On enzyme reaction

For many applications, especially studies on enzyme reaction mechanisms, we do not need to treat the entire system quantum mechanically. It is often sufficient to treat the center of interest (e.g., the active site and the reacting molecules) quantum mechanically. The rest of the molecule can be treated using classical molecular mechanics (MM see Section 7.2). The quantum mechanical technique can be ab-initio, DFT or semi-empirical. Many such techniques have been proposed and have been reviewed and classified by Thiel and co-workers [50] Two effects of the MM environment must be incorporated into the quantum mechanical system. 

Zhang Y, Liu H, Yang W (2000) Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface. J Chem Phys 112 3483-3492... 

Zhang Y, Kua J, McCammon JA (2003) Influence of structural fluctuation on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies. J Phys Chem B 107 ... 

Models for biochemical switches, logic gates, and information-processing devices that are also based on enzymic reactions but do not use the cyclic enzyme system were also introduced [76,115,117-122]. Examples of these models are presented in Table 1.3. It should also be mentioned that in other studies [108,112-114,116], models of chemical neurons and chemical neural networks based on nonenzymic chemical reactions were also introduced. 

The detection of many pesticides at extremely low levels can be best achieved not by direct detection of the pesticide itself but rather by detection of its inhibitory effects on enzyme reactions. An enzyme-electrode is first constructed and its response when exposed to a suitable concentration of its substrate determined. When an electrode is then exposed to a dilute pesticide solution, the pesticide interacts with the enzyme and diminishes (or completely destroys) its activity. This inhibition can then be easily quantified by further exposure to the initial substrate concentration and comparison with the response prior to pesticide exposure. 

The quality of extracted citrus juices depends on enzyme reactions that occur not only in the fruit during the development period, but also in the juice during processing. When juice is extracted from citrus fruit, enzymes are released from their normal restraint in the cell. Several of these enzymes catalyze reactions that adversely affect taste and appearance of the juice. Unless the reactions are controlled, the juice products will not meet the standards of quality set up by the USDA Food Safety and Quality Service. The two reactions of commercial importance are the hydrolysis of pectin to pectic acid, which clarifies juice, and the lactonization of limonoic acid A-ring lactone to the bitter compound, limonin. Research efforts to identify and characterize the reactions, to isolate and purify the enzymes, and to develop methods to control the reactions are described in this review. 

Repeatedly, researchers have found the phenomenon that enzyme molecules seem to remember the aqueous conditions from which they were prepared (Klibanov, 1995). As mentioned above, early results with enzymes in organic solvents demonstrated that enzymes work best in organic solvents if there are lyophilized from aqueous solution at or near the optimum pH value in water. No specific pH effect of organic solvents on enzyme reactions was found the piCa of amino, carboxylic, and phenolic compounds does not differ by more than 0.3 units in the aqueous and lyophilized state (Costantino, 1997). 

Activity and stability are often comparable to values in aqueous media. Many substrates which cannot be made to react in water or in pure organic solvents such as hexane owing to lack of solubility can be brought to reaction in microemulsions. Whereas enzyme structure and mechanism do not seem to change upon transition from water to the microemulsion phase (Bommarius, 1995), partitioning effects often are very important. Besides an enhanced or diminished concentration of substrates in the vidnity of microemulsion droplets and thus of enzyme molecules, the effective pH values in the water pool of the droplets can be shifted in the presence of charged surfactants. Frequently, observed acceleration or deceleration effects on enzyme reactions can be explained with such partitioning effects (Jobe, 1989). 

Understand the effects of pH, ionic strength, and temperature on enzyme reactions. 

The most common enzymatic reactions are those with two or more substrates and as many products. But many of the simpler single-substrate schemes are valuable for the development of kinetic ideas concerning effects of pH, temperature, etc., on enzyme reaction rates. Although the mechanisms of multisubstrate reactions are complicated, their kinetics can often be described by an equation of the form ... 

The stereochemistry of pyridoxal phosphate-catalyzed reactions was last summarized comprehensively in 1971 by Dunathan [2], who outlined many of the basic concepts in this field. Aspects of PLP catalysis have been discussed in other reviews on enzyme reaction stereochemistry (e.g., [9]), and a brief review, emphasizing their own work, has recently been published by the present authors [ 10]. Much work has been done in this field during the past ten years, most of it supporting the concepts laid out in Dunathan s review, often refining the picture and sometimes modifying the original ideas. 

Green discontinued research upon the birth of her two children in 1947 and 1949. She started work again, part-time, in 1951 with S. T. Cowan at the National Collection of Type Cultures of Bacteria at the Central Public Health Laboratory, Colindale, London, where they developed a series of methods for the identification of bacteria based on enzyme reactions. In 1953, she was appointed Assistant Lecturer in the Department... 

As enzyme activators and coenzymes (Bl, B2, B6, B12, pantothenic acid, folic acid, biotin, niacin) o As redox agent on enzyme reactions (Vit-C, B2, B12, folic acid, niacin)... 

The pronounced effects of pH on enzyme reactions emphasize the need to control this variable by means of adequate buffer solutions. Enzyme assays should be carried out at the pH of optimal activity, because the pH-activity curve has its minimum slope near this pH, and a small variation in pH will cause a minimal change in enzyme activity. The buffer system must be capable of counteracting the effect of adding the specimen (e.g, serum itself is a powerful buffer) to the assay system, and the effects of acids or bases formed during the reaction (e.g., formation of fatty acids by the action of lipase). Because buffers have their maximimi buffering capacity close to their pK values, whenever possible a buffer system should be chosen with a pK value within IpH unit of the desired pH of the assay (see Chapter 1). Interaction between buffer ions and other components of the assay system (e.g., activating metal ions) may eliminate certain buffers from consideration. 

Z2. Zeller, E. A., and Bisegger, A., Influence of drugs and chemotherapy on enzyme reactions. III. Cholinesterases of brain and erythrocytes. Helv. Chim. Acta 26, 1619-1630 (1943). 

Whereas the effect of changing pH on a reaction involving only small molecules can be immediately informative, the interpretation of the effects of pH on enzyme reactions is more complex, since enzymes have many ionising groups and often react by a series of chemical steps with similar rates. 

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