Enzyme catalysis factors

The previous chapters taught us how to ask questions about specific enzymatic reactions. In this chapter we will attempt to look for general trends in enzyme catalysis. In doing so we will examine various working hypotheses that attribute the catalytic power of enzymes to different factors. We will try to demonstrate that computer simulation approaches are extremely useful in such examinations, as they offer a way to dissect the total catalytic effect into its individual contributions. 

It has been frequently suggested that dynamical factors are important in enzyme catalysis (Ref. 9), implying that enzymes might accelerate reactions by utilizing special fluctuations which are not available for the corresponding reaction in solutions. This hypothesis, however, looks less appealing when one examines its feasibility by molecular simulations. That is, as demonstrated in Chapter 2, it is possible to express the rate constant as... 

Entropic Factors in Model Compounds and Their Relevance to Enzyme Catalysis... 

The entropic hypothesis seems at first sight to gain strong support from experiments with model compounds of the type listed in Table 9.1. These compounds show a huge rate acceleration when the number of degrees of freedom (i.e., rotation around different bonds) is restricted. Such model compounds have been used repeatedly in attempts to estimate entropic effects in enzyme catalysis. Unfortunately, the information from the available model compounds is not directly transferable to the relevant enzymatic reaction since the observed changes in rate constant reflect interrelated factors (e.g., strain and entropy), which cannot be separated in a unique way by simple experiments. Apparently, model compounds do provide very useful means for verification and calibration of reaction-potential surfaces... 

In view of the arguments presented in this chapter, as well as in previous chapters, it seems that electrostatic effects are the most important factors in enzyme catalysis. Entropic factors might also be important in some cases but cannot contribute to the increase of kcJKM. Furthermore, as much as the correlation between structure and catalysis is concerned, it seems that the complimentarity between the electrostatic potential of the enzyme and the change in charges during the reaction will remain the best correlator. Finally, even in cases where the source of the catalytic activity of a given enzyme is hard to elucidate, it is expected that the methods presented in this book will provide the crucial ability to examine different hypothesis in a reliable way. 

Reaction of glycosylmethylamines with aryldiazonium salts gives a class of compounds which, by acid catalysis or unknown factors of enzymic catalysis, generate glycosylmethyldiazonium ions. These, in turn, lose nitrogen, to yield highly electrophilic carbenium ions, as illustrated for the ) -d-galactosyl derivative 38 (see Scheme 8). 

The study of both carbonyl and carbon acid participation in ester hydrolysis has been used by Bowden and Last (1971) to evaluate certain of the factors suggested for important roles in enzymic catalysis. A first model concerns a comparison of the three formyl esters and shows that the proximity of the formyl to the ester group and internal strain increase in passing along the series, 1,2-benzoate, 1,8-naphthoate and 4,5-phenanthroate. The very large rate enhancements result from the proximity of the internal nucleophile once formed and from internal strain. Strain is increased or induced by the primary... 

Baldwin s rules. It is noteworthy that the EM5/EM6 ratio is reduced to a factor as small as about 2, which is less than the intrinsic entropic advantage of 5- over 6-membered ring formation. Kirby (1980) in his review lists a large number of EM data for intramolecular nucleophilic additions to carbonyl. Probably because these data derive from laboratories of chemists mainly interested in intramolecular nucleophilic catalysis and its relevance to understanding enzymic catalysis, the great majority of them refer to reactions occurring via 5- and 6-membered transition states. The only example where a 4-membered transition state is involved is (70), whose kinetics were studied... 

The factors — or at least some of them — which control reactivity in intramolecular reactions are relevant to enzyme catalysis, which also involves reactions between functional groups brought together in close and precisely defined proximity (Kirby, 1980). This has been an area of lively discussion in the recent literature [for a brief summary and leading references see Paquette et al. (1990)]. The main difficulty in making generalizations about the dependence of reactivity on geometry based on results from systems in which proximity is covalently enforced lies in the constraints imposed by particular systems. These may well affect reactivity... 

Hence the dimension ("the order") of the reaction is different, even in the simplest case, and hence a comparison of the two rate constants has little meaning. Comparisons of rates are meaningful only if the catalysts follow the same mechanism and if the product formation can be expressed by the same rate equation. In this instance we can talk about rate enhancements of catalysts relative to another. If an uncatalysed reaction and a catalysed one occur simultaneously in a system we may determine what part of the product is made via the catalytic route and what part isn t. In enzyme catalysis and enzyme mimics one often compares the k, of the uncatalysed reaction with k2 of the catalysed reaction if the mechanisms of the two reactions are the same this may be a useful comparison. A practical yardstick of catalyst performance in industry is the space-time-yield mentioned above, that is to say the yield of kg of product per reactor volume per unit of time (e.g. kg product/m3.h), assuming that other factors such as catalyst costs, including recycling, and work-up costs remain the same. 

Enzymes are extremely effective catalysts. They can increase the rate of a catalyzed reaction by a factor of 10 or more. To grasp the mechanisms involved in enzyme catalysis, we can start by looking at the course of an uncatalyzed reaction more closely. 

In terms of enzyme catalysis, the following factors are likely to influence the magnitude of the rate enhancement in enzymatic processes (a) proximity and orientation effects (b) electrostatic complementarity of the enzyme s active site with respect to the reactant s stabilized transition state configuration (c) enzyme-bound metal ions that serve as template, that alter pK s of catalytic groups, that facilitate nucleophilic attack, and that have... 

Acid-base catalysis appears to be an important factor in virtually all enzymatic reactions. The rates of proton transfer reactions have been well studied in model systems,30 but not during the course of enzyme catalysis. The protonation and deprotonation of acids and bases can be represented as... 

In enzyme catalysis entropy is probably one of the most important factors. Enzyme reactions take place with substrates that are nanoconfined in the active sites and form a very tight enzyme-substrate complex. The catalytic groups are part of the same molecule as the substrate so there is no loss of transition or rotational entropy in the TS. 

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