Enzyme-catalyzed reactions, covalent

If the enzyme-catalyzed reaction is to be faster than the uncatalyzed case, the acceptor group on the enzyme must be a better attacking group than Y and a better leaving group than X. Note that most enzymes that carry out covalent catalysis have ping-pong kinetic mechanisms. 

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 enzyme catalyzes the covalent insertion of a tyrosine at the C-terminal glutamate of the tubulin a subunit to effect the posttranslational synthesis of a peptide bond (Flavin et al., 1982 Thompson, 1982). The role of this modification reaction remains to be established... 

Once assembly of a mature peptide has been completed by the NRPS, the product remains covalently linked to the PCP domain of the last module as a thioester. Release into solution from the assembly line is accomplished by a variety of enzyme-catalyzed reactions as described below (Figure 8). 

The control via activation or inhibition of the rate(s) of an enzyme-catalyzed reaction(s). This control includes the increase or decrease in the stability or half-life of the enzyme(s). There are many different means by which control can be achieved. These include 1. Substrate availability and reaction conditions (e.g., pH, temperature, ionic strength, lipid interface activation) 2. Magnitude of Vraax sud valucs) 3. Activation (particularly, feedforward activation) 4. Isozyme formation 5. Com-partmentalization and channeling 6. Oligomerization/ polymerization 7. Feedback inhibition and cooperativity (particularly, allosterism and/or hysteresis) 8. Covalent modification and 9. Gene regulation (induction repression)... 

Fluorescence-based assays either in the measurement of enzyme activity or in the quantification of enantioselectivity all have a high degree of sensitivity, which allows the use of very dilute substrate concentrations and extremely small amounts of enzymes. Basically, there are two different approaches. One involves the use of a substrate of interest to which a fluorescent-active (or potentially active) moiety is covalently attached. The second approach makes use of a fluorescence-based sensor, which gives rise to a signal as a consequence of the enzyme-catalyzed reaction of a substrate of interest. 

The answer to these questions has two distinct but interwoven parts. The first lies in the rearrangements of covalent bonds during an enzyme-catalyzed reaction. Chemical reactions of many types take place between substrates and enzymes functional groups (specific... 

Eight enzyme-catalyzed reactions are involved in the conversion of acetyl-CoA into fatty acids. The first reaction is catalyzed by acetyl-CoA carboxylase and requires ATP. This is the reaction that supplies the energy that drives the biosynthesis of fatty acids. The properties of acetyl-CoA carboxylase are similar to those of pyruvate carboxylase, which is important in the gluconeogenesis pathway (see chapter 12). Both enzymes contain the coenzyme biotin covalently linked to a lysine residue of the protein via its e-amino group. In the last section of this chapter we show that the activity of acetyl-CoA carboxylase plays an important role in the control of fatty acid biosynthesis in animals. Regulation of the first enzyme in a biosynthetic pathway is a strategy widely used in metabolism. 

Enzyme-catalyzed reactions begin when the substrate migrates into the active site to form an enzyme-substrate complex. No covalent bonds are formed the enzyme and substrate are held together by hydrogen bonds and by... 

Previous sections of this chapter have focused on developing general principles for enzyme-catalyzed reactions based on analysis of single-substrate enzyme systems. Yet the majority of biochemical reactions involve multiple substrates and products. With multiple binding steps, competitive and uncompetitive binding interactions, and allosteric and covalent activations and inhibitions possible, the complete set of possible kinetic mechanisms is vast. For extensive treatments on a great number of mechanisms, we point readers to Segel s book [183], Here we review a handful of two-substrate reaction mechanisms, with detailed analysis of the compulsory-order ternary mechanism and a cursory overview of several other mechanisms. 

In addition to its biochemical importance, CM has drawn attention from chemists looking to study enzyme activity for three primary reasons. First, the substrate 1 binds to the enzyme CM withont forming any covalent linkages, so that major electronic reorganizations do not need to be considered. Second, unlike many enzyme-catalyzed reactions, the reaction mechanism for the conversion of 1 into 2 is the same in both the enzyme environment and in solution in the absence of the enzyme. Last, the kinetics of the enzyme activity are well known, with CM increasing the rate of the reaction by 10 over the rate in aqueous solution." This corresponds to a reduction in the activation enthalpy of 20.7 0.4 kcal moL in solution to 15.9 kcal mol in the enzymatic environment. The activation entropy is -12.9 0.4 eu in solution but is reduced to essentially nil in the enzyme. In other words, AG = 24.5 kcal moL in solution but only 15.4 kcal mol in CM. ... 

