Active site of enzymes

In recent years, biochemists have developed an arsenal of reactions that are relatively specific to the side chains of particular amino acids. These reactions can be used to identify functional amino acids at the active sites of enzymes or to label proteins with appropriate reagents for further study. Cysteine residues in proteins, for example, react with one another to form disulfide species and also react with a number of reagents, including maleimides (typically A ethylmaleimide), as shown in Figure 4.11. Cysteines also react effectively... 

What accounts for this stereospecificity It arises from the fact that the enzymes (and especially the active sites of enzymes) are inherently asymmetric structures. The nicotinamide coenzyme (and the substrate) fit the active site in only one way. Malate... 

Probing the Active Sites of Enzymes with Conformationally Restricted Substrate Analogs. BY G. L. KENYON AND J. A. FEE, Department of Chemistry, University of California, Berkeley, California. 381... 

Probing the Active Sites of Enzymes With Conformationally Restricted Sutetrate Analogs... 

They have an exceedingly high specific activity per active site the turnover number y is as high as 10 to 10 s in certain enzyme reactions, while at ordinary electrocatalysts having a number of reaction sites on the order of 10 cm , yhas a value of about 1 s at a current density of lOmA/cm. Thus, the specific catalytic activity of tfie active sites of enzymes is many orders of magnitude fiigher tfian tfiat of all other known catalysts for electrochemical (and also chemical) processes. 

The active site of enzymes usually are located in clefts and crevices in the protein. This design effectively excludes bulk solvent (water), which would otherwise reduce the catalytic activity of the enzyme. In other words, the substrate molecule is desolvated upon binding, and shielded from bulk solvent in the enzyme active site. Solvation by water is replaced by specific interactions with the protein (Warshel et al., 1989). 

The discussion of Krs values above is an attempt to show how they may be used to gain insights into transition state binding at or near the active sites of enzymes. For other examples of the explicit or implicit application of Kurz s ideas to enzymes, the reader is directed to the references cited at the start of this subsection and in the Introduction, particularly the reviews by Kraut (1988) and by Wolfenden and Kati (1991). 

The source of the enormous rate enhancements in enzymatic catalysis has been discussed from physical organic points of view (Jencks, 1969 Bruice, 1970). The kinetic behavior is attributed to factors such as an orientation effect, a microenvironmental effect and multifunctional catalysis. The active sites of enzymes are generally located in a hydrophobic hole or cleft. Therefore, the microenvironmental effect is mainly concerned with the behavior of enzyme catalytic groups in this hydrophobic microenvironment and the specific... 

Metal ions often play crucial roles at the active sites of enzymes. The analogy postulated between enzymes and micelles suggests that the combination of... 

The acido-basic properties of water molecules are greatly affected in restricted media such as the active sites of enzymes, reverse micelles, etc. The ability of water to accept or yield a proton is indeed related to its H-bonded structure which is, in a confined environment, different from that of bulk water. Water acidity is then best described by the concept of proton-transfer efficiency -characterized by the rate constants of deprotonation and reprotonation of solutes - instead of the classical concept of pH. Such rate constants can be determined by means of fluorescent acidic or basic probes. 

The aqueous cores of reverse micelles are of particular interest because of their analogy with the water pockets in bioaggregates and the active sites of enzymes. Moreover, enzymes solubilized in reverse micelles can exhibit an enhanced catalytic efficiency. Figure B4.3.1 shows a reverse micelle of bis(2-ethylhexyl)sulfosuccinate (AOT) in heptane with three naphthalenic fluorescent probes whose excited-state pK values are much lower than the ground-state pK (see Table 4.4) 2-naphthol (NOH), sodium 2-naphthol sulfonate (NSOH), potassium 2-naphthol-6,8-disulfonate (NSOH). The spectra and the rate constants for deprotonation and back-recombination (determined by time-resolved experiments) provide information on the location of the probes and the corresponding ability of their microenvironment to accept a proton , (i) NDSOH is located around the center of the water pool, and at water contents w = [H20]/[A0T] >... 

Magnetic resonance techniques have again been popular for studying enzymes which are involved in phosphate hydrolysis and transfer. 31P or 19F N.m.r.1-2 and spinlabelling3 have all been used to study the interaction of substrates with these enzymes, while affinity labelling4 5 6 7 is another technique which has been used to obtain information about the sequence and conformation of amino-acid chains at the active sites of enzymes. Recently, these experimental methods have been applied to the study of cell membranes,6-7 and these are mentioned in a new series of books concerned with enzymes in biological membranes.8 A new journal, Trends in Biochemical Sciences, which contains concise, up-to-date reviews on these and other topics is published by Elsevier on behalf of the International Union of Biochemistry. 

The main purpose of redox mediation is to increase the rate of electron transfer between the active site of enzyme biocatalysts and an electrode by eliminating the need for the enzyme to interact directly with the electrode surface. Depending on the enzyme and... 

There are several such toxic agents that cause considerable medical, public and political concern. Two examples are discussed here the heavy metal ions (e.g. lead, mercury, copper, cadmium) and the fluorophosphonates. Heavy metal ions readily form complexes with organic compounds which are lipid soluble so that they readily enter cells, where the ions bind to amino acid groups in the active site of enzymes. These two types of inhibitors are discussed in Boxes 3.5 and 3.6. There is also concern that some chemicals in the environment, (e.g. those found in industrial effluents, rubbish tips and agricultural sprays), although present at very low levels, can react with enhanced reactivity groups in enzymes. Consequently, only minute amounts concentrations are effective inhibitors and therefore can be toxic. It is suggested that they are responsible for some non-specific or even specific diseases (e.g. breast tumours). 

The first function of an enzyme is to hold the substrate for a chemical reaction. Active sites of enzymes hold the substrate molecule in a suitable position, so that it can be attacked by the reagent effectively. 

Drugs inhibit the attachment of substrate on active site of enzymes in two different ways ... 

Drugs compete with the natural substrate for their attachment on the active sites of enzymes. Such drugs are called competitive inhibitors (Fig. 16.2). 

Drug and substrate competing for active site of enzyme... 

Which forces are involved in holding the drugs to the active site of enzymes ... 

Having an increased or elevated reactivity. This term has been used in reference to the relative activity of amino acyl residues at the active sites of enzyme. The immediate environment (Le., the microenvironment) may allow simple reagents to react faster with the amino acid than would normally be expected. Thus, in labeling of proteins with active site-directed reagents, an investigator should always consider the basis of increased reactivity Is it due to facilitation of the reaction by increased affinity (Le., affinity labeling), or is it due to increased activity of the amino acyl side chain (e.g., perhaps increased nucleophilicity due to the microenvironment). 

Scheme 6.1 Active sites of enzymes employing a double hydrogen-bonding motif for substrate coordination and activation in various biochemical transformations Haloalcohol dehalogenase (1), formate dehydrogenase (2), and serine protease (3).

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