Polypeptide chain cleavage

Site of action of some endopeptidases used for polypeptide chain cleavage prior to sequence analysis. Of the four different enzymes used, trypsin is used most frequently because of its high specificity. 

A great deal is known about the photochemistry of carbenes (Chapter 2) and in the cases of the diazirine precursors given here (Table 3.1) it can confidently be predicted that the adducts formed on irradiation with proteins will be stable under most of the conditions necessary for further study (Fig. 2.1). Of course common sense should be exercized, e.g. insertion into carboxyl groups will yield esters which are unstable to hydrolysis or to treatment with hydroxylamine (e.g. Ross et al., 1982), and the possibility of reaction with peptide bonds culminating in polypeptide chain cleavage has already been mentioned (Section 2.1, Fig. 2.2). 

Generally, protein denaturation includes the complete or partial unfolding of the polypeptide chain, cleavage of disulfide linkages, and breakage of noncovalent interactions. Denaturation is sometimes reversible. The reversing process is called renaturation. 

Growing ot a polypeptide chain by attachment ot the first aminoadd to an insoluble polymer and attaching successively amirx>acids At the end cleavage of the peptide from the polymer... 

Figure 4-3. Oxidative cleavage of adjacent polypeptide chains linked by disulfide bonds (shaded) by per-formic acid (left) or reductive cleavage by 3-mercap-toethanol (right) forms two peptides that contain cysteic acid residues or cysteinyl residues, respectively.

The fragmentation of Ca -ATPase by proteolytic enzymes [42,85,235,236] and by vanadate-catalyzed photocleavage [104,105] occurs at well defined and conforma-tionally sensitive cleavage sites that delineate functional domains within the Ca -ATPase. The functional changes that follow the cleavage of the polypeptide chain provide useful hints about the role of various domains in the mechanism of Ca transport. 

Figure 12.5 Proteolytic cleavage of prothrombin by factor Xa, yielding active thrombin. Although prothrombin is a single-chain glycoprotein, thrombin consists of two polypeptides linked by what was originally the prothrombin intrachain disulfide bond. The smaller thrombin polypeptide fragment consists of 49 amino acid residues, and the large polypeptide chain contains 259 amino acids. The N-terminal fragment released from prothrombin contains 274 amino acid residues. Activation of prothrombin by Xa does not occur in free solution, but at the site of vascular damage...

As mentioned earlier, by far the largest number of zinc enzymes are involved in hydrolytic reactions, frequently associated with peptide bond cleavage. Carboxypeptidases and ther-molysins are, respectively, exopeptidases, which remove amino acids from the carboxyl terminus of proteins, and endopeptidases, which cleave peptide bonds in the interior of a polypeptide chain. However, they both have almost identical active sites (Figure 12.4) with two His and one Glu ligands to the Zn2+. It appears that the Glu residue can be bound in a mono- or bi-dentate manner. The two classes of enzymes are expected to follow similar reaction mechanisms. 

The NC-IUBMB classifies peptidases (EC 3.4) into exopeptidases (EC 3.4.11-19), which remove one or a few amino acids, and endopeptidases (proteinases, EC 3.4.21-99), which catalyze the cleavage of peptide bonds away from either end of the polypeptide chain (Fig. 2.1). Exopeptidases are further subdivided into enzymes that carry out hydrolysis at the N-terminus or the C-terminus (Figs. 2.1 and 2.2). Thus, aminopeptidases (EC 3.4.11) cleave a single amino acid from the N-terminus [3] those removing a dipep-... 

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