Peptide bonds proton-catalyzed hydrolysis

Such a difference in partial double-bond character has implications for the mechanism, and, hence, the reaction rate, of acid-catalyzed hydrolysis (Fig. 6.15). In delocalized peptide bonds (Fig. 6.15,a), protonation involves the carbonyl O-atom with its partial negative charge. In non-delocalized peptide bonds (Fig. 6.15,b), protonation involves the N-atom, which is rendered more basic by the lack of delocalization [73],... 

Activation reactions catalyzed by serine proteases (including kallikreins) are an example of limited proteolysis in which the hydrolysis is limited to one or two particular peptide bonds. Hydrolysis of peptide bonds starts with the oxygen atom of the hydroxyl group of the serine residue that attacks the carbonyl carbon atom of the susceptible peptide bond. At the same time, the serine transfers a proton first to the histidine residue of the catalytic triad and then to the nitrogen atom of the susceptible peptide bond, which is then cleaved and released. The other part of the substrate is now covalently bound to the serine by an ester bond. The charge that develops at this stage is partially neutralized by the third (asparate) residue of the catalytic triad. This process is followed by deacylation, in which the histidine draws a... 

Stage 2 Water adds to the carbonyl group of the peptide bond. The rate of this nucleophilic addition is accelerated by coordination of the carbonyl oxygen to Zn and/or to one of the N—protons of Arg-127 (not shown). The product is a tetrahedral intermediate stabilized by coordination to zinc. Stabilization of the tetrahedral intermediate may be the major factor for the rapid rate of the carboxypeptidase-catalyzed hydrolysis. 

Hybrid potentials have been used to understand the mechanism of the human immunodeficiency virus (HIV) protease with the ultimate aim of being able to help in the design of inhibitors which could be useful as AIDS therapies. This enzyme, which catalyzes the hydrolysis of peptide bonds, is a homodimer. Its active center is at the interface of the two chains and consists of two catalytic aspartic acid residues from identical positions in each of the two chains. Although the aspartates are equivalent in the sequence, they are not equivalent when the substrate is present. It is known that when the enzyme is active one of the aspartic residues is protonated and it is thought that there is a lytic water molecule that is also involved in the catalysis. 

As an example of application to a reaction involving a macromolecule, we indicate below the transition state obtained by the combined classical quantum force field in a study of the peptide hydrolysis reaction catalyzed by thermolysin. The subsystem is limited to the substrate, a water molecule, a zinc atom, the side chains of His 143, Glul66, the whole glutamic acid and the histidine 146 moieties (see Figure 10). The transition state represented here corresponds to the proton transfer from Glul43 to the nitrogen atom of the peptidic bond before the breaking of the bond. 

Fig. 31. Mechanistic proposal for peptide hydrolysis catalyzed by carboxypeptidase A (Christianson and Lipscomb, 1989). (a) The precatalytic Michaelis complex with substrate carbonyl hydrogen bonded to Arg-127 allows for nucleophilic attack by a water molecule promoted by zinc and assisted by Glu-270 (an outer-sphere C==O Zn interaction is not precluded), (b) Tbe stabilized tetrahedral intermediate collapses, with required proton donation by Glu-270 (Monzingo and Matthews, 1984) Glu-270 may play a bifunctional catalytic role (Schepartz and Breslow, 1987), which results in the product complex (c). [Reprinted with permission from Christianson, D. W., Lipscomb, W. N. (1989) Acc. Chem. Res. 22,62-69. Copyright 1989 American Chemical Society.]...

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. ... 

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