Mechanisms enzyme-catalyzed

Knowing how the protein chain is folded is a key ingredient m understanding the mechanism by which an enzyme catalyzes a reaction Take carboxypeptidase A for exam pie This enzyme catalyzes the hydrolysis of the peptide bond at the C terminus It is... 

Enzyme-Catalyzed Reactions Enzymes are highly specific catalysts for biochemical reactions, with each enzyme showing a selectivity for a single reactant, or substrate. For example, acetylcholinesterase is an enzyme that catalyzes the decomposition of the neurotransmitter acetylcholine to choline and acetic acid. Many enzyme-substrate reactions follow a simple mechanism consisting of the initial formation of an enzyme-substrate complex, ES, which subsequently decomposes to form product, releasing the enzyme to react again. 

Enzymes. Protein engineering has been used both to understand enzyme mechanism and to selectively modify enzyme function (4,5,62—67). Much as in protein stabiUty studies, the role of a particular amino acid can be assessed by replacement of a residue incapable of performing the same function. An understanding of how the enzyme catalyzes a given reaction provides the basis for manipulating the activity or specificity. 

The pH dependency of enzyme-catalyzed reactions also exhibits an optimum. The pH optima for enzyme-catalyzed reactions cover a wide range of pH values. Eor instance, the subtihsins have a broad pH optima in the alkaline range. Other enzymes have a narrow pH optimum. The nature of the pH profile often gives clues to the elucidation of the reaction mechanism of the enzyme-catalyzed reaction. The temperature at which an experiment is performed may affect the pH profile and vice versa. 

FIGURE 27.4 The mechanism of transamination. All the steps are enzyme-catalyzed. 

One class of enzymes that follow a ping-pong-type mechanism are aminotransferases (previously known as transaminases). These enzymes catalyze the transfer of an amino group from an amino acid to an a-keto acid. The products are a new amino acid and the keto acid corresponding to the carbon skeleton of the amino donor ... 

Any or all of these mechanisms may contribute to the net rate acceleration of an enzyme-catalyzed reaction relative to the uncatalyzed reaction. A thorough understanding of any enzyme would require that the net acceleration be accounted for in terms of contributions from one or (usually) more of these mechanisms. Each of these will be discussed in detail in this chapter, but first it is important to appreciate how the formation of the enzyme-substrate (ES) complex makes all these mechanisms possible. 

If the enzyme-catalyzed reaction is to be faster than the uncatalyzed case, the acceptor group on the enzyme must be a better attacking group than Y and a better leaving group than X. Note that most enzymes that carry out covalent catalysis have ping-pong kinetic mechanisms. 

Figure 29 14 MECHANISM Mechanism of the enzyme-catalyzed, PLP-dependent transamination of an a-amino acid to give an a-keto acid. Individual steps are explained in the text.

Hart, R. C., Stempel, K. E., Boyer, P. D., and Cormier, M. J. (1978). Mechanism of the enzyme-catalyzed bioluminescent oxidation of coelenterate-type luciferin. Biochem. Biophys. Res. Commun. 81 980-986. 

An example for proteases are the (3-lactamases that hydrolyse a peptide bond in the essential (3-lactam ring of penicillins, cephalosporins, carbapenems and monobac-tams and, thereby, iireversibly inactivate the diug. 13-lactamases share this mechanism with the penicillin binding proteins (PBPs), which are essential enzymes catalyzing the biosynthesis of the bacterial cell wall. In contrast to the PBPs which irreversibly bind (3-lactams to the active site serine, the analogous complex of the diug with (3-lactamases is rapidly hydrolyzed regenerating the enzyme for inactivation of additional (3-lactam molecules. 

The kinetics of enzyme reactions were first studied by the German chemists Leonor Michaelis and Maud Menten in the early part of the twentieth century. They found that, when the concentration of substrate is low, the rate of an enzyme-catalyzed reaction increases with the concentration of the substrate, as shown in the plot in Fig. 13.41. However, when the concentration of substrate is high, the reaction rate depends only on the concentration of the enzyme. In the Michaelis-Menten mechanism of enzyme reaction, the enzyme, E, and substrate, S, reach a rapid preequilibrium with the bound enzyme-substrate complex, ES ... 

