Side-chains of peptides

Many enzymes contain small nonprotein molecules and metal ions that participate directly in substrate binding or catalysis. Termed prosthetic groups, cofactors, and coenzymes, these extend the repertoire of catalytic capabilities beyond those afforded by the limited number of functional groups present on the aminoacyl side chains of peptides. 

Solid-Phase Glycosylation of the Hydroxy Side Chain of Peptides... 

As discussed in Section 9.4.4, the incorporation of a metal ligand binding group in the side chain of peptidic structures can be used to induce and stabilize secondary structures and in the development metallopeptide molecular devices. Along these lines and based on the unique complexing ability toward metal cations of EDTA, several amino acids containing aminodiacetic adds have been reported. 

The question sometimes arises as to why multiple frameworks are desirable in antibody Hbraries. There is a good reason why nature uses more than one framework in the antibody repertoire. As already mentioned above, antigens not only contact the CDRs, but also framework residues (Fig. 2.3). For example, large antigens make additional contact to the outer loop, or CDR4 mentioned above, while small haptens, but also side chains of peptide antigens, often bind in a deep cavity near the pseudo-2-fold axis of the antibody [15]. 

Figure 9.2.12 Typical arrangement of side chains of peptides. (From Voyer and Lamothe, 1995.)...

The vibrational transitions of protein side-chain groups are highly localized (Table 7.7), therefore they can be applied directly to investigate the side chains of peptides and proteins (Singh, 2000). 

The technique of isobaric tag for relative and absolute quantification (iTRAQ) is based on covalently labeling the amines at N-termini and the side chains of peptides with isotope-coded tags after the proteins have been isolated form biological systems, denatured, and enzymatically digested. Here the isotope labeling is carried out at a much later stage than in both SILAC and ICAT. iTRAQ is an MS/MS technique that uses CID-derived ions for both the identification and quantification of proteins. 

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 ammo 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... 

Fig. 3. (a) Chemical stmcture of a synthetic cycHc peptide composed of an alternating sequence of D- and L-amino acids. The side chains of the amino acids have been chosen such that the peripheral functional groups of the dat rings are hydrophobic and allow insertion into Hpid bilayers, (b) Proposed stmcture of a self-assembled transmembrane pore comprised of hydrogen bonded cycHc peptides. The channel is stabilized by hydrogen bonds between the peptide backbones of the individual molecules. These synthetic pores have been demonstrated to form ion channels in Hpid bilayers (71). 

The most important aspect of Table 27.1 is that the 20 anino acids that occur in proteins share the common feature of being a-anino acids, and the differences fflnong them are in their side chains. Peptide bonds linking carboxyl and a-anino groups characterize the structure of proteins, but it is the side chains that are mainly responsible for theh properties. The side chains of the 20 commonly occuning amino acids encompass both large and small differences. The major differences between amino acid side chains concern ... 

Thermitase, pH 7.5, 55°, 50% DMSO, 3-140 min. This method was used to avoid the degradation of base-sensitive side chains during peptide synthesis. The method is compatible with the Fmoc group. ... 

Aspaityl proteinases are proteinases that utilize the terminal carboxyl moiety of the side chain of aspartic acid to effect peptide bond hydrolysis. 

Cleavage of a peptide bond is an example of a nucleophilic attack. The nucleophile in the reaction is either an activated water molecule or part of the side-chain of an amino acid, and peptidases are described as having either a water nucleophile or a protein nucleophile. Peptidases with a water nucleophile either utilize one or two metal ions as ligands for the water molecule, in which case the peptidase generally acts... 

It is known that native collagen contains tripeptide sequences which, because of being homopolypeptides, are not able to give rise to triple-helical tertiary structures (e.g. Gly-Pro-Leu, Gly-Pro-Ser). The reason for this and for the above-mentioned low thermostability of the synthetic homopolypeptides is presumably to be found in the fact that in the case of the model peptides with their monotonously repeated tripeptide sequences, special interactions between the side chains of the different amino acid residues as postulated by Ward and Mason are no more possible157). 

Peptoids are an archetypal and relatively conservative example of a peptidomimetic oligomer (Tab. 1.1). In fact, the sequence of atoms along the peptoid backbone is identical to that of peptides. However, peptoids differ from peptides in the marmer of side chain appendage. Specifically, the side chains of peptoid oligo-... 

For the synthesis and structural studies of /9-peptides, Seebach and coworkers have prepared acycHc /9-amino acids with different substitution pattern (including /9A, y 3,3, 3,3 -amino acids) and with the side chains of natural... 

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