Glutamate residues, predominance

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... 

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. 

Since crystals form through contacts between protein molecules, it can be expected that altering the surface residues on a protein will alter the ability to form crystals. Altering surface residues to allow better crystal surface contacts can work extremely well for improving crystals (D Arcy et al., 1999 Lorber et al., 2002). Two residues in particular, lysine and glutamic acid, seem to be particularly good residues for mutation. Both are found predominantly on the surface of proteins, and both seem to be disfavored in protein-protein interaction surfaces. Since crystals depend on forming contacts between proteins, this approach may improve the crystal contact surfaces of the proteins in the crystal (Mateja et al., 2002). 

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. 

Glutamic acid is an electrically charged amino acid. Charged amino acid residues in membrane proteins possess an environment that is very well defined, that is, they are very rarely present in the membrane and are predominantly located in extramembrane regions. Glutamic acid may be found in the membrane only if its environment possesses a high propensity for finding it in the membrane. 

Type n aldolases are found predominantly in bacteria and fungi, and are Zn " -dependent enzymes (Scheme 2.182) [1378]. Their mechanism of action was recently affirmed to proceed through a metal-enolate [1379] an essential Zn " atom in the active site (coordinated by three nitrogen atoms of histidine residues [1380]) binds the donor via the hydroxyl and carbonyl groups. This facilitates pro-(/ )-proton abstraction from the donor (presumably by a glutamic acid residue acting as base), rendering an enolate, which launches a nucleophilic attack onto the aldehydic acceptor. 

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