Peptide covalent bonding

The primary structure of enzymes is determined by peptide covalent bonds joining each amino acid to the neighboring one, as well as by disulfide bonds joining sulfur atoms in two cysteine radicals. 

A Peptide Covalent Bond Between Carbon Nanotube and DNA... 

The substrate specificity of enzymes shows the following differences. The occurrence of a distinct functional group in the substrate is the only prerequisite for a few enzymes, such as some hydrolases. This is exenqtlified by nonspecific lipases (cf. Table 3.21) or peptidases (cf. 1.4.5.2.1) which generally act on an ester or peptide covalent bond. 

Since the peptide units are effectively rigid groups that are linked into a chain by covalent bonds at the Ca atoms, the only degrees of freedom they have are rotations around these bonds. Each unit can rotate around two such bonds the Ca-C and the N-Ca bonds (Figure 1.6). By convention the angle of rotation around the N-Ca bond is called phi (<[)) and the angle around the Ca-C bond from the same C atom is called psi (y). 

By changing Ser 221 in subtilisin to Ala the reaction rate (both kcat and kcat/Km) is reduced by a factor of about 10 compared with the wild-type enzyme. The Km value and, by inference, the initial binding of substrate are essentially unchanged. This mutation prevents formation of the covalent bond with the substrate and therefore abolishes the reaction mechanism outlined in Figure 11.5. When the Ser 221 to Ala mutant is further mutated by changes of His 64 to Ala or Asp 32 to Ala or both, as expected there is no effect on the catalytic reaction rate, since the reaction mechanism that involves the catalytic triad is no longer in operation. However, the enzyme still has an appreciable catalytic effect peptide hydrolysis is still about 10 -10 times the nonenzymatic rate. Whatever the reaction mechanism... 

The peptide linkage is usually portrayed by a single bond between the carbonyl carbon and the amide nitrogen (Figure 5.3a). Therefore, in principle, rotation may occur about any covalent bond in the polypeptide backbone because all three kinds of bonds (N——C, and the —N peptide bond) are sin-... 

By far the majority of carbohydrate material in nature occurs in the form of polysaccharides. By our definition, polysaccharides include not only those substances composed only of glycosidically linked sugar residues but also molecules that contain polymeric saccharide structures linked via covalent bonds to amino acids, peptides, proteins, lipids, and other structures. 

A second kind of covalent bonding in peptides occurs when a disulfide linkage, RS-SR, is formed between two cysteine residues. As we saiv in Section 18.8, a disulfide is formed by mild oxidation of a thiol, RSH, and is cleaved by mild reduction. 

DNA synthesizers operate on a principle similar to that of the Merrifield solid-phase peptide synthesizer (Section 26.8). In essence, a protected nucleotide is covalently bonded to a solid support, and one nucleotide at a time is added to the growing chain by the use of a coupling reagent. After the final nucleotide has been added, all the protecting groups are removed and the synthetic DNA is cleaved from the solid support. Five steps are needed ... 

Alkylating agent, a reactive chemical that forms a covalent bond with chemical moieties on the biological target (usually a protein). For instance, p-haloalkylamines generate an aziridinium ion in aqueous base that inserts into -SH, -CHOH, or other chemical structures in peptides. Once inserted, the effects of the alkylating agent are irreversible. 

Macromolecules are formed from many fragments of smaller molecules which are connected to each other by covalent bonds. For example, protein molecules are assembled from amino acids which are interconnected by peptide bonds (see Fig. 4.1). Typical amino acids are given in Fig. 4.2. 

Ni(salen)-DNA adduct formation is closely related to that formed by the Ni(peptide) systems, although there are different mechanisms proposed for both types of complexes. In the case of Ni(salen), the addition of a phenol radical to the guanine heterocycle and formation of a covalent bond to guanine C8 (Equation (9)) is suggested. 

A peptide linker-chelate analog, glycyl-tyrosyl-lysine-N-e-DTPA (GYK-DTPA), was incorporated onto B72.3 antibody and labeled with 11 In and 90y.81,82 In vitro and in vivo evaluations in dogs were conducted. Results indicated that the 11 in chelate was stable in vivo however, the 90Y version showed a biphasic decay pattern. The covalent bond between the peptide and DTPA precluded use of one of the coordinating arms that is necessary to coordinate 90Y in a stable fashion. 

Figure 16.3 Conceptual illustration of two peptides before (left) and after (right) a chemical reaction with formaldehyde. The amino acids are represented as circles. In this particular peptide, a tyrosine (Y) is located within the epitope (shaded circles). An arginine (R) is located elsewhere in the peptide. Formaldehyde results in the formation of a covalent bond between the two residues, due to a Mannich condensation reaction, as shown on the right. The new configuration prevents antibodies from binding to the epitope on the left. 

However, all of these studies were performed using model components in vitro—none have examined formaldehyde-induced modifications in vivo. Further, while modification sites have been mapped by MS/MS, intact cross-linked peptide species have not been observed in such experiments.49 This possibly indicates that the covalent bonds of the formaldehyde cross-links are not as strong as those of the peptide backbone. The resulting fragment ion spectra are similar to that of the unmodified peptide with the exception of 12Da or 30Da additions at modifications sites. Thirty Dalton modifications correspond to the addition of formaldehyde while 12 Da modifications indicate water elimination. 

Biosynthesis of the polypeptide chain is realised by a complicated process called translation. The basic polypeptide chain is subsequently chemically modified by the so-called posttranslational modifications. During this sequence of events the peptide chain can be cleaved by directed proteolysis, some of the amino acids can be covalently modified (hydroxylated, dehydrogenated, amidated, etc.) or different so-called prosthetic groups such as haem (haemoproteins), phosphate residues (phosphoproteins), metal ions (metal-loproteins) or (oligo)saccharide chains (glycoproteins) can be attached to the molecule by covalent bonds. Naturally, one protein molecule can be modified by more means. 

The rational synthesis of peptide-based nanotubes by self-assembling of polypeptides into a supramolecular structure was demonstrated. This self-organization leads to peptide nanotubes, having channels of 0.8 nm in diameter and a few hundred nanometer long (68). The connectivity of the proteins in these nanotubes is provided by weak bonds, like hydrogen bonds. These structures benefit from the relative flexibility of the protein backbone, which does not exist in nanotubes of covalently bonded inorganic compounds. 

Finally, special mention must be made of Cys, which, when present alone, can be considered to belong to the polar uncharged group described above. It can, however, when correctly positioned within the three-dimensional (3-D) structure of a protein, form disulfide bridges with another Cys residue (Figure 4.2). These are the only covalent bonds, apart from the peptide bond of course, that we usually find in proteins2. 

Depending on the structure calculation program used, special covalent bonds such as disulfide bridges or cyclic peptide bonds have to be enforced by distance constraints. Disulfide bridges may be fixed by restraining the distance between the two sulfur atoms to 2.0-2.1 A and the two distances between the Cb and the sulfur atoms of different residues to 3.0-3.1 A [7]. 

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