Serine peptides, hydrolysis

S. A. Bizzozero, H. Dutler, Stereochemical Aspects of Peptide Hydrolysis Catalyzed by Serine Proteases of the Chymotrypsin Type , Bioorg. Chem. 1981, 10, 46 - 62 ... 

The stereochemical aspects of peptide hydrolysis catalyzed by chymotrypsin and related serine proteases has been recently analyzed with respect to requirements for stereoelectronic control of bond cleavage and this analysis has led to a much more complete understanding of the reaction mechanism (9-14). 

Proteins are hydrolyzed very slowly with storage in water at neutral pH. However, addition of proteases can increase the rate of hydrolysis about 10 billion times over the spontaneous rate. The chymotrypsin mechanism depicted in Figure 2.53 is shared by trypsin and elastase. These three proteases are members of a family called the serine proteases (named after Ser 195), Carboxypeptidase Aand pepsin catalyze peptide hydrolysis by different mechanisms and are not part of this family. 

Figure 1.24 Mechanism of peptide hydrolysis by a serine protease and enzyme inhibition by forming stable tetrahedral intermediate.

As with peptide hydrolysis, several enzyme systems exist that catalyze carboxylic and phosphoric ester hydrolysis without the need for a metal ion. They generally involve a serine residue as the nucleophile in turn, serine may be activated by hydrogen-bond formation—or even proton abstraction—by other acid-base groups in the active site. The reaction proceeds to form an acyl- or phosphory 1-enzyme intermediate, which is then hydrolyzed with readdition of a proton to the serine oxygen. Mechanisms of this type have been proposed for chymotrypsin. In glucose-6-phosphatase the nucleophile has been proposed to be a histidine residue. ... 

Amino-acid Protection. - Carboxyamidomethyl (CAM) esters have been shown to be useful protecting groups in a-chymotrypsin and papain-catalysed peptide hydrolysis and synthesis.5 10 1,3-Dioxans (582) can be obtained from Na-protected serine derivatives by acid-catalysed transacetalation and are sufficiently robust to survive both amino deprotection and peptide coupling reactions. 11 (L)-Histidine benzyl ester can be prepared as the ditosylate salt... 

It is worth noting that hydrolysis of the peptide bond can also occur with other amino acids. For example, salmon calcitonin undergoes hydrolysis at the cysteine -serine peptide bond where the cysteine remains linked to the peptide by a disulfide bond [34]. 

Aldehydes can react with one molecule of an alcohol to form a hemiacetal (see Chapter 11). Because the catalytic site of elastase contains an active serine hydroxyl group, it is reasonable that an aldehyde derivative of a peptide substrate of elastase would react with the serine -OH group to form a hemiacetal, which is a tetrahedral analogue of the transition state of the peptide hydrolysis reaction. (See also Robert C. Thompson and Carl A. Bauer. [1979]. Biochemistry 18, 1552-1558.)... 

Bizzozero SA, Duller H (1981) Stereochemical aspects of peptide hydrolysis catalyzed by serine proteases of the chymotrypsin type. Bioorgan Chem 10 46-62... 

It is reasonable to inquire whether recognition of such a concept might apply to mechanistic ideas about enzyme reactions. It now appears that the stereoelectronic theory that Deslongchamps and co-workers have developed is specifically applicable to peptide hydrolyses by serine proteases. Hydrolysis of simple esters will be used first to illustrate the approach. 

At the C-terminus of the Lon peptide resides Lon s proteolytic domain. Lon is a serine protease and requires a nucleophilic serine for hydrolysis and substrate proteolysis. In the majority of organisms. 

Peptidases or proteases are enzymes that hydrolyse peptide bonds [9]. Proteolytic enzymes can be classified in five classes on basis of their catalytic mechanism aspartic, metallo-, cysteine, threonine and serine peptidases, whereby the latter three follow the same basic mechanism (Scheme 7.3) [10], Another classification of peptidases on the basis of statistically significant similarities in amino acid sequences was presented by Rawlings et al. (MEROPS database) [11], Serine proteases (SP) alone cover approximately one-third of all known proteases, and can accelerate the peptide hydrolysis very efficiently 10 fold) [6,11,12], SPs also hydro-... 

Figure 11.4 Serine proteinases catalyze the hydrolysis of peptide bonds within a polypeptide chain. The bond that is cleaved is called the scissile bond. (Ra) and (Rb)j/ represent polypeptide chains of varying lengths.

FIGURE 5.5 (a) The hydroxy amino acids serine and threonine are slowly destroyed during the course of protein hydrolysis for amino acid composition analysis. Extrapolation of the data back to time zero allows an accurate estimation of the amonnt of these amino acids originally present in the protein sample, (b) Peptide bonds involving hydrophobic amino acid residues snch as valine and isolencine resist hydrolysis by HCl. With time, these amino acids are released and their free concentrations approach a limiting value that can be approximated with reliability. 

Elastase-like proteinases are serine proteinases that recognized peptide residues with linear aliphatic side chains (alanyl, valyl, leucyl or isoleucyl residues) and that effect hydrolysis of the polypeptide chain on the carboxy-terminal side of these residues. Examples of elastase-like proteinase are pancreatic elastase, neutrophil elastase and proteinase-3. 

Serine proteinases are proteinases that utilise the terminal hydroxyl group of the side chain of serine to affect peptide bond hydrolysis. 

FIGURE 11.2 Hydrolysis of esters and peptides by serine proteases reaction scheme (a) and mechanism of action (b) (after Polgar15). (a) ES, noncovalent enzyme-substrate complex (Michaelis complex) EA, the acyl-enzyme PI and P2, the products, (b) X = OR or NHR (acylation) X = OH (deacylation). 

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