Enzymes specificity, enzyme-catalyzed reactions

Although the validity of specific models for specific enzyme-catalyzed reactions may be open to question, the most general physical chemical principles are likely to be common to both enzymatic and nonenzy-matic catalysis. I would therefore like to make a plea for the consideration of the significance of such a general phenomenon to catalysis, both by metaUoenzymes and in nonbiological systems. I refer to the structure of the so-called second coordination sphere of metal complexes and its relevance to catalysis. This is an aspect of the field which has not been too widely discussed previously, either at the present symposium or elsewhere. 

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. 

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. 

This represents an acceleration of at least lO u over the rate of the spontaneous reaction (4). Another striking and biochemically important aspect of enzyme catalyzed reactions is their specificity for the reaction catalyzed and the structure of the substrate utilized. 

Monitoring enzyme catalyzed reactions by voltammetry and amperometry is an extremely active area of bioelectrochemical interest. Whereas liquid chromatography provides selectivity, the use of enzymes to generate electroactive products provides specificity to electroanalytical techniques. In essence, enzymes are used as a derivatiz-ing agent to convert a nonelectroactive species into an electroactive species. Alternatively, electrochemistry has been used as a sensitive method to follow enzymatic reactions and to determine enzyme activity. Enzyme-linked immunoassays with electrochemical detection have been reported to provide even greater specificity and sensitivity than other enzyme linked electrochemical techniques. 

In this chapter we have seen that enzymatic catalysis is initiated by the reversible interactions of a substrate molecule with the active site of the enzyme to form a non-covalent binary complex. The chemical transformation of the substrate to the product molecule occurs within the context of the enzyme active site subsequent to initial complex formation. We saw that the enormous rate enhancements for enzyme-catalyzed reactions are the result of specific mechanisms that enzymes use to achieve large reductions in the energy of activation associated with attainment of the reaction transition state structure. Stabilization of the reaction transition state in the context of the enzymatic reaction is the key contributor to both enzymatic rate enhancement and substrate specificity. We described several chemical strategies by which enzymes achieve this transition state stabilization. We also saw in this chapter that enzyme reactions are most commonly studied by following the kinetics of these reactions under steady state conditions. We defined three kinetic constants—kai KM, and kcJKM—that can be used to define the efficiency of enzymatic catalysis, and each reports on different portions of the enzymatic reaction pathway. Perturbations... 

This equation is fundamental to all aspects of the kinetics of enzyme action. The Michaelis-Menten constant, KM, is defined as the concentration of the substrate at which a given enzyme yields one-half of its maximum velocity. is the maximum velocity, which is the rate approached at infinitely high substrate concentration. The Michaelis-Menten equation is the rate equation for a one-substrate enzyme-catalyzed reaction. It provides the quantitative calculation of enzyme characteristics and the analysis for a specific substrate under defined conditions of pH and temperature. KM is a direct measure of the strength of the binding between the enzyme and the substrate. For example, chymotrypsin has a Ku value of 108 mM when glycyltyrosinylglycine is used as its substrate, while the Km value is 2.5 mM when N-20 benzoyltyrosineamide is used as a substrate... 

In addition to KM and vmax, the turnover number (molar activity) and the specific activity are two important parameters in enzyme catalyzed reactions. The turnover number indicates the number of substrate molecules converted per unit time by a single enzyme molecule. The specific activity is given in units and one international unit (i.u.) is the amount of enzyme that consumes or forms 1 pmol of substrate or 1 pmol of product per minute under standard conditions. 

Group specificity, in which the enzyme catalyzes reactions of only one type of functional group. 

Cyclodextrins as catalysts and enzyme models It has long been known that cyclodextrins may act as elementary models for the catalytic behaviour of enzymes (Breslow, 1971). These hosts, with the assistance of their hydroxyl functions, may exhibit guest specificity, competitive inhibition, and Michaelis-Menten-type kinetics. All these are characteristics of enzyme-catalyzed reactions. 

