Hydrolysis, peptide bond

Aspaityl proteinases are proteinases that utilize the terminal carboxyl moiety of the side chain of aspartic acid to effect peptide bond hydrolysis. 

Bada, XL., Schoeninger, M.J. and Schimmelmann, M. 1989 Isotopic fractionation during peptide bond hydrolysis. Geochimica et CosmochimicaActa 53 3337-3341. 

M. N. James, and A. R. Sielecki, Stereochemical analysis of peptide bond hydrolysis catalyzed by the aspartic proteinase penicillopepsin, Biochemistry 24 3701 (1985). 

Fig. 3.10. Mechanism of peptide bond hydrolysis by pepsin, an aspartic endopeptidase [2]...

The present chapter focuses on specific aspects of these challenges, namely peptide bond hydrolysis (chemical and enzymatic) and intramolecular reactions of cyclization-elimination (Fig. 6.4). This will be achieved by considering, in turn a) the enzymatic hydrolysis of prodrugs containing a peptide pro-moiety (Sect. 6.2), b) the chemical hydrolysis of peptides (Sect. 6.3), c) the enzymatic hydrolysis of peptides containing only common amino acids (Sect. 6.4), d) the hydrolysis of peptides containing nonproteinogenic amino acids (Sect. 6.5), and, finally, e) the hydrolysis of peptoids, pseudopeptides and peptidomimetics (Sect. 6.6). 

The individual contributions of the H20, H+, and HO- catalysts to the mechanism of the reaction were further evaluated by means of the kinetics parameters (Table 6.4). At neutral pH, Reactions a and c were both dominated by fcH2<> The second-order rate constants ku+ and kHO- were identical, indicating similar efficiencies of the H+ and HO catalysts. Interestingly, the second-order rate constants for the hydrolysis of Gly-D-Val (6.48) to yield Gly and D-Val (6.49) (Reaction b) could also be calculated (Table 6.4). The similarity to the corresponding rate constants of Reactions a and c suggests that the rate of peptide bond hydrolysis is not particularly sensitive to substitution at or protonation of the flanking amino and carboxy groups [69],... 

The tripeptides in Fig. 6.17 underwent a few breakdown reactions (N-ter-minus elimination, Qm formation, peptide bond hydrolysis), some of which will be considered later in this section. Of relevance here was that, of the two amidated tripeptides, the amide at the C-terminus underwent deamidation predominantly (Fig. 6.17, Reaction a), which, perhaps, explains the somewhat lesser stability compared to the free carboxylic acid forms. While the hexapeptide (6.52, Fig. 6.17) followed a different pattern of decomposition [76b], deamidation was also a predominant hydrolytic reaction at all pH values. Thus, the procedure to extrapolate results from small model peptides to larger medicinal peptides appears to be an uncertain one, since small modifications in structure can cause large differences in reactivity. 

Under mildly acidic (pH 4-5) and neutral (pH 6-8) conditions, isomerization to the iso-aspartyl peptide predominated over peptide bond hydrolysis. However, an additional pathway was observed under these conditions,... 

A. Radzicka, R. Wolfenden, Rates of Uncatalyzed Peptide Bond Hydrolysis in Neutral Solution and the Transition State Affinities of Proteases , J. Am. Chem. Soc. 1996, 118, 6105 - 6109. 

R. A. Kenley, N. W. Warne, Acid-Catalyzed Peptide Bond Hydrolysis of Recombinant Human Interleukin 11 , Pharm. Res. 1994, 11, 72-76. 

Whereas standard proteases use serine, cysteine, aspartate, or metals to cleave peptide bonds, the proteasome employs an unusual catalytic mechanism. N-terminal threonine residues are generated by self-removal of short peptide extensions from the active yS-subunits and act as nucleophiles during peptide-bond hydrolysis [23]. Given its unusual catalytic mechanism, it is not surprising that there are highly specific inhibitors of the proteasome. The fungal metabolite lactacystin and the bacterial product epoxomicin covalently modify the active-site threonines and in-... 

Proteasome jS-subunits are synthesized with N-terminal extensions and are inactive because a free N-terminal threonine is required for peptide-bond hydrolysis [130]. The precursor jS-subunits assemble with a-subunits to form half proteasomes com-... 

The arrangement of S965, H746, and the oxyanion hole suggests that the classical steps of peptide-bond hydrolysis follow the sequence of the trypsin-like serine proteases, namely the formation of the tetrahedral adduct, the acyl-enzyme complex, and hydrolysis. Tricorn has been shown to exhibit both tryptic and chymotryp-tic specificities (Tamura et al. 1996a). The X-ray structure reveals that specificity for basic PI residues is conferred by D936 which is provided by the diad-related subunit (see Figures 10.9 and 10.10). 

Radzicka, A. and Wolfenden, R. (1996). Rates of uncatalyzed peptide bond hydrolysis in neutral solution and the transition state affinities of proteases. J. Am. Chem. Soc.,... 

Many enzymic reactions have high negative AG° values, for example glycosyl or peptide bond hydrolysis reactions in aqueous media, oxidations with oxygen as substrate etc. Some thermodynamic data of industrially applied enzymic reactions are described by Bmns and Schulze (1962), Tewari (1990) and Biselli, Kragl and Wandrey (1995). 

For comparison, the solubility-pH profile of the deamidated protein was added to the plot containing the profiles for the pronase E-treated proteins (Figure 5). The deamidated protein, with 2.6% peptide bond hydrolysis, showed improved minimum solubility, comparable to the protein with 5.7% peptide bond hydrolysis and no deamidation. The shape of solubility-pH profile for the deamidated sample resembled that of the intact protein more than those of the pronase E-treated samples. For the deamidated sample, both the increase in solubility and the slight shift of minimum solubility to the acid side were the result of the increase in negative charges from deamidation. Obviously, deamidation was more capable of maintaining the original protein structure than proteolysis, which is essential for the development of desirable functional properties. 

Figure 3. Deamidation and peptide bond hydrolysis of soy protein during germination of soybean seeds.

In limited proteolysis, proteases such as pronase E hydrolyzed the 7S subunits of soy proteins more than the IIS subunits, resulting in enhanced protein solubility. Deamidation with relatively insignificant peptide bond hydrolysis that occurred during the germination of soybeans imparted to the storage protein improved solubility and emulsifying activity. On the other hand, the incorporation of phosphorus in soy proteins by the protein kinase cAMPdPK was too low to effect significant... 

Proteolysis. Proteolysis is the cleavage of amide bonds that comprise the backbone of proteins and peptides. The reaction can occur spontaneously in aqueous medium under acidic, neutral, or basic conditions. This process is accelerated by proteases, ubiquitous enzymes that catalyze peptide-bond hydrolysis at rates much higher than occur spontaneously. In humans, these enzymes only recognize sequences of L-amino acids but not d-amino acids. They are found in barrier tissues (nasal membranes, stomach and intestinal linings, vaginal and respiratory mucosa, ocular epithelium), blood, all internal solid organs, connective tissue, and fat. The same protease may be present in multiple sites in the body. 

There is no evidence that the overall compositional changes in the enamel at any stage of development is principally due to compositional changes in the individual protein and peptide component per se. It is proposed that if peptide bond hydrolysis occurs during enamel maturation, it is catalyzed in part by the enamel crystals290. ... 

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