Amino acids coordinating side chains

The predominance of aspartate and glutamate residues in the Ca -coordination spheres of proteins was quantified in Section III,D. They constitute 29% and 18%, respectively, of the Ca " -coordinating ligands from the proteins presented in Table II. An analysis of the hydrogenbonding networks around the Ca -binding sites of these proteins (Color Plate 2 and Fig. 7) indicates several reasons for the prevalence of these negatively charged amino acids. The side-chain carboxylate moiety of... 

Amino acids with coordinating side-chains such as methionine (and the binding sites of some metals in metalloproteins) are described in more detail in Chapter 20.2. 

Amino Acids with Non-coordinating Side Chains 740... 

Amino Acids with Coordinating Side Chains 746... 

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. 

Figure 1 Schematic structure of some amino acids with coordination side chains, and prothetic groups found in metalloproteins.

In the case of the common peptides the comparison of the stability constants of zinc(II) and cadmium(II) complexes reveals the same trends as reported for the amino acids Favored complexation with zinc(II) in almost all cases, except for the thiolate ligands. The binding of several side chain residues may enhance the stability of cadmium(II) complexes but the extent of this stabihzation is relatively low. This is true even for the aspartyl or histidyl residues which are generally considered as the most strongly coordinating side chains in the corresponding... 

FIGURE 27.19 Proposed mechanism of hydrolysis of a peptide catalyzed by carboxypeptidase A. The peptide is bound at the active site by an ionic bond between its C-terminal amino acid and the positively charged side chain of arginine-145. Coordination of Zn to oxygen makes the carbon of the carbonyl group more positive and increases the rate of nucleophilic attack by water. 

Electrochemical studies performed in the 7 x Cys-Aspl4 D. afri-canus Fdlll indicate that the reduced [3Fe-4S] center can react rapidly with Fe to form a [4Fe-4S] core that must include noncysteinyl coordination (101). The carboxylate side chain of Asp 14 was proposed as the most likely candidate, since this amino acid occupies the cysteine position in the typical sequence of a 8Fe protein as indicated before. The novel [4Fe-4S] cluster with mixed S and O coordination has a midpoint redox potential of 400 mV (88). This novel coordinated state with an oxygen coordination to the iron-sulfur core is a plausible model for a [4Fe-4S] core showing unusual spin states present in complex proteins (113, 114). 

Natural a-amino acids provide a moderately effective N,OJ chelating donor set derived from carboxylate and amino groups, respectively. Several side-chain donor atoms may also be involved in metal ion coordination, especially those of Cys (thiol sulfur) and His (imidazole nitrogen(s)). (Abbreviations for amino acid residues are those recommended by IUPAC-IUB.1702)... 

In addition to the backbone donor system the amino acid residues can contain a variety of donor centers (679E). The most important of these are the imidazole N atoms of His, the S atom of Cys, and to some extent the, 3-carboxylate O atom of Asp. Other side chain donors like the O atoms of Ser and phenolic O atoms of Tyr or amino N atoms of Lys are of minor importance for coordination of Ni11 ions. Also, thioether S-donors of Met play only a minor role in the interactions with Ni11 ions.1730... 

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