Rate enhancement and specificity

Rate enhancement and specificity - the two striking phenomena associated with enzyme-catalysed reactions are the rate enhancement and specificity 

The same example may be used to illustrate specificity. The enzyme also forms an anhydride from the non-specific thiol ester, succinyl methyl mercaptopropionate 

It is relatively easy to rationalise how enzymes discriminate against substrates 

It is of interest to note that the efficient enzymes, catalase, carbonic anhydrase and the nitrogenases have very small substrates (HjOj, CO2 and Nj, respectively) for which it is not easy to distinguish between reacting and non-reacting parts. It is a great challenge to quantitatively understand the forces of interaction between these substrates and their enzymes. 

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With the exception of enzymes such as proteases, nucleases, and amylases, which act on macromolecular substrates, enzyme molecules are considerably larger than the molecules of their substrates. Consideration of the structure of an enzyme s active site and its relationship to the structures of the enzyme s substrate(s) in its ground and transition states is necessary to understand the rate enhancement and specificity of the chemical reactions performed by the enzyme,... 

It seems that a major contribution to the rate enhancement and specificity exhibited by enzymes is complementarity between the electrostatic potentials of the substrate and the enzyme in the transition state. 

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... 

K. L. Saenger, N. Smith, S. L. Dexheimer, C. Engleke, and D. E. Pritchard. Role of initial rotation on vibrationally inelastic collisions enhancements and specificity in level to level rate constants for Li. J. Chem. Phys., 79 4076-4084 (1983). 

The kinetics and electronic mechanisms of conventional chemical catalysts- are contrasted with those in enzymes. The analogy between certain attributes of surfactants and phase-transfer catalysis and enzyme active sites are made and the limitations of surface catalysts and zeolites are pointed out. The principle features that give enz3nnes their unusual rate enhancements and remarkable specificity are discussed and ways in which these can be realized in man-made catalysts are proposed. The catalytic activation of CO2 by both enzymatic and non-enzymatic means, including a detailed analysis of the electronic reaction sequence for the metalloenzyme carbonic anhydrase, is used to illustrate the above themes. 

The 17-[Zn]3 efficiently catalyzed the cleavage of RNA dinucleotides 21, by the cooperative action of the Zn° centers, with high rate enhancement and significant nucleobase specificity. The catalytic rates for dinucleotides having different nudeobases was observed in the order of GpG UpU ApA. The heterotiinudear complex 17-[Zn2Cu] has been found to be even more active (99AGE3189). 

In summary, for an enzyme model to be operative, a certain number of criteria, characteristic of enzyme catalysis, must be fulfilled, among which is substrate specificity—that is, selective differential binding. The enzymelike catalyst must also obey Michaelis-Menten kinetics (saturation behavior), lead to a rate enhancement, and show bi- and/or multifunctional catalysis (348). 

Certain factors and product precursors are occasionally added to various fermentation media to iacrease product formation rates, the amount of product formed, or the type of product formed. Examples iaclude the addition of cobalt salts ia the vitamin fermentation, and phenylacetic acid and phenoxyacetic acid for the penicillin G (hen ylpenicillin) and penicillin V (phenoxymethylpenicillin) fermentations, respectively. Biotin is often added to the citric acid fermentation to enhance productivity and the addition of P-ionone vastly iacreases beta-carotene fermentation yields. Also, iaducers play an important role ia some enzyme production fermentations, and specific metaboHc inhibitors often block certain enzymatic steps that result in product accumulation. 

Depending on the peroxide class, the rates of decomposition of organic peroxides can be enhanced by specific promoters or activators, which significantly decrease the energy necessary to break the oxygen—oxygen bond. Such accelerated decompositions occur well below the peroxides normal appHcation temperatures and usually result in generation of only one usehil radical, instead of two. An example is the decomposition of hydroperoxides with multivalent metals (M), commonly iron, cobalt, or vanadium ... 

