Examples, Enzyme Catalysis

Elucidating Mechanisms for the Inhibition of Enzyme Catalysis An inhibitor interacts with an enzyme in a manner that decreases the enzyme s catalytic efficiency. Examples of inhibitors include some drugs and poisons. Irreversible inhibitors covalently bind to the enzyme s active site, producing a permanent loss in catalytic efficiency even when the inhibitor s concentration is decreased. Reversible inhibitors form noncovalent complexes with the enzyme, thereby causing a temporary de-... 

In this chapter we shall illustrate some fundamental aspects of enzyme catalysis using as an example the serine proteinases, a group of enzymes that hydrolyze peptide bonds in proteins. We also examine how the transition state is stabilized in this particular case. 

Many examples are known in the field of enzyme catalysis, the groups HA and B both being situated in the active site of the enzyme. 

Clearly, proximity and orientation play a role in enzyme catalysis, but there is a problem with each of the above comparisons. In both cases, it is impossible to separate true proximity and orientation effects from the effects of entropy loss when molecules are brought together (described the Section 16.4). The actual rate accelerations afforded by proximity and orientation effects in Figures 16.14 and 16.15, respectively, are much smaller than the values given in these figures. Simple theories based on probability and nearest-neighbor models, for example, predict that proximity effects may actually provide rate increases of only 5- to 10-fold. For any real case of enzymatic catalysis, it is nonetheless important to remember that proximity and orientation effects are significant. 

Nitrilases catalyze the synthetically important hydrolysis of nitriles with formation of the corresponding carboxylic acids [4]. Scientists at Diversa expanded the collection of nitrilases by metagenome panning [56]. Nevertheless, in numerous cases the usual limitations of enzyme catalysis become visible, including poor or only moderate enantioselectivity, limited activity (substrate acceptance), and/or product inhibition. Diversa also reported the first example of the directed evolution of an enantioselective nitrilase [20]. An additional limitation had to be overcome, which is sometimes ignored, when enzymes are used as catalysts in synthetic organic chemistry product inhibition and/or decreased enantioselectivity at high substrate concentrations [20]. 

Several dozens of aldolases have been identified so far in nature [23,24], and many of these enzymes are commercially available at a scale sufficient for preparative applications. Enzyme catalysis is more attractive for the synthesis and modification of biologically relevant classes of organic compounds that are typically complex, multifunctional, and water soluble. Typical examples are those structurally related to amino acids [5-10] or carbohydrates [25-28], which are difficult to prepare and to handle by conventional methods of chemical synthesis and mandate the laborious manipulation of protective groups. 

Binding to transport proteins may be of particular interest, since binding not only assays the affinities of the binding site on the transporter protein but also the translocation equilibria [67], In terms of enzyme catalysis, a transport protein transforms a substrate, a molecule located at one side of the membrane, into a product, the same molecule at the other side of the membrane, without chemical modification. Substrate must bind to a particular conformation of the enzyme with the binding sites accessible only from, for example, the outside. Similarly, the release of the product has to occur from a conformation which opens the binding site to the inside only this implies at least one transition step between the two types of conformations (see Fig. 

Baldwin s rules. It is noteworthy that the EM5/EM6 ratio is reduced to a factor as small as about 2, which is less than the intrinsic entropic advantage of 5- over 6-membered ring formation. Kirby (1980) in his review lists a large number of EM data for intramolecular nucleophilic additions to carbonyl. Probably because these data derive from laboratories of chemists mainly interested in intramolecular nucleophilic catalysis and its relevance to understanding enzymic catalysis, the great majority of them refer to reactions occurring via 5- and 6-membered transition states. The only example where a 4-membered transition state is involved is (70), whose kinetics were studied... 

In the field of enzyme catalysis, heme-proteins such as cytochrome P450, for example, exhibit both types of 0-0 bond cleavages in organic hydroperoxides and peroxy acids (178). Heterolytic cleavage of HOOH/ROOH yields H20 or the corresponding alcohol, ROH and a ferryl-oxo intermediate (Scheme 4). Homolytic 0-0 bond cleavage results in the formation of a hydroxyl (HO ) or an alkoxyl (RO ) radical and an iron-bound hydroxyl radical. 

See for example the pioneering work of Breslow Bres-low, R. Dong, S. D. Biomimetic Reactions Catalyzed by Cyclodextrins and their Derivatives Chem. Rev. 1998, 98,1997-2011 and Breslow, R. Biomimetic Chemistiy and Artificial Enzymes - Catalysis by Design Acc Chem. Res. 1995,28,146-153. 

Catalysis by imidazole in aqueous systems has received widespread attention because of its central position as the catalytic group in many hydrolytic enzymes. Many imidazole derivatives with long aliphatic chains have been synthesized and their catalytic role in the presence of detergents has been reported as models of hydrolytic enzymes. Representative examples of the hydrolysis ofp-nitrophenyl acetate (8) are summarized in Table 2. 

Abstract This chapter introduces the basic principles used in applying isotope effects to studies of the kinetics and mechanisms of enzyme catalyzed reactions. Following the introduction of algebraic equations typically used for kinetic analysis of enzyme reactions and a brief discussion of aqueous solvent isotope effects (because enzyme reactions universally occur in aqueous solutions), practical examples illustrating methods and techniques for studying enzyme isotope effects are presented. Finally, computer modeling of enzyme catalysis is briefly discussed. 

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