Solution-phase Enzymatic Reactions

Hydrolysis ofp-nitrophenyl-(3-D-galactopyranoside was performed in buffered media, whereas transgalactosylation of p-nitrophenyl-2-acetamide-2-deoxy-beta-D-glucopyranoside was conducted in buffer-acetonitrUe solvent system. The authors did not use immobilized enzyme. The reaction was performed by separate loading of the enzyme in phosphate buffer solution and the substrate solution in 

Hydrolysis and P-galactosidase PMMA microchip with Y-junction at the inlet  

Glass microchip with Y junctions at the inlet and a single outlet continuous flow operation 

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The efficiency of solution-phase (two aqueous phase) enzymatic reaction in microreactor was demonstrated by laccase-catalyzed l-DOPA oxidation in an oxygen-saturated water solution, and analyzed in a Y-shaped microreactor at different residence times (Figure 10.24) [142]. Up to 87% conversions of l-DOPA were achieved at residence times below 2 min. A two-dimensional mathematical model composed of convection, diffusion, and enzyme reaction terms was developed. Enzyme kinetics was described with the double substrate Michaelis-Menten equation, where kinetic parameters from previously performed batch experiments were used. Model simulations, obtained by a nonequidistant finite differences numerical solution of a complex equation system, were proved and verified in a set of experiments performed in a microreactor. Based on the developed model, further microreactor design and process optimization are feasible. 

Computer simulation techniques offer the ability to study the potential energy surfaces of chemical reactions to a high degree of quantitative accuracy [4]. Theoretical studies of chemical reactions in the gas phase are a major field and can provide detailed insights into a variety of processes of fundamental interest in atmospheric and combustion chemistry. In the past decade theoretical methods were extended to the study of reaction processes in mesoscopic systems such as enzymatic reactions in solution, albeit to a more approximate level than the most accurate gas-phase studies. 

This chapter presents the implementaiton and applicable of a QM-MM method for studying enzyme-catalyzed reactions. The application of QM-MM methods to study solution-phase reactions has been reviewed elsewhere [44]. Similiarly, empirical valence bond methods, which have been successfully applied to studying enzymatic reactions by Warshel and coworkers [19,45], are not covered in this chapter. 

The main point of this exercise and considerations is that you can easily examine the feasibility of the desolvation hypothesis by using well-defined thermodynamic cycles. The only nontrivial numbers are the solvation energies, which can however be estimated reliably by the LD model. Thus for example, if you like to examine whether or not an enzymatic reaction resembles the corresponding gas-phase reaction or the solution reaction you may use the relationship... 

DKPs are simple and easy to obtain and are quite common by-products of synthetic, spontaneous, and biological formation pathways. DKP formation has been well documented as side reactions of solid-phase and solution-phase peptide synthesis. In addition, DKPs have been shown to be decomposition products of various peptides, proteins, and other commercial pharmaceuticals. Cyclic dipeptides were found to be present in solutions of human growth hormone, bradykinin, histerlin, and solutions of agents within the classes of penicillins and cephalosporins. " DKPs are also enzymatically synthesized in several protists and in members of the plant kingdom. Hydrolysates of proteins and polypeptides often contain these compounds and they are commonly isolated from yeasts, lichens, and fungi. ... 

For liquid-phase catalytic or enzymatic reactions, catalysts or enzymes are used as homogeneous solutes in the hquid, or as sohd particles suspended in the hquid phase. In the latter case, (i) the particles per se may be catalysts (ii) the catalysts or enzymes are uniformly distributed within inert particles or (hi) the catalysts or enzymes exist at the surface of pores, inside the particles. In such heterogeneous catalytic or enzymatic systems, a variety of factors that include the mass transfer of reactants and products, heat effects accompanying the reactions, and/or some surface phenomena, may affect the apparent reaction rates. For example, in situation (iii) above, the reactants must move to the catalytic reaction sites within catalyst particles by various mechanisms of diffusion through the pores. In general, the apparent rates of reactions with catalyst or enzymatic particles are lower than the intrinsic reaction rates this is due to the various mass transfer resistances, as is discussed below. 

When the gel with entrapped enzyme was placed in water containing 47.3 mM ethyl butylate at 28.9 °C, a swollen state was reached from the beginning of the measurement, while it took more than 80 min for the enzyme free gel to swell in enzyme/substrate solution. The rapid swelling is due to the change of solvent composition within or at the very vicinity of the gel phase by the enzymatic reaction shown above. 

Proton abstraction from a model carbon acid, hydroxyacetaldehyde, by formate anion has been examined theoretically for the gas phase and for aqueous solution.152 The reaction shows an early transition state, whereas its enzymatic equivalent has a late transition state. Solvation brings the transition state foiward. The factors that contribute to producing the later transition state in enzymes are discussed. 

Thus this technique is especially suited to studying enzymatic reactions with considerable advantage. Until now the procedure for determining the active centrum of an enzyme was rather complex because enzymatic reactions are performed only in aqueous solutions and at very low concentrations. Thus, IR-spectroscopy and normal Raman techniques failed. Also, experiments to study enzymatic reactions in the crystalline phase will not succeed, for the native conformation of the enzymes in solution is a prerequisite for optimal reactivity. The usual technique, therefore, is a stepwise modification of the functional groups of either the enzyme or its substratum and the measurement of their kinetic behaviour. This very laborious procedure then provides some information concerning the active centrum. 

Figure 4 A schematic representation of the experimentai approach for time-resoived XAS measurements. XAS provides local structural and electronic information about the nearest coordination environment surrounding the catalytic metal ion within the active site of a metalloprotein in solution. Spectral analysis of the various spectral regions yields complementary electronic and structural information, which allows the determination of the oxidation state of the X-ray absorbing metal atom and precise determination of distances between the absorbing metal atom and the protein atoms that surround it. Time-dependent XAS provides insight into the lifetimes and local atomic structures of metal-protein complexes during enzymatic reactions on millisecond to minute time scales, (a) The drawing describes a conventional stopped-flow machine that is used to rapidly mix the reaction components (e.g., enzyme and substrate) and derive kinetic traces as shown in (b). (b) The enzymatic reaction is studied by pre-steady-state kinetic analysis to dissect out the time frame of individual kinetic phases, (c) The stopped-flow apparatus is equipped with a freeze-quench device. Sample aliquots are collected after mixing and rapidly froze into X-ray sample holders by the freeze-quench device, (d) Frozen samples are subjected to X-ray data collection and analysis.

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