Polypeptide chain termination requirements

Figure 39-15. The leucine zipper motif. A shows a helical wheel analysis of a carboxyl terminal portion of the DNA binding protein C/EBP. The amino acid sequence is displayed end-to-end down the axis of a schematic a-helix. The helical wheel consists of seven spokes that correspond to the seven amino acids that comprise every two turns of the a-helix. Note that leucine residues (L) occur at every seventh position. Other proteins with "leucine zippers" have a similar helical wheel pattern. B is a schematic model of the DNA binding domain of C/EBP. Two identical C/EBP polypeptide chains are held in dimer formation by the leucine zipper domain of each polypeptide (denoted by the rectangles and attached ovals). This association is apparently required to hold the DNA binding domains of each polypeptide (the shaded rectangles) in the proper conformation for DNA binding. (Courtesy ofS McKnight)...

As suggested above, the presence of an N-terminal Ser or Thr in a protein can be used to generate a reactive carbonyl group. This will be at a unique site, as there is only one N-terminus per polypeptide chain. Furthermore, that site is exactly the one required for there to be contiguity of the backbone of the chimeric molecule under construction. 

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... 

A large number of components are required for the synthesis of a polypeptide chain. These include all the amino acids that are found in the finished product, the mRNA to be translated, tRNAs, functional ribosomes, energy sources, and enzymes, as well as protein factors needed for initiation, elongation, and termination of the polypeptide chain. 

The N-terminal portion of the 522-residue polypeptide chain of colicin El appears to be required for transport into the membrane and the central part for binding to the receptor the channelforming property is characteristic of the C-terminal region.k A similar organization has been established for the smaller colicin N translocation domain, (residues 1-66), receptor domain, (residues 67-182), and pore-forming domain (residues 183-387). 

The start of protein synthesis is signalled by specific codon-anticodon interactions. Termination is also signalled by a codon in the mRNA, although the stop signal is not recognized by tRNA, but by proteins that then trigger the hydrolysis of the completed polypeptide chain from the tRNA. Just how the secondary and tertiary structures of the proteins are achieved is not yet clear, but certainly the mechanism of protein synthesis, which we have outlined here, requires little modification to account for preferential formation of particular conformations. 

Determining the order of amino acids involves the sequential removal and identification of successive amino acid residues from one or the other free terminal of the polypeptide chain. However, in practice it is extremely difficult to get the required specific cleavage reaction of the desired products to proceed with 100% yield. This obstacle becomes significant when sequencing long polypeptides, because the fraction of the total material of minimum polypeptide chain length becomes constantly smaller as the successive removal of terminal residues continues. Conversely, the amino acid released from the polypeptide chain becomes increasingly contaminated with amino acids released from previously unreacted chains. 

A procollagen triple helix is assembled in the endoplasmic reticulum helix formation is aided by disulfide bonds between N- and C-terminal propeptides, which align the polypeptide chains. Post-translational modification of procollagen is crucial in allowing for collagen fibril formation. For example, in cells deprived of ascorbate, as in the disease scurvy, the procollagen chains are not hydroxylated sufficiently to form stable triple helices at normal body temperature (hydrox-ylation is through the activity of prolyl hydroxylase, which requires the cofactor ascorbic acid). 

The action of these two pancreatic exopeptidases on synthetic substrates, proteins, and peptides has been reviewed in detail by Neurath (1960). The specificity requirements which were deduced from studies with synthetic peptides have been confirmed by studies with polypeptides. The structural requirements of specific substrates for both types of carboxy-peptidase are analogous except for the nature of the amino acids which contain the free, ionized a-carboxyl group at the terminus of the substrate. Carboxypeptidase B hydrolyzes most rapidly those bonds formed by terminal lysyl and arginyl residues, whereas carboxypeptidase A hydrolyzes terminal bonds formed by a variety of aromatic, neutral, or acidic amino acids. Of the natural amino acids only carboxyl-terminal prolyl residues are resistant to the action of the enzyme. The rate of hydrolysis depends upon the nature of the side chains of the amino acids which form the susceptible bonds. Thus, differences in the rate of hydrolysis of different substrates may vary several thousandfold. The methods for application of these peptidases to hydrolysis of proteins have been discussed in detail by Canfield and Anfinsen (1963). 

Selenium is incorporated into Se-requiring enzymes by the modification of serine. This serine is not modified when it is in the free state or when it occurs in a polypeptide chain. The serine residue in question is modified when it occurs boimd to transfer RNA, that is, eis the aminoacyl-tRNA derivative. Seryl-tRNA is converted to selenocysteinyl-tRNAby the action of selenocysteine synthase (Stur-chler et al, 1993). The codon for selenocysteine is UGA (TGA in DNA UGA in mRNA). The fact that this particular triplet of bases codes for an amino acid is very imusual, as UGA normally is a stop codon. Stop codons occur in mRNA and signal the termination of synthesis of the protein however, in the case of the UGA codons that code for selenocysteine residues, regions of the mRNA that lie beyond the coding sequence somehow convert the UGA from a codon that halts translation to one that codes for selenocysteine (Figure 10.55). The structure of selenocysteine is shown in Figure 10.56. 

CHAPTER 36, FIGURE 6 Cofactor proteins, factor V and factor VIII. Factor V and factor VIII coagulant (not the von Willebrand factor carrier of factor VIII) contain six distinct structural domains. The two A domains. A, and Aj at the N-terminal end of the polypeptide chain, are separated from the Aj domain by a highly glycosylated B domain. The two C domains are at the C-terminal end of the molecule. The A domain sequences are homologous to the A domains of ceruloplasmin. Both factor Va and factor Villa act as catalysts in the activation of prothrombin and factor X, respectively. Activation sites are indicated by green arrows inactivation sites by red arrows. In factor Va, complete inactivation requires cleavage of Arg ° . 

The cycle of peptide-chain elongation continues until one of the three stop codons (UAA, UAG, UGA) is reached. There is no aminoacyl-tRNA complementary to these codons, and instead a termination factor or a release factor (RF) with bound GTP binds to the ribosome and induces hydrolysis of both the aminoacyl-linkage and GTP, thereby releasing the completed polypeptide chain from the ribosome. The 475 amino acid-long sequence of rabbit liver RF has been deduced from its cDNA sequence, and it shows 90% homology with mammalian trypto-phanyl-tRNA synthetase (Lee et al., 1990). It has also been reported that for efficient and accurate termination, an additional fourth nucleotide (most commonly an A or a G) after the stop codon is required (Tate and Brown, 1992). The exact role of the fourth nucleotide in the termination of protein synthesis is not fully understood at present. 

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