Dielectric Film Deposition. Dielectric films are found in all VLSI circuits to provide insulation between conducting layers, as diffusion and ion implantation (qv) masks, for diffusion from doped oxides, to cap doped films to prevent outdiffusion, and for passivating devices as a measure of protection against external contamination, moisture, and scratches. Properties that define the nature and function of dielectric films are the dielectric constant, the process temperature, and specific fabrication characteristics such as step coverage, gap-filling capabihties, density stress, contamination, thickness uniformity, deposition rate, and moisture resistance (2). Several processes are used to deposit dielectric films including atmospheric pressure CVD (APCVD), low pressure CVD (LPCVD), or plasma-enhanced CVD (PECVD) (see Plasma technology). 

Trickle Bed Hydrodesulfurization The first large-scale apph-cation of trickle bed reactors was to the hydrodesulfurization of petroleum oils in 1955. The temperature is elevated to enhance the specific-rate and the pressure is elevated to improve the solubihty of the... 

The catalytic triad consists of the side chains of Asp, His, and Ser close to each other. The Ser residue is reactive and forms a covalent bond with the substrate, thereby providing a specific pathway for the reaction. His has a dual role first, it accepts a proton from Ser to facilitate formation of the covalent bond and, second, it stabilizes the negatively charged transition state. The proton is subsequently transferred to the N atom of the leaving group. Mutations of either of these two residues decrease the catalytic rate by a factor of 10 because they abolish the specific reaction pathway. Asp, by stabilizing the positive charge of His, contributes a rate enhancement of 10. ... 

Mutations in the specificity pocket of trypsin, designed to change the substrate preference of the enzyme, also have drastic effects on the catalytic rate. These mutants demonstrate that the substrate specificity of an enzyme and its catalytic rate enhancement are tightly linked to each other because both are affected by the difference in binding strength between the transition state of the substrate and its normal state. 

Most importantly, microwave processing frequently leads to dramatically reduced reaction times, higher yields, and cleaner reaction profiles. In many cases, the observed rate enhancements may be simply a consequence of the high reaction temperatures that can rapidly be obtained using this non-classical heating method, or may result from the involvement of so-called specific or non-thermal microwave effects (see Section 2.5). 

Significant rate accelerations and higher loadings are observed when the micro-wave-assisted and conventional thermal procedures are compared. Reactions times are reduced from 12-48 h with conventional heating at 80 °C to 5-15 min with microwave flash heating in NMP at temperatures up to 200 °C. Finally, kinetic comparison studies have shown that the observed rate enhancements can be attributed to the rapid direct heating of the solvent (NMP) rather than to a specific nonthermal microwave effect [17]. 

The microwave-assisted PTC transesterification of several carbohydrates in basic medium with methyl benzoate or laurate has been studied [96], Small amounts of DMF were necessary to provide good yields within 15 min at 160 °C. Rate enhancements were compared to conventional heating (A) under the same conditions and specific microwave activation was mostly seen when the less reactive fatty compounds were involved (Eq. (44) and Tab. 3.19)... 

The first report suggesting specific activation of an organic reaction by MW was that of Berlan et al. [28] who observed that some Diels-Alder reactions occurred more rapidly on MW heating than under conventional heating at the same temperature (95 °C). The reactions were performed in two different solvents, xylene and dibutyl ether and the rate enhancements were slightly higher in xylene, the less polar solvent. For example the rate enhancement of the reaction of 2,3-dimethyl-l,3-butadiene 21 with methyl vinyl ketone 22 was 8 times in xylene and 2.3 times in dibutyl ether, based on the half lives of the reactions. Reaction of anthracene 3 with diethyl maleate 23 in xylene (Scheme 4.12) resulted in an approximately fourfold rate in-... 

For example, large rate enhancements have been reported in the synthesis of chal-cones by crossed-aldol condensations in open vessels, suggesting the participation of specific MW effects [41]. The chalcone 24 was synthesized from cyclohexanone and benzaldehyde in ethanol, in the presence of a catalytic amount of sodium hydroxide (Scheme 4.13), in a MW oven in 90% yield in only 1 min. 

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