Alcohol dehydrogenase model systems

Uncovering of the three dimentional structure of catalytic groups at the active site of an enzyme allows to theorize the catalytic mechanism, and the theory accelerates the designing of model systems. Examples of such enzymes are zinc ion containing carboxypeptidase A 1-5) and carbonic anhydrase6-11. There are many other zinc enzymes with a variety of catalytic functions. For example, alcohol dehydrogenase is also a zinc enzyme and the subject of intensive model studies. However, the topics of this review will be confined to the model studies of the former hydrolytic metallo-enzymes. 

We then coupled the regeneration system 1 to the horse liver alcohol dehydrogenase (HLADH) catalyzed oxidation of cyclohexanol to cyclohexanone as a model system (Fig. 9). 

This zinc metalloenzyme [EC 1.1.1.1 and EC 1.1.1.2] catalyzes the reversible oxidation of a broad spectrum of alcohol substrates and reduction of aldehyde substrates, usually with NAD+ as a coenzyme. The yeast and horse liver enzymes are probably the most extensively characterized oxidoreductases with respect to the reaction mechanism. Only one of two zinc ions is catalytically important, and the general mechanistic properties of the yeast and liver enzymes are similar, but not identical. Alcohol dehydrogenase can be regarded as a model enzyme system for the exploration of hydrogen kinetic isotope effects. 

We shall now briefly outline some of the features of the zinc metalloenzymes which have attracted most research effort several reviews are available, these are indicated under the particular enzyme, and for more detailed information the reader is referred to these. Attention is focussed here, albeit briefly, on carbonic anhydrases,1241,1262,1268 carboxypeptidases, leucine amino peptidase,1241,1262 alkaline phosphatases and the RNA and DNA polymerases.1241,1262,1462 Finally, we examine alcohol dehydrogenases in rather more detail to illustrate the use of the many elegant techniques now available. These enzymes have also attracted much effort from modellers of the enzymic reaction and such studies, which reveal much interesting coordination chemistry and often new catalytic properties in their own right—and often little about the enzyme system itself (except to indicate possibilities), will be mentioned in the next section of this chapter. 

We have already seen a number of models for the zinc(II) containing enzymes such as carbonic anhydrase in Section 11.3.2. Zinc is an essential component in biochemistry, and forms part of the active site of more then 100 enzymes, of which hydrolases (such as alkaline phosphatase and carboxypeptidase A), transferases (e.g. DNA and RNA polymerase), oxidoreductases (e.g. alcohol dehydrogenase and superoxide dismutase) and lysases (carbonic anhydrase) are the most common. In addition, the non-enzyme zinc finger proteins have an important regulatory function. In many of these systems, the non-redox-active Zn2+ ion is present as a Fewis acidic centre at which substrates are coordinated, polarised and hence activated. Other roles of zinc include acting as a template and playing a structural or regulatory role. 

The problem of biomimetic model design simulating the action mechanism of corresponding enzymes is based on the idea of structural-functional conformity. In 1971, alcohol dehydrogenase was primarily synthesized [123], In this biomimetic system the product is formed due to direct electron transfer from the reduced co-factor (NADH) analog to aldehyde. Note that the display of alcohol dehydrogenase catalytic activity requires the presence of zinc (II) ion. 

The reaction catalysed by alcohol dehydrogenases is a transfer of hydride ion from the alcohol to the 4-position of the pyridinium ring of the coenzyme NAD+ (Scheme 6), [For a review of hydride transfer in model systems, see Watt (1988).] The two hydrogen atoms at the 4-position of the dihydro-pyridine ring of NADH are diastereotopic, and over the years it has become apparent that some alcohol dehydrogenases transfer the pro-/ ... 

Hard electrophiles like Mg(C104)2 are used to activate abiotic systems. In the enzyme liver alcohol dehydrogenase (LAD) a considerably different catalytic apparatus is present a zinc ion coordinated to two cysteines and a histidine serves as a coordinating site for the carbonyl compound/alcoholate, as illustrated in equation (10). This zinc ion has amphoteric properties consistent with the capacity to activate the reaction in both directions without being consumed, in other words to act as a catalyst. Synthetic models of this catalytically active zinc have been shown to possess some catalytic activity in analogy to the enzyme (see Section L3.3.5.1iii). 

To date, the only experimental examples where a 2° Swain-Schaad relationship resulted in a breakdown of semidassical models and implicated tunneling and coupled motion were from studies of alcohol dehydrogenases (ADH). Furthermore, all these studies were conducted on the oxidation of the alternative substrate benzyl alcohol to aldehyde. The only attempt so far to conduct similar measurements used a very different system (DHFR). These experiments revealed no deviation from the semidassical EXP [45]. Until such experiments are extended to other systems or at least extended to the reduction of aldehyde to alcohol for the same system, the generalization of their interpretation should be taken with some discretion. These examples are discussed in great detail in Chapter 10, Section 10.5.1.1, and only a concise summary of two seminal examples is presented below. 

Finally, we examine alcohol dehydrogenases in rather more detail to illustrate the use of the many elegant techniques now available. These enzymes have also attracted much effort from modellers of the enzymic reaction and such studies, which reveal much interesting coordination chemistry and often new catalytic properties in their own right—and often little about the enzyme system itself (except to indicate possibilities), will be mentioned in the next section of this chapter. 

Zinc ion is essential for the catalytic activities of both yeast and liver alcohol dehydrogenase. Until recently, model systems have been notably unsuccessful in accounting for the participation of Zn(II) in the enzyme-catalyzed oxidoreductive interconversion of aldehyde and alcohol. The studies of Creighton and Sigman (20) and of Shinkai and Bruice (21, 22) conclusively demonstrate that Lewis (general) acid catalysis by Zn + (and other divalent metal ions) can effectively promote aldehyde reduction by the reduced 1,4-dihydropyridine moiety. 

As a test of the applicability of S/G-1 to large systems, we applied this method to a Zn(ll) dependent system recently studied using the SIBFA procedure. To this end, the Zn(ll)-alcohol dehydrogenase (ADH) active site (de Courcy et al., 2008) was calculated, GEM was used to model the Zn(ll) cation and the remaining system was treated with SIBFA. As can be seen in Fig. 8.4, S/G-1 successfully reproduced the RVS values for a complicated hetero-polyligated complex (Chaudret et al., 2014). 

The mechanism of liver alcohol dehydrogenase (LADH) has been extensively studied. For a recent overview the reader is referred to Ref [93]. Reaction field effects on the transition structure of model hydride transfer systems have been calculated at ab initio 4-3IG basis set level [93, 94]. The active site of enzymes are usually assumed to be designed to receive molecules in the transition state for the reaction they catalyze. This special sort of surrounding medium effects has been computationally documented recently [95]. From the reaction geodesic passing through the transition state for hybride transfer in the pyridium cation/methanolate model system, only the TS-structure could be fitted into the LADH active site. The normal mode analysis carried out on the TS showed an excellent agreement with isotopic substitution experiments [95]. Reaction field calculations on this model systems have also been performed. For an overview of biomolecular interactions the reader is referred to Ref [96]. 

A better model for the investigation of this hypothesis is the gene system in D. melanogaster. Gene sequences which are located on the second and third chromosomes are especially convenient for analysis. Genes of alcohol dehydrogenase (Adh-50.1), phenol oxidase (Tyr-52.4), and kinurenin hydroxylase (cn-57.5) are lo-... 

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