This article will describe the different chemical strategies used by enzymes to achieve rate acceleration in the reactions that they catalyze. The concept of transition state stabilization applies to all types of catalysts. Because enzyme-catalyzed reactions are contained within an active site of a protein, proximity effects caused by the high effective concentrations of reactive groups are important for enzyme-catalyzed reactions, and, depending on how solvent-exposed the active site is, substrate desolvation may be important also. Examples of acid-base catalysis and covalent (nucleophilic) catalysis will be illustrated as well as examples of "strain" or substrate destabilization, which is a type of catalysis observed rarely in chemical catalysis. Some more advanced topics then will be mentioned briefly the stabilization of reactive intermediates in enzyme active sites and the possible involvement of protein dynamics and hydrogen tunneling in enzyme catalysis. 

Several enzyme-catalyzed reactions involve the nucleophilic attack of an active site amino acid side chain on the substrate, which results in an immediate reaction that is attached covalently to the enzyme. This type of catalysis is known as nucleophic (or covalent) catalysis. 

The absolute amounts of aniline covalently bonded to the soil fulvic acid in the presence and absence of the peroxidase were not measured. However, the relative signal to noise ratios obtained in the NMR spectra indicate that significantly more aniline was taken up by the fulvic acid in the enzyme catalyzed reaction. It should also be pointed out that, in the execution of the peroxidase experiment, the solution containing the fulvic acid, aniline, and peroxidase darkened instantaneously upon addition of the hydrogen peroxide, indicating significantly faster kinetics than in the nonenzyme reaction. 

The information within an enzyme s active site (its shape and charge distribution) constrains the motions and allowed conformations of the substrate, making it appear more like the transition state. In other words, the information in the structure of the enzyme is used to optimally orient the substrate. As a result of this information transfer, the energy of the enzyme-substrate complex becomes closer to the AG, which means that the energy needed for the reaction to proceed to product is reduced. Consequently there is an increase in the rate of the enzyme-catalyzed reaction. Other factors, such as electrostatic effects, general acid-base catalysis, and covalent catalysis (discussed on pp. 177-180), also contribute to the increased rates of enzyme-catalyzed reactions over non-enzyme catalyzed reactions. 

The examples in this section have been chosen to provide an in-depth presentation showing how RSSF currently has been applied to the study of biological systems. These applications include the study of isotope effects on enzyme-catalyzed reactions, the investigation of substrate-metal ion interactions in metalloenzymes, the search for and identification of covalent intermediates in enzyme-catalyzed processes, the analysis of the effects of site-directed mutations on enzyme catalytic mechanism, and the exploitation of natural and artificial chromophores as probes of allosteric processes. 

This compound has been isolated and characterized (108,109) ite crystallographic structure differs from that of the apoenzyme and its NAD compound (34). The pyruvate is covalently linked to NAD, and the compound appears to be formed from enolpyruvate by nucleophilic attack of pyruvate C-3 at the nicotinamide C-4 in a relatively slow enzyme-catalyzed reaction formally analogous to lactate oxidation (106). It is formed more rapidly—and dissociates to give active enzyme more slowly—with heart isozymes than with muscle isozymes, and the halftime for the formation of the complex from enzyme, NAD, and pyruvate unexpectedly increases with the enzyme concentration (103). The explanation seems to be that it is formed primarily from enzyme subunits produced by reversible dissociation of the tetramer in dilute solution (107). This does not preclude the existence of the complex in the tissue, and Everse and Kaplan (79) have suggested a hypothesis for its involvement in metabolic control. 

Noncovalent forces have also been reported to play an important role in these enzyme-catalyzed reactions [50,56]. Moreover, Hofsten and Lalasidis [50] were of the opinion that covalent forces did not play a role in these reactions. Several investigators have shown that the product produced during the plastein reaction is composed of aggregates held together by hydrophobic and ionic bonds [57,58]. Others [59] emphasized an entropy-driven aggregation process. Trans-peptidation has been considered by a number of authors [46,60,61] as the mechanism of enzymatic modification processes (resynthesis, plastein reaction, EPM). That means that a great number of peptide bonds are split and new covalent bonds formed in the course of the enzymatic process. 

Methionine-enriched protein was produced also from an enzymatically prehydrolyzed milk protein using an enzymatic peptide modification method with a-chymotrypsin as catalyst. Amino acid incorporation leading to methionine enrichment of the product proceeded via formation of covalent bonds. The concentration of the substrate was 25% (w/v). Methionine was added to the reaction mixture in the form of methionine methyl ester hydrochloride. An ester/substrate ratio of 1 5 was used in the enzymatic peptide modification reaction. The methionine content of the product was twice as high as that of the substrate. The slight change in the degree of hydrolysis revealed that part of the amino acids were bound to the peptide chains and that transpeptidation was the main force during this enzyme-catalyzed reaction. The newly incorporated Met was located in C- and N-termi-nals in a ratio of 3 1 [82],... 

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