C-terminal carboxyl group

Amidation refers to the replacement of a protein s C-terminal carboxyl group with an amide group (COOH — CONH2). This PTM is usually characteristic of peptides (very short chains of amino acids), as opposed to the longer polypeptides, but one therapeutic polypeptide (salmon calcitonin, Chapter 11) is amidated, and amidation is required for full functional activity. Overall, the function(s) of amidation is not well understood, although in some cases at least it appears to contribute to peptide/polypeptide stability and/or activity. 

It should be noted that the majority of the derivatization techniques modify the peptide s N-terminus. The reason is that the N-terminal amine group is easier to modify than the C-terminal carboxyl group. Also, due to differences in pKa value in the e-amino group of lysine, there are possible reaction that modify the N-terminus only, while the lysine side chains remain intact. Modifications of carboxyl groups... 

U. H. Mortensen, S. J. Remington, K. Breddam, Site-Directed Mutagenesis on (Serine) Carboxypeptidase Y. A Hydrogen Bond Network Stabilizes the Transition State by Interaction with the C-Terminal Carboxylate Group of the Substrate , Biochemistry 1994, 33, 508-513. 

In addition to the 0-methylation of aspartate and glutamate residues, the C-terminal carboxyl group of GTPases are methylated. In the G-protein family C-terminal cysteines are prenylated at the sequence CZZX, where Z is a hydrophobic amino acid and X represents any residue. Once the ZZX sequence is cleaved by a special protease, the isoprenylcysteine carboxymethyltransferase (Icmt) methylates the C-terminal carboxyl group and effectively creates a more hydrophobic enzyme. ... 

Alterobactin A is a cyclodepsipeptide from Alteromonas luteoviolacea, with A -DHB-(4S),8-diamino-(3/ )-hydroxy-octanolyl-D-Ser-Gly-L-Arg-L-f/ireo-3-hydroxy-Asp-Gly-L-f/treo-3-hydroxy-Asp having an ester bond between the C-terminal carboxyl group and Ser. It is accompanied by its hydrolysis product alterobactin B (Fig. 8, 26, 27) (298). Alterobactin A forms a 1 1 complex with Fe " with an... 

Fig. 2.15A. Pattern of ubiquitinylation of proteins and degradation in the proteosome. Ubiquitin (Ub)is initially activated by an enzyme El, whereby the C-terminal carboxyl group of ubiquitin becomes attached to a SH group of El via a thioester bond. Ubiquitin is then transferred from El-Ub to E2, from which it is transferred with the help of E3 to the target protein. Several ubiquitin molecules can attach to the target protein in a hnear or in a crosshnked fashion. The mono- or polyubiquitinylated protein is degraded to peptides in the 26S proteosome. In the above diagram the filled circles represent the ubiquitin residues attached to the target protein. K lysine residues of the target protein.

Rather than perform individual syntheses of all possible combinations of these nonpeptide units, members of each ring type or scaffold family were pooled in equimolar amounts prior to incorporation into the sequence DArg-Arg-X-Y-Arg. Since each individual member of a given pool was constructed on a similar carbocyclic scaffold, the chemical environment of the N-terminal amino group and C-terminal carboxylate groups were expected to follow similar kinetic and thermodynamic controls during the attachment of the nonpeptide residue to the growing peptide chain. The use of these smaller, directed libraries made it readily practical to obtain HPLC and mass spectral data for each and therefore confirm the composition of the library. 

A third lipid anchor is provided by the polyprenyl farnesyl (15-carbon) and geranylgeranyl (20-carbon) groups in thioether linkage to cysteine residues. These must be present in specific recognition sequences at the C termini of proteins, most often with the sequence CAAX.211-215 The prenylation (also called isoprenyla-tion) reaction is followed by proteolytic removal of the last three residues (AAX) and methylation of the new C-terminal carboxyl group as is discussed in Chapter 11, Section D,3. See also Chapter 22, Section A,4. 

Comparison of the deduced sequence of A. saitoi carboxypeptidase with other known serine carboxypeptidase sequences shows that they share a low degree of similarity 32% with wheat carboxypeptidase II, 32.3% with malt carboxypeptidase II and 26.2% with yeast carboxypeptidase Y (Figure 19) [88], However, all of the sequences conserve the catalytic domains (indicated by boxes II to IV in Figure 19) and the domain (box I in the Figure 19) which contains the amino acid residues recognizing the C-terminal carboxylate group of peptide substrates. There are also present in the sequence ten potential sites for N-linked glycosylation. 

During solid phase synthesis peptides are bound to the solid support by means of the C-terminal carboxyl group. The properties of the anchor group positioned between the growing oligomer and the solid support are crucial for the success of a solid phase synthesis. Usually, specialised linkers are used which provide either peptide carboxylic acids or peptide carboxylic amides upon cleavage [4]. A cleavage mechanism that proceeds by a nucleophilic attack... 

The attachment of the first amino acid is a special procedure in both Fmoc-and t-Boc-chemistry if the intended peptide should contain a C-terminal carboxyl group. However, the stepwise synthesis in both Fmoc- and t-Boc chemistry follows the same general outline. 

Some uncertainties exist concerning the attachment of the sugar molecules and the exact formula of the hydroxy acid. The C-terminal carboxyl group of D-alanine is linked as an ester to a hydroxyl group of one of the sugar molecules. 

A series of glycosylphosphatidylinositol (GPI) anchors that are covalently linked to a variety of proteins utilize diacylglycerol or alkylacylglycerol for attachment to a bilayer. The proteins are joined through their C-terminal carboxyl groups to the diacylglycerol by a chain of covalently linked ethano-lamine, phosphate, mannose, glucosamine, and myo-inositol as shown in Fig. The proteins are linked... 

B. The side chains of the amino acid residues in proteins contain functional groups with different pKs. Therefore, they can donate and accept protons at various pH values and act as buffers over a broad pH spectrum. There is only one N-terminal amino group (pK=9) and one C-terminal carboxyl group (pK= 3) per polypeptide chain. Peptide bonds are not readily hydrolyzed, and such hydrolysis would not provide buffering action. Hydrogen bonds have no buffering capacity. 

A recently developed method for lsO-based quantification of peptides uses catalysis with hydrochloric acid instead of standard proteases for labeling. Unlike proteolytic labeling, acid catalysis labels all carboxyl groups present in a peptide (Asp, Glu, carboxymethylated Cys, C-terminal carboxyl groups). Thus, most peptides labeled by this strategy have a mass difference >4 Da, making data analysis simpler and more reliable than conventional proteolytic labeling approaches (104). 

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