Figure 3. Mitochondrial fatty acid oxidation. Long-chain fatty acids are converted to their CoA-esters as described in the text, and their fatty-acyl-groups transferred to CoA in the matrix by the concerted action of CPT 1, the acylcarnitine/carnitine exchange carrier and CPT (A) as described in the text. Medium-chain and short-chain fatty acids (Cg or less) diffuse directly into the matrix where they are converted to their acyl-CoA esters by a acyl-CoA synthase. The mechanism of p-oxidation is shown below (B). Each cycle of P-oxidation removes -CH2-CH2- as an acetyl unit until the fatty acids are completely converted to acetyl-CoA. The enzymes catalyzing each stage of P-oxidation have different but overlapping specificities. In muscle mitochondria, most acetyl-CoA is oxidized to CO2 and H2O by the citrate cycle (Figure 4) some is converted to acylcamitine by carnitine acetyltransferase (associated with the inner face of the inner membrane) and exported from the matrix. Some acetyl-CoA (if in excess) is hydrolyzed to acetate and CoASH by acetyl-CoA hydrolase in the matrix. Enzymes ...

Enzymes act as catalysts in biological systems to effectively regulate the rate of reactions and determine which products are formed. Enzyme-catalyzed reactions are often described by the Michaelis-Mentin mechanism that is represented by the following steps ... 

Mildvan AS, Grisham CM (1974) The Role of Divalent Cations in the Mechanism of Enzyme Catalyzed Phosphoryl and Nucleotidyl. 20 1-21 Mingos DMP, Hawes JC (1985) Complementary Spherical Electron Density Model. 63 1-63 Mingos DMP, Johnston RL (1987) Theoretical Models of Cluster Bonding. 68 29-87 Mingos DMP, McGrady JE, Rohl AL (1992) Moments of Inertia in Cluster and Coordination Compounds. 79 1-54... 

Another consequence of application of organic solvents as a reaction medium is associated with the mechanism of enzyme-catalyzed transformations. According to the commonly accepted mechanism, the first product of the interaction of a hydrolytic (serine) enzyme with an ester is an O-acylenzyme (Scheme 5.4). When the reaction is performed in an aqueous solution, water acts as a nucleophile in the next step, to give acid B. If more nucleophilic hydrogen peroxide is present in the reaction mixture, peroxycarboxylic acids C are formed. However, in organic solvents the O-acylenzyme also reacts readily with other nucleophiles, such as... 

Information relevant to the mechanism of an enzyme-catalyzed reaction can, in general, only be obtained from irreversible inhibitors which react specifically at the active site and thereby inactivate the enzyme. As active-site-directed inhibition is treated in detail in Ref. 142 general aspects will be discussed here only briefly. In order to be suitable as an active-site-directed inhibitor, a compound must fulfil the following requirements. 

Figure 15-8. Mechanisms of control of an enzyme-catalyzed reaction. Circled numbers indicate possible sites of action of hormones. .Alteration of membrane permeability conversion of an inactive to an active enzyme, usually in-...

Such a pathway has both flow and direction. The enzymes catalyzing nonequilibrium reactions are usually present in low concentrations and are subject to a variety of regulatory mechanisms. However, many of the reactions in metabolic pathways cannot be classified as equilibrium or nonequilibrium but fall somewhere between the two extremes. 

ALLOSTERIC HORMONAL MECHANISMS ARE IMPORTANT IN THE METABOLIC CONTROL OF ENZYME-CATALYZED REACTIONS... 

ALASl. This repression-derepression mechanism is depicted diagrammatically in Figure 32-9. Thus, the rate of synthesis of ALASl increases greatly in the absence of heme and is diminished in its ptesence. The turnover rate of ALASl in rat liver is normally rapid (half-life about 1 hour), a common feature of an enzyme catalyzing a rate-limiting reaction. Heme also affects translation of the enzyme and its transfer from the cytosol to the mitochondrion. 

E---S + R E---P->E + P The enzyme is regenerated at the end of this sequence, making it available to bind another substrate molecule. Note that the steps in this enzyme-catalyzed biochemical mechanism are similar to the steps in chemical heterogeneous catalysis binding with bond weakening, reaction at the bound site, and release of products. 

The mechanism predicts that the rate of this reaction depends on the concentrations of enzyme (E) and the reactant that binds to it (S) but does not depend on additional reactants (R). This makes sense from a mechanistic point of view provided there is enough of R present that the third step proceeds rapidly once distortion is complete. Experimentally, many enzyme-catalyzed reactions obey this form of rate law. 

As described in Section 15.7, enzymes are the catalysts of biological reactions. Without enzymes, most of the reactions that occur in a cell would be imperceptibly slow. Cations of transition metals play essential roles in the mechanisms of many enzyme-catalyzed reactions. Here we introduce just one representative example, superoxide dismutase. 

Leuenberger, M.G., Engeloch-Jarret, C., and Woggon, W.-D., The reaction mechanism of the enzyme-catalyzed central cleavage of P-carotene to retinal, Angew. Chem. Int. Ed, 40, 2613, 2001. 

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