Aspartate residues, predominance

Access of iron to the interior of the protein could be through channels, which traverse the shell along the three- and four-fold axes of symmetry of the protein. The three-fold channels are predominantly hydrophilic, with three glutamate and three aspartate residues at each end of the funnel-shaped channel. In contrast, the four-fold channels are essentially lined with hydrophobic residues. 

Further insights into the influence of pH on the reactivity at aspartic acid residues are provided by a study of the model peptide Val-Tyr-Pro-Asp-Gly-Ala (Fig. 6.28,a) [93], At pH 1 and 37°, the tm value for degradation was ca. 450 h, with cleavage of the Asp-Gly bond predominating approximately fourfold over formation of the succinimidyl hexapeptide. At pH 4 and 37°, the tm value was ca. 260 h due to the rapid formation of the succinimidyl hexapeptide, which was slowly replaced by the iso-aspartyl hexapeptide. Cleavage of the Asp-Gly bond was a minor route. At pH 10 and 37°, the tm value was ca. 1700 h, and the iso-aspartyl hexapeptide was the only breakdown product seen. In Sect. 6.3.3.2, we will compare this peptide with three analogues to evaluate the influence of flanking residues. 

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... 

TOF-TOF instruments can also analyse small intact proteins but this instrument leads to low sequence coverage. Indeed, as observed for CID, proteins above 5000 Da produce sequential b and y fragment ions principally at the termini of the protein. Nevertheless, the most predominant fragment ions correspond to cleavage at the C-terminal to aspartic or glutamic acid residues and at the N-terminal to proline residues in the protein [73],... 

GcL contains 544 amino acids in a single chain folded into one domain, making it one of the largest structural domains observed to date in a protein. Like RmL, GcL is an a structure with a central, predominantly parallel jS sheet. There are 11 strands in the central sheet, 3 more in a small additional sheet, and 17 a helices (Fig. 2). The catalytic Ser-217, a part of the G-X-S-X-G pentapeptide, is located at a tight turn between the C terminus of a /3 strand and an N terminus of an a helix, exactly as observed in RmL. The hydroxyl of Ser-217 is hydrogen bonded to the imidazole of His-463, which in turn donates a hydrogen bond to Glu-354. Thus, GcL constitutes the first known example of a serine hydrolase in which the acid residue of the triad is a glutamate and not an aspartate. 

Sericin, the protein that binds the pairs of fibroin filaments as they emerge from the silkworm, and which may have a role in dehydrating the fibroin and encouraging its crystallisation, has a markedly different composition and structure to that of fibroin. It is largely amorphous and is rich in serine (—32%), aspartic acid (—14%) and glycine (—13%) there is a much greater proportion of residues with polar and/or bulky side-chains. The predominance of these polar, hydrophilic groups means that sericin is readily soluble in hot water. 

Elevated levels of isoaspartate residues have been noted within aged proteins. A extracted from parenchyma contains predominantly isoaspartate residues at positions 1 and 7. The aspartic acid residue at position 23 seems largely unaffected, perhaps because of steric protection by the neighbouring valine. It was found that synthetic A with these substitutions resulted in more stable -sheets. These two alterations are found near the beginning and... 

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