Specificity, enzymes towards substrates

Les.), and Couceiro, de Almeida, and Freire (1953) have localized it histo-chemically in the electrical tissue of Electwphorus electricus L. The distribution of carbonic anhydrase in several tissues of two teleosts and its inhibition in vivo by the sulfonamides have been investigated by Maetz (1953a,b). The presence of cathepsin in the stomachs of various animals including pike and trout has been established by Buchs (1954). A new advance has also been made in the comparative study of pepsin. This enzyme, previously crystallized from salmon (Norris and Elam, 1940), halibut (Eriksen, 1943), and shark (Sprissler, 1942), has now been crystallized from three species of tuna (Norris and Mathies, 1953). These interesting researches have shown that fish pepsins differ in crystal structure, amino acid composition, and specificity from swine or bovine pepsins and show a closer relationship to one another. As pointed out by Velick and Udenfriend (1953), specificity requirements toward substrates are less exacting with extracellular enzymes. 

The study of evolutionary trees seems to indicate that almost no natural selection was invoked in the choice of proteins [1]. The selection appears to be random. One thus tends to think the selection was guided by the stability of the protein and the efficiency in the active site region. A different view has emerged recently. The synthesis of proteins after all went through a selection process, but one implemented at the molecular level, and the fitness was determined by none other than water. We describe and develop this view briefly here. The process of selection by elimination of error in protein synthesis is known as kinetic proofreading (KPR), which is applied generally to the selectivity of enzymes towards substrate absorption and conversion to product. However, more specifically, it applies to the avoidance of error in protein synthesis. Here we shall first discuss KPR from a general point of view, with application to protein synthesis and DNA replication. 

Each enzyme has a working name, a specific name in relation to the enzyme action and a code of four numbers the first indicates the type of catalysed reaction the second and third, the sub- and sub-subclass of reaction and the fourth indentifies the enzyme [18]. In all relevant studies, it is necessary to state the source of the enzyme, the physical state of drying (lyophilized or air-dried), the purity and the catalytic activity. The main parameter, from an analytical viewpoint is the catalytic activity which is expressed in the enzyme Unit (U) or in katal. One U corresponds to the amount of enzyme that catalyzes the conversion of one micromole of substrate per minute whereas one katal (SI unit) is the amount of enzyme that converts 1 mole of substrate per second. The activity of the enzyme toward a specific reaction is evaluated by the rate of the catalytic reaction using the Michaelis-Menten equation V0 = Vmax[S]/([S] + kM) where V0 is the initial rate of the reaction, defined as the activity Vmax is the maximum rate, [S] the concentration of substrate and KM the Michaelis constant which give the relative enzyme-substrate affinity. 

Classical bacterial exotoxins, such as diphtheria toxin, cholera toxin, clostridial neurotoxins, and the anthrax toxins are enzymes that modify their substrates within the cytosol of mammalian cells. To reach the cytosol, these toxins must first bind to different cell-surface receptors and become subsequently internalized by the cells. To this end, many bacterial exotoxins contain two functionally different domains. The binding (B-) domain binds to a cellular receptor and mediates uptake of the enzymatically active (A-) domain into the cytosol, where the A-domain modifies its specific substrate (see Figure 1). Thus, three important properties characterize the mode of action for any AB-type toxin selectivity, specificity, and potency. Because of their selectivity toward certain cell types and their specificity for cellular substrate molecules, most of the individual exotoxins are associated with a distinct disease. Because of their enzymatic nature, placement of very few A-domain molecules in the cytosol will normally cause a cytopathic effect. Therefore, bacterial AB-type exotoxins which include the potent neurotoxins from Clostridium tetani and C. botulinum are the most toxic substances known today. However, the individual AB-type toxins can greatly vary in terms of subunit composition and enzyme activity (see Table 2). 

Regulation of Flavonoid Synthesis in C. americanum. Biosynthesis of methylated flavonol glucosides seems to be under tight regulation, not only by the substrate specificity of the enzymes involved, but also by other factors, among which are (a) the strict position specificity of these enzymes towards their hydroxylated or partially methylated substrates (b) the apparent difference in microenvironment of the different methyl-transferases, whereby those earlier in the pathway utilized aglycones whereas later enzymes accepted only glucosides as substrates (c) the subtle characteristic differences in methyl-transferases with respect to their pH optima, pi values and requirement for Mg ions, despite their similar molecular size ... 

