2 evaluation using enzymatic reactions

Next we evaluate the PDLD + EVB surface for the enzymatic reaction using eq. (5.17). The resulting surface is shown in Fig. 5.6. As seen from the ligure, the protein can reduce Aby stabilizing the ionic state more than water. In fact, in the specific case of papain the protein inverts the stabilization of the covalent and ionic states relative to their order in solution. 

However, the active site is only a conceptual tool and the assignment of the active-site atoms is more or less arbitrary. It is not possible to know beforehand which residues and protein interactions that will turn out to be important for the studied reaction. Hybrid QM/MM methods have been used to extend the active site only models by incorporating larger parts of the protein matrix in studies of enzymatic reactions [19-22], The problem to select active-site residues appears both for active-site and QM/MM models, but in the latter, explicit effects of the surrounding protein (i.e. atoms outside the active-site selection) can at least be approximately evaluated. As this and several other contributions in this volume show, this is in many cases highly desirable. 

Solids were characterized by XRD, N2.BET surface area, and FT-IR. The antacid capacity of the synthesized zeolites was evaluated using the methodology reported by Rivera et al. [7] and Linares et al. [6]. The pepsin enzymatic activity was determined by the reaction between a specific mass of the solid and a denatured haemoglobin solution [8]. 

The evaluation of the KM and vmax values for enzymatic reactions is usually carried out using a linear plot of Eq. 14. The Lineweaver-Burke equation is widely used to this aim ... 

Figure 2 Effect of enzyme immobilization on luminescent image spatial resolution evaluated using coupled enzymatic reactions on nylon net as a model system, (a) Immobilized 3a-hydroxysteroid dehydrogenase (b) immobilized 3a-hydroxysteroid dehydrogenase and FMN-NADH oxidoreductase (c) immobilized 3a-hydroxysteroid dehydrogenase, FMN-NADH oxidoreductase, and bacterial luciferase. (From Ref. 47. Copyright John Wiley Sons Ltd. Reproduced with permission.)...

To demonstrate the ability of the system to perform a matrix experiment as described above, concentrations of enzyme, substrate, and ATP were varied across the 24 wells in a row of an SBS 384-well microtiter plate. Results of these types of evaluations for the optimization of an assay for a protein kinase A and Kemptide system were presented by Wu et al.12 All the reactions were carried out in lOOmM HEPES, pH 7.4, lOmM MgCl2, lOmM DTT, and 0.015% Brij-35. No quenching agent was used. A sample from each of the 24 wells was analyzed in parallel every 6.5 min as the 24 enzymatic reactions progressed. 

Inhibiting the production of the Aft peptides represents the most direct approach to curtailing their potential to accumulate as amyloid plaques, by inhibiting either the ft-sec-retase at step 1 or the y-secretase at step 2. Because these are enzymatic reactions with measurable products, a biochemical assay using a purified enzyme preparation can be integrated into an HTS platform, facilitating the rapid evaluation of large numbers of compounds for inhibition of the enzymatic activity. 

Any semi-quantitative evaluation of photon emission derived from the luciferin/luciferase enzymatic reaction by in vivo imaging requires prior study of the diffusion to all organs of the enzyme substrate, D-luciferin, at a concentration sufficient to saturate the reporter enzymatic activity (4). Indeed the diffusion of the substrate may change depending on the strain of mouse used or the specific formulation of the substrate. Here follows the protocol we adopted to this aim ... 

Enzyme kinetics were evaluated in a PDMS-glass chip using a continuous-flow system. A biotinylated enzyme (HRP or (5-galactosidase) was coupled to streptavidin-coated beads via the amide coupling of an aminocaproyl spacer. These beads (15.5 pm) were retained by a weir in the chip. The channel wall was passivated by 1 mg/mL BSA. The apparent enzyme kinetic parameters were evaluated using the Lilly-Homby model, as developed for the packed-bed enzymatic reactor systems. It was found that the apparent Michaelis constant (Km) approached the tme Km value of the free enzyme at zero-flow rate of a homogeneous reaction [845]. 

The evaluations of the activities were done by extracting the necessary product concentration out of the chromatogram, calculating conversion of the enzymatic reaction, and using the intracellular protein concentration, measured by the method of Bradford [33]. 

If any analytical evaluation of the progress of the reaction is wanted, then an aliquot can be diluted with 95% ethanol (or methanol) and titrated with 0.02 N methanolic NaOH with cresol red as the endpoint indicator. An alternate approach is to employ a titrimeter (Radiometer, microtitration assembly, Copenhagen), but it is important to realize that most phospholipases A2 adhere strongly to glass surfaces. Thus a vessel resistant to the solvents used in the reaction is mandatory, as is rigorous attention to cleaning the electrode after titration. The extent of the enzymatic reaction can be calculated using as a control a reaction mixture with no enzyme added. 

In the preparation of dynamic nitroaldol systems, different aldehydes and nitroalkanes were first evaluated for reversible nitroaldol reactions in the presence of base to avoid any side- or competitive reactions, and to investigate the rate of the reactions. 1H-NMR spectroscopy was used to follow the reactions by comparison of the ratios of aldehyde and the nitroalcohols. Among various bases, triethylamine was chosen as catalyst because its reactions provided the fastest exchange reaction and proved compatible with the enzymatic reactions. Then, five benzaldehydes 18A-E and 2-nitropropane 19 (Scheme 9) were chosen to study dynamic nitroaldol system (CDS-2) generation, because of their similar individual reactivity and product stabilities in the nitroaldol reaction. Ten nitroaldol adducts ( )-20A-E were generated under basic conditions under thermodynamic control, showing... 

The resulting dynamic aminonitrile systems were first subjected to lipase mediated resolution processes at room temperature. A-Methy] acetamide was observed as a major product from the lipase amidation resolution. In this case, free methylamine A was generated during the dynamic transimination process and transformed by the lipase. To avoid this by-reaction, the enzymatic reaction was performed at 0 °C, and the formation of this amide was thus detected at less than 5% conversion. To circumvent potential coordination, and inhibition of the enzyme by free Zn(II) in solution [54], solid-state zinc bromide was employed as a heterogeneous catalyst for the double dynamic system at 0 °C. The lipase-catalyzed amidation resolution could thus be used successfully to evaluate /V-substituted a-aminonitrile substrates from double dynamic systems in one-pot reactions as shown in Fig. 7d. Proposedly, the heterogeneous catalyst interfered considerably less or not at all in the chemo-enzymatic reaction because the two processes are separated from each other. Moreover, the rate of the by-reaction was reduced due to strong chelation between the amine and zinc bromide in the heterogeneous system. 

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