Modifications of the polypeptide chain

In addition to proteolytic processing (i.e. removal of the signal peptide sequence), the polypeptide is subject to other covalent modifications N- and 0-glycosylation and 0-phosphorylation. After synthesis and transportation across the ER lumen, the proteins pass to the Golgi apparatus and thence, 

The Golgi complex is also the locus of casein micelle formation. In association with calcium, which is actively accumulated by Golgi vesicles, the polypeptide chains associate to form submicelles, and then micelles, prior to secretion. 

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Molecular weights are now readily determined for these molecules with very high precision and accuracy. Variation between the experimental and the predicted MW of a protein (predicted from its DNA code) help in the determination of post-translational modifications of the polypeptide chain. Noncovalent interactions between biomolecules and ligands may also be studied using soft ionization methods. 

A closer examination of these essential residues, including the catalytic triad, reveals that they are all part of the same two loop regions in the two domains (Figure 11.10). The domains are oriented so that the ends of the two barrels that contain the Greek key crossover connection (described in Chapter 5) between p strands 3 and 4 face each other along the active site. The essential residues in the active site are in these two crossover connections and in the adjacent hairpin loops between p strands 5 and 6. Most of these essential residues are conserved between different members of the chymotrypsin superfamily. They are, of course, surrounded by other parts of the polypeptide chains, which provide minor modifications of the active site, specific for each particular serine proteinase. 

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. 

Another potential site of reactivity for anhydrides in protein molecules is modification of any attached carbohydrate chains. In addition to amino group modification in the polypeptide chain, glycoproteins may be modified at their polysaccharide hydroxyl groups to form ester derivatives. Esterification of carbohydrates by acetic anhydride, especially cellulose, is a major industrial application for this compound. In aqueous solutions, however, esterification may be a minor product, since the oxygen of water is about as strong a nucleophile as the hydroxyls of sugar residues. 

Another potential site of reactivity for anhydrides in protein molecules is modification of any attached carbohydrate chains. In addition to amino group modification in the polypeptide chain, glycoproteins may be modified at their polysaccharide hydroxyl groups to form esterified... 

Most of the other posttranslational modifications involving the N- or C-terminus (Table 1) as well as the side-chain functionalities (Table 2) of the polypeptide chains occur under the control of enzymes that also dictate the regioselectivity of such chemical transformations. This regioselectivity is difficult to attain by synthetic procedures. Sophisticated protection schemes are required when additional chemistry must be performed on preassembled peptides, unless enzymatic methods can be used to supplement the synthetic strategies. As a consequence, the use of suitably modified amino acids as synthons is generally the preferred approach as will be discussed in the following sections. 

As discussed for N-myristoylation and S-prenylation, even S-acylation of proteins with a fatty acid which in the vast majority of cases is the C16 0 palmitic acid, plays a fundamental role in the cellular signal-transduction process (Table l). 2-5 14 While N-myristoylation and S-prenylation are permanent protein modifications due to the amide- and sulfide-type linkage, the thioester bond between palmitic acid and the peptide chain is rather labile and palmi-toylation is referred to as a dynamic modification. 64 This reversibility plays a crucial role in the modulation of protein functions since the presence or absence of a palmitoyl chain can determine the membrane localization of the protein and can also be used to regulate the interactions of these proteins with other proteins. Furthermore, a unique consensus sequence for protein palmitoylation has not been found, in contrast to the strict consensus sequences required for N-myristoylation and S-prenylation. Palmitoylation can occur at N- or C-terminal parts of the polypeptide chain depending on the protein family and often coexists with other types of lipidation (see Section 6.4.1.4). Given the diversity of protein sequences... 

How are the possible choices for newly formed proteins made Much seems to depend upon the amino acid sequences at the ends of the polypeptide chains. As they emerge from a ribosome, some N-terminal signal sequences bind to recognition proteins. One such protein labels the ends of proteins destined for secretion into the vesicles of the ER. This protein ensures that the protein end binds to the signal recognition particle (SRP), enters a translocon pore, and undergoes cotranslational passage into the periplasmic space in bacteria or the ER in eukaryotes. Cotranslational modification reactions also occur both in the... 

Recall that collagen is an extracellular matrix protein that serves as a major constituent of many connective tissues (see figs. 4.10 to 4.13). Collagen fibrils have a distinctive banded pattern with a periodicity of 680 A. Individual fibrils are composed of three polypeptide chains wound around one another in a right-handed helix with a total length of 3,000 A. Each of the polypeptide chains in the triple helix has a repetitious tripeptide sequence, Gly-X-Y, where X is frequently a proline and Y is frequently a hy-droxyproline. The latter amino acid is not one of the 20 that are specified genetically, so it must be formed posttransla-tionally by a modification of some of the prolines. 

Another example of post-translational modification is the cleavage of the polypeptide chain. Chymotrypsin is produced in the inactive form, the proenzyme, as chymotrypsinogen. This type of inactive precursor to an enzyme is known as a zymogen. 

Association between elements of the secondary structure form structural domains with properties determined both by the chiral properties of the polypeptide chain and by the packing requirements which effectively minimize the molecule s hydrophobic surface area. Association of domains in proteins results in the formation of the protein s tertiary structure. Furthermore, protein subunits can pack together to form quaternary structure, which can either serve a structural role or provide a structural basis for modification of the protein s functional properties [132]. 

The protein molecule ultimately needed by a cell often differs from the polypeptide chain synthesized. Modification of the synthesized chain occurs in several ways ... 

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