Amide group linkage

Proteins form in a sequence of condensation reactions in which the amine end of one amino acid combines with the carboxyl end of another, eliminating a water molecule to create an amide linkage. The amide group that connects two amino acids is called a peptide linkage, and the resulting molecule is known as a peptide. When two amino acids are linked, the product is a dipeptide. A dipeptide formed from alanine and glycine is shown in Figure 13-33. 

Figure 1.69 SAMSA is an anhydride compound containing a protected thiol. Reaction with protein amine groups yields amide bond linkages. Deprotection of the acetylated thiol produces free sulfhydryl groups for conjugation.

Figure 1.84 Glutaric anhydride reacts with amines in a ring-opening process to create an amide bond linkage and a terminal carboxylate group.

Figure 3.3 EDC may be used in tandem with sulfo-NHS to create an amine-reactive protein derivative containing active ester groups. The activated protein can couple with amine-containing compounds to form amide bond linkages.

Figure 3.9 An azlactone reacts with amine groups through a ring-opening process, creating amide bond linkages with the attacking nucleophile.

Figure 6.1 The Wedekind trifunctional crosslinker can react with amine groups via its p-nitrophenyl ester to form amide bond linkages. The phenyl azide group then can be photoactivated with UV light to generate covalent bond formation with a second molecule. The biotin side chain provides binding capability with avidin or streptavidin probes.

Cascade Blue cadaverine and Cascade Blue ethylenediamine both contain a carboxamide-linked diamine spacer off the 8-methoxy group of the pyrene trisulfonic acid backbone. The cadaverine version contains a 5-carbon spacer, while the ethylenediamine compound has only a 2-carbon arm. Both can be coupled to carboxylic acid-containing molecules using a carbodiimide reaction (Chapter 3, Section 1). Since Cascade Blue derivatives are water-soluble, the carbodiimide EDC can be used to couple these fluorophores to proteins and other carboxylate-containing molecules in aqueous solutions at a pH range of 4.5-7.5. The reaction forms amide bond linkages (Figure 9.39). 

Figure 9.61 QDs containing carboxylate groups can be coupled to amine-containing proteins or other molecules using the EDC/sulfo-NHS reaction to form amide bond linkages. The intermediate sulfo-NHS ester is negatively charged and will help maintain particle stability due to like charge repulsion between particles.

Figure 10.1 DTPA reacts with amine-containing molecules via ring opening of its anhydride groups to create amide bond linkages. The potential also exists for both anhydride groups to react and cause crosslinking of modified molecules, which is undesirable.

Figure 11.3 The active ester group of NHS-biotin reacts with amine-containing compounds to form amide bond linkages.

The Derivative, 5-(biotinamido)pentylamine, contains a 5-carbon cadaverine spacer group attached to the valeric acid side chain of biotin (Thermo Fisher). The compound can be used in a carbodi-imide reaction process to label carboxylate groups in proteins and other molecules, forming amide bond linkages (Chapter 3, Section 1). However, the main use of this biotinylation reagent is in the determination of factor XHIa or transglutaminase enzymes in plasma, cell, or tissue extracts. 

Figure 18.11 NHS-PEG4-azide can be used to modify an amine-containing molecule to create an amide derivative terminating in azido groups. The azide modifications then can be used in a click chemistry reaction that forms a triazole linkage with an alkyne-containing molecule. Alternatively, the azide derivative can be used in a Staudinger ligation reaction with a phosphine derivative, which results in an amide bond linkage.

Figure 19.15 The carbodiimide EDC can be used in the presence of sulfo-NHS to create reactive sulfo-NHS ester groups on a carrier protein. Subsequent coupling with an amine-containing hapten can be done to create amide bond linkages.

Figure 20.18 The bifunctional chelating reagent DTPA may be used to modify amine groups on antibody molecules, forming amide bond linkages. Indium-111 then may be complexed to the chelator group to create a radiolabeled-targeting reagent.

Figure 22.19 Biotinylated liposomes may be formed using biotinylated PE. Reaction of NHS-LC-biotin with PE results in amide bond linkages and a long spacer arm terminating in a biotin group.

Figure 28.12 Sulfo-SBED first is used to label a bait protein through reaction of the sulfo-NHS ester with available amine groups on the protein, yielding an amide bond linkage. This labeled bait protein then is added to a sample containing proteins that potentially could interact with the bait. After an incubation period, the sample is exposed to UV light to photoactivate the phenyl azide group. This reaction causes any interacting prey proteins to be crosslinked with the bait protein, forming a complex containing a biotin affinity tag.

The third step of ubiquitinylation, the transfer of ubiquitin to the target protein, is catalyzed by a ubiquitin-protein-ligase, or E3 enzyme. In this reaction ubiquitin is linked by its C-terminal glycine in an amide isopeptide linkage to an e-NH2-group of the substrate proteins Lys residues. 

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