Biocatalysis analysis

So, in the final analysis, biocatalysis should not be considered in a separate sector available only to the specialist bioorganic chemist. It is one method, in the portfolio of catalytic techniques, that is available to all chemists for the solution of present and future problems in organic synthesis. To erect a Chinese wall between the natural and non-natural catalysts is totally illogical and prevents some creative thinking, particularly in the area of coupled natural/ non-natural catalysts11611 and biomimetic systems11621. 

Homann M.J., Suen W.-C., Zhang, N. and Zaks, A., Comparative analysis of chemical and biocatalytic syntheses of drug intermediates. In Biocatalysis in the Pharmaceutical and Biotechnology Industries, Patel, R.N. (ed.), CRC Press, 2007, pp. 645-659 and references cited therein. 

Hailing, P.J., Thermodynamic predictions for biocatalysis in nonconventional media theory, tests, and recommendations for experimental design and analysis. Enzyme Microb. TechnoL, 1994,16, 178-206. 

In order to provide dTDP-deoxy sugars by combinatorial biocatalysis we have utiHzed the enzymes for the dTDP- 3-L-rhamnose pathway. The successful combination of pathway enzymes with optimized enzyme productivities (amount of product per unit of enzyme) needs a concise kinetic and inhibition analysis. Scheme 5.1 depicts the biosynthetic pathway of dTDP- 3-L-rhamnose with important km and Ki constants. The enzymes RmlA and RmlB are highly controlled by the intermediate, dTDP-4-keto-6-deoxy-a-D-glucose 3, the product 5 or by... 

Zlokarnik M. Dimensional Analysis, Scale-Up. In Elickinger MC, Drew SW, eds. Encyclopedia of Bioprocess Technology Eermentation, BioCatalysis, and Bioseparation. New York John Wiley and Sons Inc., 1999 840-861. 

M. Zlokarnik. Dimensional Analysis, Scale-Up. In Encyclopedia of Bio process Technology Fermentation, Biocatalysis, Bioseparation. Vol. 2, 840-861. (M.C. Flickinger and S. W. Drew, eds.) Wiley, 1999. 

Zlokarnik, M. Dimensional analysis, scale-up. In Encyclopedia of Bioprocess Technology Fermentation. Biocatalysis and Bioseparation. Flickinger, M.C., Drew, St. W., eds. Wiley, New York. 1999, pp 840-861. 

The last 20 or 30 years have witnessed the coincidence of two of the most powerful trends in technology development in human history the simultaneous exponential growth of the capacity of microchips and the capacity for DNA sequencing. These two forces have created an environment which enables the collection and analysis of large amounts of DNA sequences for relevant information regarding enzyme function and thus also biocatalysis. 

This chapter outlines the principles of green chemistry, and explains the connection between catalysis and sustainable development. It covers the concepts of environmental impact, atom economy, and life-cycle analysis, with hands-on examples. Then it introduces the reader to heterogeneous catalysis, homogeneous catalysis, and biocatalysis, explaining what catalysis is and why it is important. The last two sections give an overview of the tools used in catalysis research, and a list of recommended books on specialized subjects in catalysis. 

Microreactor technology offers the possibility to combine synthesis and analysis on one microfluidic chip. A combination of enantioselective biocatalysis and on-chip analysis has recently been reported by Beider et al. [424]. The combination of very fast separations (<1 s) of enantiomers using microchip electrophoresis with enantioselective catalysis allows high-throughput screening of enantioselective catalysts. Various epoxide-hydrolase mutants were screened for the hydrolysis of a specific epoxide to the diol product with direct on-chip analysis of the enantiomeric excess (Scheme 4.112). 

Another example in which biocatalysis is combined with analysis is the system reported by Honda et al. [436]. A microreaction system, consisting of an enzyme-immobilized microreactor, for optical resolution of racemic amino acids was devel-... 

Figure 2.17a reports in more detail the process simplification possible by biocatalysis in the case of cephalexin synthesis [154]. Figure 2.17b shows the results of a life cycle analysis (Chapter 5) of the old chemical route versus the new white biotech route [154]. The significant improvement in the sustainability of the new process is clearly evidenced. 

Abstract This chapter discusses the potential usefulness of ionic liquids with respect to biocatalysis by illustrating the stability and activity of enzymes in ionic liquids in the presence or absence of water. Ionic liquids are a class of coulombic fluids composed of organic cations like alkyl-substituted imidazolium, pyrrolidin-ium, and tetraalkylammonium ions and anions such as halides, tetrafluoroborates, hexafluorophosphates, tosylates, etc. The possibility of tunable solvent properties by alternation of cations and anions has made ionic liquids attractive to study biocatalysis which warrants an understanding of enzyme stability and activity in ionic liquids. This chapter systematically outlines the recent studies on the stability of enzymes and their reactivity toward a wide range of catalytic reactions. A careful approach has been taken toward analysis of relationship between stabil-ity/activity of enzymes versus chaotropic/kosmotropic nature of cations and anions of ionic liquids. 

