Theories of biocatalysis

So far in this chapter, the chemical biology reader has been introduced to examples of biocatalysts, kinetics assays, steady state kinetic analysis as a means to probe basic mechanisms and pre-steady-state kinetic analysis as a means to measure rates of on-catalyst events. In order to complete this survey of biocatalysis, we now need to consider those factors that make biocatalysis possible. In other words, how do biocatalysts achieve the catalytic rate enhancements that they do This is a simple question but in reality needs to be answered in many different ways according to the biocatalyst concerned. For certain, there are general principles that underpin the operation of all biocatalysts, but there again other principles are employed more selectively. Several classical theories of catalysis have been developed over time, which include the concepts of intramolecular catalysis, orbital steering , general acid-base catalysis, electrophilic catalysis and nucleophilic catalysis. Such classical theories are useful starting points in our quest to understand how biocatalysts are able to effect biocatalysis with such efficiency. 

General base catalysis is said to occur when the measured rate /cb of a given chemical reaction changes according to the nature of the base B used to catalyse the reaction. Quite frequently, the measured rate varies systematically with the strength of the various bases used to catalyse the reaction according to the first Bronsted equation 

Thereafter, these equations and others can be rearranged to give solutions for all the enzyme species including and [E + S] for instance. These solutions are then substituted back 

This equation is still relatively complicated if concise. Therefore, we will have to apply some boundary conditions to reduce this further in order to obtain useful information. Let us assume that [S] [Ks] (i.e. kcat conditions), then making the usual substitution for Vmax (see above) we arrive at 

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In the enzyme design approach, as discussed in the first part of this chapter, one attempts to utilize the mechanistic understanding of chemical reactions and enzyme structure to create a new catalyst. This approach represents a largely academic research field aiming at fundamental understanding of biocatalysis. Indeed, the invention of functional artificial enzymes can be considered to be the ultimate test for any theory on enzyme mechanisms. Most artificial enzymes, to date, do not fulfill the conditions of catalytic efficiency and price per unit necessary for industrial applications. 

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... 

According to the most advanced theories of enzyme catalysis, differential stabilisation of reaction transition states relative to ground states is the most effective way to effect catalysis irrespective of whether there is an excess or lack of substrate available for biocatalysis (see Chapter 8 Figure 10.17). Therefore, in order for an antibody to act as an enzyme, the antibody... 

Integral theory of solution, potentials of mean force, RPA theory Proteins and biocatalysis... 

The above-mentioned common example of water formation also points out the limits of the equilibrium theory. In biochemistry this theory is very useful in explaining energetics and the nature of biocatalysis, but it would be a gross mistake to assume that the organism is anywhere near chemical equilibrium (AF = 0). L. V. Bertalanffy put it succinctly A closed system at equilibrium neither needs energy for its maintenance, nor can energy be obtained from it. The chemical equilibrium, for this reason, is unable to produce work. In order for a system to perform work, it must not be at equilibrium, but rather it must tend toward equilibrium. And in order for the system to be able to persist in its tendency, it must be kept in a steady state. Such is the situation with the organism, whose constant capacity for work is insured by the fact that it is an open system. ... 

As discussed in part 2.2.3 biocatalysis may be used both in asymmetric synthesis and resolution in order to obtain enantiopure compounds. A major difference between asymmetric synthesis and resolution is that the former in theory may give 100% yield of the wanted enantiomer. Resolution on the other hand can only give 50% yield since the starting point is a mixture of 50% of each enantiomer. This is the classical disadvantage of resolution. 

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. 

A Chapter on biocatalysis is not really complete without introducing the idea of transition state theory and the concept of transition state stabilisation as the most fundamental means in biocatalysis for biocatalysts to effect rate enhancements. 

Koper, M. T. M., and Heering, H. A. 2010. Comparison of electrocatalysis and hio-electrocatalysis of hydrogen and oxygen redox reactions, A. Wiecleowski and A. H. Heering, (Eds), Fuel Cell Science Theory, Fundamentals and Biocatalysis, pp. 71-110. Hoboken, NJ John Wiley Sons, Inc. 

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