Zinc proteases carboxypeptidase A and thermolysin have been extensively studied in solution and in the crystal (for reviews, see Matthews, 1988 Christianson and Lipscomb, 1989). Both carboxypeptidase A and thermolysin hydrolyze the amide bond of polypeptide substrates, and each enzyme displays specificity toward substrates with large hydrophobic Pi side chains such as phenylalanine or leucine. The exopeptidase carboxypeptidase A has a molecular weight of about 35K and the structure of the native enzyme has been determined at 1.54 A resolution (Rees et ai, 1983). Residues in the active site which are important for catalysis are Glu-270, Arg-127, (liganded by His-69, His-196, and Glu-72 in bidentate fashion), and the zinc-bound water molecule (Fig. 30). 

As modified so far the polyethylenimines, in contrast to enzymes, are weak in structural specificity toward substrates. This need not be a defect, however, for these macromolecular catalysts do not have to operate in a cellular environment and hence need not be subject to constraints designed to maintain the stability of a very complex, integrated biochemical network. Nevertheless, circumstances may arise where substrate specificity may be an essential requirement. We have some ideas on how this might be achieved with these relatively elastic macromolecular frameworks. For example, preliminary experiments show that we can attach —SH groups covalently to the polymer. It should be possible thereafter to add to the polymer solution an inhibitor with a structure analogous to the potential substrate and then to expose the solution to air... 

Enzymes are usually impressively specific in their action. The specificity toward substrate is sometimes almost absolute. For many years urea was believed to be the only substrate for the enzyme urease and succinate the only substrate for succinate dehydrogenase. Even after much searching for other substrates, only... 

There is one case in which strain or induced fit could be useful in a type of specificity. These mechanisms are unimportant where competition between substrates is concerned. But given a situation in which there is no specific substrate present, these mechanisms could be of use in providing a low absolute activity of the enzyme toward, say, water. For example, induced fit could prevent hexokinase from being a rampant ATPase in the absence of glucose (although its absence is extremely unlikely). 

A meaning of specificity that is really a misuse of the term refers to the activity of an enzyme toward an alternative substrate in the absence of a specific substrate, as can happen in an experiment in vitro. In such a test tube experiment, a substrate is often described as poor because it involves either a high value of Km or a low value of cat. In biological systems both cat and KM are important. 

In vitro Metabolism. Numerous variables simultaneously modulate the in vivo metabolism of xenobiotics therefore their relative importance cannot be studied easily. This problem is alleviated to some extent by in vitro studies of the underlying enzymatic mechanisms responsible for qualitative and quantitative species differences. Quantitative differences may be related directly to the absolute amount of active enzyme present and the affinity and specificity of the enzyme toward the substrate in question. Because many other factors alter enzymatic rates in vitro, caution must be exercised in interpreting data in terms of species variation. In particular, enzymes are often sensitive to the experimental conditions used in their preparation. Because this sensitivity varies from one enzyme to another, their relative effectiveness for a particular reaction can be sometimes miscalculated. 

Enzymes provide the catalytic entities in biological transformations. The unique characteristics of biocatalysts, namely, activation of substrates and acceleration of reaction rates at ambient temperatures, specificity towards substrates, and stereospecificity and chiroselectivity towards product formation, generate most sophisticated and effective catalysts [101]. Accordingly, extensive efforts of chemists and biochemists are directed towards harnessing chemical transformations by means of technological approaches utilizing enzymes [102, 103]. 

It is well known that the specificity of an enzyme such as thrombin and plasmin is very close to that of trypsin. In this respect, inverse substrates for trypsin also are expected to be susceptible to the catalysis by these enzymes. In the kinetic analysis of trypsin-like enzymes toward p-amidinophenyl esters, it was found that the inverse concept is also applicable to thrombin, plasmin, urokinase, kallikrein, and trypsins from various origins 74 - 75). These enzymes are not distinctively different from bovine-... 

Efficient catalysis requires a specific configuration of substrates and reactive residues, with groups (selected from a small number of suitable candidates) to serve as nucleophiles and electrophiles under physiological conditions. In enzymes catalysing similar reactions, some convergence towards similar spatial arrangements and functional groups at the active site must be expected. 

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