As evident from the above discussion, ILs have emerged as alternative solvent systems for biocatalysis which has already established with a range of different class of enzymes performing better or at least comparable to conventional orgattic solvents. The added advantages of easy work up procedure, possibility of recycling the solvent and multiple uses of enzymes were also noted. However, the complexity in the nature of ILs has resulted variation in enzyme performance in terms of reaction rate and enantioselectivity. A brief comparative analysis of enzyme activity versus nature of the component of ILs would be helpful for better understanding of the subject and careful selection of ILs for a desired reaction. 

We have examined several systems chosen to illustrate the current role of theory and simulation in biomimetics and biocatalysis. It should be clear that the theory is not done in a vacuum (so to speak) but rather that the theory becomes interesting only for systems amenable to experimental analysis. However, the examples illustrate how the theory can provide new insights and deeper understanding of the experiments. As experience with such simulations accumulates and as predictions are made on more and more complex systems amenable to experiment, it will become increasingly feasible to use the theory on unknown systems. As the predictions on such unknown systems are tested with experiment and as the reliability of the predictions increases, these techniques will become true design tools for development of new biological systems. 

Biocatalysis is the study of biological catalysts with regard to their kinetics, mechanisms, specificity, and application in synthesis and analysis. In addition to the traditional study of mechanistic enzymology, biocatalysis is concerned with the use of recombinant DNA technology, site-specific mutagenesis, directed evolution, pathway engineering, substrate design, and structure-based approaches as tools for the development of novel catalysts and reactions. 

Another area of intensive research in the field of applied genomics is the gene expression analysis by DNA microarrays and similar methods. As of now, most applications of these techniques are either based on their scientific merits or on medial/pharmaceutical/toxicological applications. It is probably only a matter of time until these methods find their way into research on biocatalysis. Possible applications include the analysis of coordinated regulation of enzymes not linked in operons, or the identification of new enzymes on the basis of their expression pattern. ... 

But first, in order to study biocatalysis, there needs to be a ready supply of a biocatalyst of interest made available through techniques such as those described in Chapter 3. Structure is always very helpful to interpret function (Chapters 4-6). After this, there need to be techniques of analysis and a sound theoretical framework with which to interpret biocatalysis data and elaborate those key mechanisms of biocatalyts that make biocatalysis possible. For this reason, we will begin this chapter with a detailed discussion of ways to acquire and analyse biocatalytic data using various models of biocatalysis. Following this, we will take a look at those theories... 

For the purposes of the following analysis, biocatalysis is assumed to be irreversible and each biocatalyst E possesses only a single catalytic site. Hence, if the total concentration of biocatalyst is [E]o, then this must be the sum of free enzyme, [E], and Michaelis complex, [ES], concentrations as indicated in... 

The Michaelis-Menten equation (8.8) and the irreversible Uni Uni kinetic scheme (Scheme 8.1) are only really applicable to an irreversible biocatalytic process involving a single substrate interacting with a biocatalyst that comprises a single catalytic site. Hence with reference to the biocatalyst examples given in Section 8.1, Equation (8.8), the Uni Uni kinetic scheme is only really directly applicable to the steady state kinetic analysis of TIM biocatalysis (Figure 8.1, Table 8.1). Furthermore, even this statement is only valid with the proviso that all biocatalytic initial rate values are determined in the absence of product. Similarly, the Uni Uni kinetic schemes for competitive, uncompetitive and non-competitive inhibition are only really applicable directly for the steady state kinetic analysis for the inhibition of TIM (Table 8.1). Therefore, why are Equation (8.8) and the irreversible Uni Uni kinetic scheme apparently used so widely for the steady state analysis of many different biocatalytic processes A main reason for this is that Equation (8.8) is simple to use and measured k t and Km parameters can be easily interpreted. There is only a necessity to adapt catalysis conditions such that... 

In this case. Equation (8.26) and the irreversible Uni Uni kinetic scheme for four catalytic sites is appropriate for the steady state kinetic analysis of homo-tetrameric, human mitochondrial MnSOD biocatalysis (Figure 8.8, Table 8.1) with one catalytic site containing one manganese ion per subunit. These sites are not only independent, but each turnover of a catalytic site involves one substrate superoxide radical being transformed to only one of two possible redox products depending upon the oxidation state of the manganese ion involved. 

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