence of satisfying the demands of the metal ion for a preferred stereochemistry and a set of donors with bond distances within a limited range. Thus, coordinate bond formation has consequences that clearly alter the local environment around the metal ion, but may also alter polymer chain conformation over an extended range. Since three-dimensional shape in biopolymers plays a role in function, 'natural' complexation evolved by Nature usually plays a positive role whereas 'unnatural' complexation through the addition of 'foreign' metal ions may be deleterious to function.

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