Amidation, posttranslational

Fig. 6 Sequence alignment of the deduced amino acid sequence from the identified cDNA encoding PBAN and related peptides from Helicoverpa zea and Bombyx mori. The putatively expressed peptides are shown in boxes. The conserved amino acids are underlined in the B. mori sequence. Putative proteolytic posttranslational processing sites are shown in bold with glycine contributing the C-terminal amide. Sequences of PBAN-like peptides are also shown in Table 1. GenBank accession numbers H. zea - PI 1159 and B. mori - BAA05971...

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. 

Some proteins can be posttranslationally modified by the addition of prenyl groups. Prenyl groups are long-chain, unsaturated hydrocarbons that are intermediates in isoprenoid synthesis. The farnesyl group has 15 carbons, and the geranylgeranyl has 20 carbons. They are attached to a cysteine residue near the end of the protein as a thiol ether (Protein-S-R). Other proteins can have a long-chain fatty acid (C14=myristoyl, C16=palmitoyl) attached to the amino terminus as an amide. These fatty acid modifications can increase the association of proteins with the membrane. 

The most common posttranslational modifications, discussed in the following sections, include phosphorylation, sulfation, disulfide formation, N-methylation, O-methylation, S-methylation, N-acetylation, hydroxylation, glycosylation, ADP-ribosylation, prenylation, biotinylation, lipoylation, and phosphopan-tetheine tethering. Many of the posttranslational modifications are proven to be cross talks. Other modifications exist in a smaller extent and include oxidation of methionine, C-methylation, ubiquitylation, carboxylation, and amidation. These topics will not be covered in this chapter which is meant to focus primarily on the recent literature (2005-08). For a more complete coverage of all posttranslational modifications and earlier literature (up to 2005), the reader is referred to Professor Christopher T. Walsh s book Posttranslational Modification of Proteins Expanding Nature s Inventory ... 

Other kinds of modifications may be necessary to convert a newly synthesized protein to its biologically active form. The N-formyl group of the initiating methionine in prokaryotes is removed by a deformylase. A methionine amino-peptidase removes the initiating residue in many eukaryotic proteins. Other posttranslational modifications may include acetylation, amidation, hydroxy lation, methylation, phosphorylation, and sulfation of specific amino acid resi-... 

The elements of protein structure are divided into four classes primary, secondary, tertiary, and quaternary. Primary structure refers to the linear sequence of amino acids linked by amide bonds along protein chains. These polymer chains vary in length from a few amino acid residues (oligopeptides) to molecules containing 2000 or more amino acids. Most proteins are from 100 to 500 amino acid residues in length. One or more of each of 20 natural amino acids may be present in each protein molecule. In some cases the amino acids undergo posttranslational chemical modification, which introduces still more variety into protein structure. 

Many a.a. residues undergo posttranslational enzymatic amidation, hydroxyla-tion, oxidation, esterification, glycosylation, methylation, or cross-linking. Some segments of the polypeptide chains may be removed (Figure 7.1). Modified residues in a given protein can be used for analytical purposes, e.g., hydroxyproline (ProOH), which is characteristic for collagens. 

Very little lipoate exists in the cell as the free acid unless the cell is supplemented with substantial quantities of the molecule. Instead, it is found almost exclusively in its cofactor form, appended in an amide linkage to a specific lysyl residue on an LCP. The pathways in E. coli by which LCPs are posttranslationally modified with lipoic acid have recently begun to be illuminated and then extended to other organisms through comparative bioinformatics, and biochemical and genetic approaches. E. coli and many other organisms use two distinct routes for the construction of the lipoyl cofactor (Figure 9). One route, often referred to as the... 

This folding is influenced by many surroimding proteins, by the state of glycosylation of side chains, and by other posttranslational modifications, by the presence of cis amide linkages in unfolded or folded forms (pp. 82,83 Box 9-F), and by possibility for formation of disulfide bridges (pp. 521,522). ... 

As discussed in Chapter 6, transmembrane proteins usually have a number of posttranslational modifications that provide additional chemical groups to fulfill requirements of the three-dimensional structure. The amino terminus (residues 1-34) extends out of the membrane and has branched high mannose oligosaccharides linked through N -glycosidic bonds to the amide of asparagine (see Fig. 7.10). It is anchored in the lipid plasma membrane by a palmitoyl group that forms a thioester with the SH residue of a cysteine. The COOH terminus, which extends... 

Contains an unusual ring to the N-end amine group, which forces the CO-NH amide sequence into a fixed conformation. Can disrupt protein folding structures like a-hetix or P sheet, forcing the desired kink in the protein chain. Common in collagen, where it often undergoes a posttranslational modification to hydroxyproline. Uncommon elsewhere. 

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