The use of the symbol E in 5.1 for the environment had a double objective. It stands there for general environments, and it also stands for the enzyme considered as a very specific environment to the chemical interconversion step [102, 172], In the theory discussed above catalysis is produced if the energy levels of the quantum precursor and successor states are shifted below the energy value corresponding to the same species in a reference surrounding medium. Both the catalytic environment E and the substrates S are molded into complementary surface states to form the complex between the active precursor complex Si and the enzyme structure adapted to it E-Si. In enzyme catalyzed reactions the special productive binding has been confussed with the possible mechanisms to attain it lock-key represents a static view while the induced fit concept... 

Scheme 1 is a gross over-simplification for almost any enzyme-catalyzed reaction of a specific substrate, based as it is on a one-step reaction with a single, rate-determining transition state but it is appropriate for many, if not most reactions catalyzed by simple enzyme mimics. Most important for present purposes, it emphasises the most important properties of enzyme reactions which the design of mimics, or artificial enzymes, must address, namely ... 

The high specificity and stereoselectivity of enzymes, as well as the mild conditions under which they react, make enzyme-catalyzed reactions versatile tools in the synthesis of glycoconjugates. In some instances, an enzymic one-step transformation affords higher yields then the conventional and more-complex chemical synthesis. The application of enzymes in glycopeptide synthesis is under active development for selective deprotection and glycosylation purposes. 

Virtually all biological reactions are stereospecific. This generalization applies not only to the enzyme-catalyzed reactions of intermediary metabolism, but also to the processes of nucleic acid synthesis and to the process of translation, in which the amino acids are linked in specific sequence to form the peptide chains of the enzymes. This review will be restricted mainly to some of the more elementary aspects of the stereospecificity of enzyme reactions, particularly to those features of chirality which have been worked out with the help of isotopes. 

Site-directed mutagenesis is one of the most powerful methods of studying mechanisms of enzyme-catalyzed reactions. Since this technique makes it possible to replace a specific amino acid residue of an enzyme by an arbitrary one, it is particularly useful to specify the amino acid residue(s) which is responsible for the activity [20 - 22]. In the case of AMDase, one of four cysteine residues was presumed to be involved in the catalytic site by the titration experiments. To determine which Cys is located at the active site, preparation of four mutant enzymes, in each of which one of the cysteines is replaced another amino acid, and kinetic studies on them, are expected to be most informative. Which amino acid should be introduced in place of cysteine To decide on the best candidate. 

Typically, a specific enzyme catalyzes each chemical reaction in the metabolism of an organism. This specificity is required to properly regulate metabolism. One needs to be able to independently control the rates of aU, or almost all, metabolic reactions, enzyme by enzyme. 

Aconitase was first described 50 years ago by Martius (1,2) and soon there after named by Breusch (3). The enzyme demonstrated the then surprizing ability to distinguish between the chemicadly identical acetyl arms of citrate (4). The stereo-specificity of enzyme catalyzed reactions was not fully understood until the late 1940 s when Ogston point out that as long as a substrate attaches to an asymmetric enzyme at three points, the enzyme can differentiate between two identical amis of a symmetrical molecule (5). 

An enzyme-catalyzed reaction involving two substrates and one product. There are two basic Bi Uni mechanisms (not considering reactions containing abortive complexes or those catagorized as Iso mechanisms). These mechanisms are the ordered Bi Uni scheme, in which the two substrates bind in a specific order, and the random Bi Uni mechanism, in which either substrate can bind first. Each of these mechanisms can be either rapid equilibrium or steady-state systems. 

Stereochemical probes of the specificity of substrates, products, and effectors in enzyme-catalyzed reactions, receptor-ligand interactions, nucleic acid-ligand interactions, etc. Most chirality probe studies attempt to address the stereospecificity of the substrates or ligands or even allosteric effectors. However, upon use of specific kinetic probes, isotopic labeling of achiral centers, chronfium-or cobalt-nucleotide complexes, etc., other stereospecific characteristics can be identified, aU of which will assist in the delineation of the kinetic mechanism as well as the active-site topology. A few examples of chirality probes include ... 

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