Specificity of enzyme catalysis

Enzymes are highly specific and usually catalyze only one type of reaction. Some enzymes show absolute specificity. For example, pyruvate kinase catalyzes the transfer of a phosphate group only from phosphoenolpyruvate to adenosine diphosphate during glycolysis (Chapter 13). Examples of enzymes that show less specificity are  

Many enzymes show stereoisomeric specificities. For example, human a-amylase catalyzes the hydrolysis of glucose from the linear portion of starch but not from cellulose. Starch and cellulose are both polymers of glucose, but in the former the sugar residues are connected by q (1 4) linkages, whereas in the latter they are con- 

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As already stated, Fischer was deeply intrigued by the phenomenon of enzyme activity. He realized that the substances were proteins and this undoubtedly was why he next undertook the study of amino acids and peptides. He fully appreciated that the specificity of enzyme catalysis depended on the occurrence of a complementarity for interacting dissymmetric surfaces. In this regard, he wrote (3) ... 

Enzymes are structurally complex, highly specific catalysts each enzyme usually catalyzes only one type of reaction. The enzyme surface binds the interacting molecules, or substrates, so that they are favorably disposed to react with one another (fig. 1.15). The specificity of enzyme catalysis also has a selective effect, so that only one of several potential reactions takes place. For example, a simple amino acid can be used in the synthesis of any of the four major classes of macromolecules or can simply be secreted as waste product (fig. 1.16). The fate of the amino acid is determined as much by the presence of specific enzymes as by its reactive functional groups. 

In the 1960 s and 1970 s, much indirect evidence was obtained in favour of protein intramolecular mobility, i.e. the entropy and energy specificity of enzyme catalysis (Likhtenshtein, 1966, 1976a, b, 1979, 1988 Lumry and Rajender, 1970 Lumry and Gregory, 1986). The first observations made concerned the transglobular conformational transition during substrate-protein interaction (Likhtenshtein, 1976), the reactivity of functional groups inside the protein globule, and proteolysis. 

In the recent past, multianalyte determination has found increased applications, i.e. specific and multiple reactions favor a system that allows the specific determination of each reaction, using the same principal measurement methods, detectors and conditions. In keeping with this idea, a flow injection thermometric method based on an enzyme reaction and an integrated sensor device was proposed for the determination of multiple analytes. In principle the technique relies on the specificity of enzyme catalysis and the universality of... 

Examples of this sort are not unusual, although most biochemists would accept the high specificity of enzyme catalysis as axiomatic. However, this does not imply that there is a one-to-one relationship between the enzyme and the specific reaction. A good case can be made for suggesting that the enzymes which are responsible for some metabolic pathways are multifunctional (section 6.3.2). This feature of their catalysis, coupled with our poor understanding of their behaviour outside of a wholly aqueous environment, suggests that enzyme catalysis may have more to offer the organic chemist than we presently realize. 

In concluding this chapter, it should be noted that we have presented various models of enzyme mechanisms in which metal ions participate. We have seen that reactions catalyzed by metalloenzymes or enzymes activated by metal ions span a remarkably broad spectrum of reaction types. Of course many facets such as the remarkable speed and specificity of enzyme catalysis have not received complete explanation on the basis of model system chemistry. However, the missing link may be found at the point where biological molecules deviate from the model systems. Here, perhaps the most interesting chemical features will be found (258,259). 

Fig. 1.11 Specificity of enzyme catalysis. (From httpMsls-text3.c.u-tokyo.ac.jp/large fig/fig04 05.html. Copyright 2011 Division of Life Sciences, Komaba Organization for Educational Excellence, College of Arts and Sciences, The University of Tokyo).

The chemical reaction catalyzed by triosephosphate isomerase (TIM) was the first application of the QM-MM method in CHARMM to the smdy of enzyme catalysis [26]. The study calculated an energy pathway for the reaction in the enzyme and decomposed the energetics into specific contributions from each of the residues of the enzyme. TIM catalyzes the interconversion of dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde 3-phosphate (GAP) as part of the glycolytic pathway. Extensive experimental studies have been performed on TIM, and it has been proposed that Glu-165 acts as a base for deprotonation of DHAP and that His-95 acts as an acid to protonate the carbonyl oxygen of DHAP, forming an enediolate (see Fig. 3) [58]. 

As with chemical synthesis, the first step when prospecting for a particular biotransformation is to perform a literature search to check whether a suitable precedent has been described. Extensive technical literature resources in the public domain provide both examples of specific enzyme-catalysed reactions and descriptions of transformations where enzyme activity is inferred if not explicitly described. Currently, searches of online databases such as PubMed reveal over 2000 new publications per annum in the subject of enzyme catalysis (excluding reviews). 

The outstanding characteristic of enzyme catalysis is that the enzyme specifically binds its substrates, with the reactions taking place in the confines of... 

Complexation could occur in many different ways, but for the intimate com-plexation required for catalysis, the enzyme must have, or must be able to assume, a shape complementary to that of the substrate. Originally, it was believed that the substrate fitted the enzyme somewhat like a key in a lock this concept has been modified in recent years to the induced-fit theory, whereby the enzyme can adapt to fit the substrate by undergoing conformational changes (Figure 25-18), Alternatively, the substrate may be similarly induced to fit the enzyme. The complementarity is three-dimensional, an important factor in determining the specificity of enzymes to the structure and stereochemical configuration of the substrates. 

General-Base and General-Acid Catalysis Avoids the Need for Extremely High or Low pH Electrostatic Interactions Can Promote the Formation of the Transition State Enzymatic Functional Groups Provide Nucleophilic and Electrophilic Catalysis Structural Flexibility Can Increase the Specificity of Enzymes... 

The extraordinary specificity of enzymatic catalysis is due to the shape recognition. Enzymes are proteins having a stereospecific binding site. At this site, the two reactants (in the above example, D-glucose and oxygen) are brought together in a precise and favorable orientation for the reaction to take place. 

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