Side chains amino acid, metal-binding

Figure 3.1 Principal protein amino acid side-chain metal-ion binding modes (the metal ion represented as a dark filled circle) and (right) the structure of the Ca2+-binding y-carboxyglutamate found in proteins of the blood-clotting cascade.

Transition metals such as iron can catalyze oxidation reactions in aqueous solution, which are known to cause modification of amino acid side chains and damage to polypeptide backbones (see Chapter 1, Section 1.1 Halliwell and Gutteridge, 1984 Kim et al., 1985 Tabor and Richardson, 1987). These reactions can oxidize thiols, create aldehydes and other carbonyls on certain amino acids, and even cleave peptide bonds. The purposeful use of metal-catalyzed oxidation in the study of protein interactions has been done to map interaction surfaces or identify which regions of biomolecules are in contact during specific affinity binding events. 

The major metal-binding amino acid side chains in proteins (Gurd and Wilcox, 1956 see Voet and Voet, 1990) (Table II) are carboxyl (aspartic acid and glutamic acid), imidazole (histidine), indole (tryptophan), thiol (cysteine), thioether (methionine), hydroxyl (serine, threonine, and tyrosine), and possibly amide groups (asparagine and glutamine, although... 

The specific amino acid side chains on a-lactalbumin responsible for binding to the metal support are not known however, a-lactalbumin is a metalloprotein. Under physiological conditions, it carries one Ca(II) per molecule hence, there are metal binding sites on the protein. Column-bound a-lactalbumin is eluted by a solution of the free ligand imidazole. A flowchart outlining these procedures is shown in Figure E4.3. 

The chemical modification studies have thus not yet led to a much more conclusive picture of the active site than that outlined in Fig. 12, and the identification of amino acid side chains involved in catalysis or substrate binding may have to await the completion of the crystal structure determination. The reporter properties of the Co(II) enzyme clearly show, however, that an open coordination position is of decisive functional importance, that the metal ion is intimately associated with the basic group participating in the reaction, and that the metal ion is probably also involved in the binding of one of the substrates, HCO3. 

The binding of metal ions to peptides and proteins is a consequence of these molecules containing a great number of potential donor atoms through both the peptide backbone and amino acid side chains. The complexes formed exist in a variety of conformations that are sensitive to the pH environment of the complex [2,3]. With at least 20 amino acid combinations available, some with coordinating side chains, which can be linked in any particular order and length, the number of ligands that... 

The selectivity of peptide motifs for certain metals comes from the coordinating contribution from amino acid side chains, the common coordination number of the metal, hardness/softness of the metal ion, ligand field stabilisation effects and the hardness/softness of any coordinating side chains of the amino acid sequence. An example of the influence of side chains and the importance of the position of the side chain comes from the tripeptides Gly-Gly-His, also known as copper binding peptide. The side chain imidazole ring of the His residue has a very efficient nitrogen donor (the imidazole N), which can form a tetradentate chelate ring for coordination as in Scheme 10.3. 

A helical structure can be stabilized by introducing ligand units to the amino acid side-chains. On addition of appropriate metal ions the a-helix (Figure 1.3.3A) is formed by use of the metal as a cross-linking unit [5]. Attachment of metal binding sites to the end of well-chosen decapentapeptides and coordination of the random coil peptide to appropriate metal ions leads to induction of an a-helix... 

The particular arrangement of an enzyme s amino acid side chains in the active site determines the type of molecules that can bind and react there there are usually about five such side chains in any particular enzyme. In addition, many enzymes have small nonprotein molecules associated with or near the active site that determine substrate specificity. These molecules are called cofactors if they are noncovalently linked to the protein they are called prosthetic groups if covalently bound. In some enzymes a specific metal ion is required for activity. 

Because cobalt(III) complexes bind to the N-terminal amino acid residue of peptides, only the N-terminal peptide bond is hydrolyzed. It would be advantageous if the metal complex could coordinate to various parts of a peptide chain, thus allowing for cleavage of other areas of the peptide chain. Recently this has become an active area of research, and there have been several publications on the cleavage of the polypeptide backbone of proteins promoted by metal complexes. The advantage that these complexes have over the cobalt(III) complexes is that they can be selectively introduced on to various amino acid side chains, allowing for cleavage of peptide bonds at locations other than the N-terminus. This is of interest because,... 

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