Dehydrogenase catalysis models

Goward, C.R. Nicholls, D.J. (1994) Malate dehydrogenase a model for structure, evolution, and catalysis. Protein Sci. 3, 1883-1888. 

The NAD+-dependent alcohol dehydrogenase from horse liver contains one catalytically essential zinc ion at each of its two active sites. An essential feature of the enzymic catalysis appears to involve direct coordination of the enzyme-bound zinc by the carbonyl and hydroxyl groups of the aldehyde and alcohol substrates. Polarization of the carbonyl group by the metal ion should assist nucleophilic attack by hydride ion. A number of studies have confirmed this view. Zinc(II) catalyzes the reduction of l,10-phenanthroline-2-carbaldehyde by lV-propyl-l,4-dihy-dronicotinamide in acetonitrile,526 and provides an interesting model reaction for alcohol dehydrogenase (Scheme 45). The model reaction proceeds by direct hydrogen transfer and is absolutely dependent on the presence of zinc(II). The zinc(II) ion also catalyzes the reduction of 2- and 4-pyridinecarbaldehyde by Et4N BH4-.526 The zinc complex of the 2-aldehyde is reduced at least 7 x 105 times faster than the free aldehyde, whereas the zinc complex of the 4-aldehyde is reduced only 102 times faster than the free aldehyde. A direct interaction of zinc(II) with the carbonyl function is clearly required for marked catalytic effects to be observed. 

Recently, a controversial debate has arisen about whether the optimization of enzyme catalysis may entail the evolutionary implementation of chemical strategies that increase the probability of tunneling and thereby accelerate reaction rates [7]. Kinetic isotope effect experiments have indicated that hydrogen tunneling plays an important role in many proton and hydride transfer reactions in enzymes [8, 9]. Enzyme catalysis of horse liver alcohol dehydrogenase may be understood by a model of vibrationally enhanced proton transfer tunneling [10]. Furthermore, the double proton transfer reaction in DNA base pairs has been studied in detail and even been hypothesized as a possible source of spontaneous mutation [11-13]. 

On the basis of the crystal structure of a Bacillus stearothermophilus pyruvate dehydrogenase subcomplex formed between the heterotetrameric El and the peripheral subunit binding domain of E2 with an evident stmctural dissymmetry of the two active sites, a direct active center communication via an acidic proton tunnel has been proposed (Frank et ak, 2004). According to this, one active site is in a closed state with an activated cofactor even before a substrate molecule is engaged, whereas the activation of the second active site is coupled to decarboxylation in the first site. Our own kinetic NMR studies on human PDH El (unpublished) support the model suggested, but similar studies on related thiamin enzymes, such as pyruvate decarboxylase, transketolase or pyruvate oxidase reveal that half-of-the-sites reactivity is a unique feature of ketoacid dehydrogenases. In line with this. X-ray crystallography studies on intermediates in transketolase catalysis indicated an active site occupancy close to unity in both active sites (Fiedler et al., 2002 and G. Schneider, personal communication). 

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. 

Holbrook JJ, Stinson RA (1973) The use of ternary complexes to study ionizations and isomerizations during catalysis by lactate dehydrogenase. Biochem J 131 739-748 Hoshide F, Ohi S, Baba N, Oda J, Inouye Y (1982) Asymmetric reduction with bis(NADH) model compounds. Agric Biol Chem 46 2173-2175 Hoshide F, Baba N, Oda J, Inouye Y (1983) Asymmetric reduction by an NADH model compound with L-prolinamide in the N1 substituent. Agric Biol Chem 47 2141-2143... 

The latter method, called the PI-FEP/UM approach, allows accurate primary and secondary kinetic isotope effects to be computed for enzymatic reactions. These methods are illustrated by applications to three enzyme systems, namely, the proton abstraction and reprotonation process catalyzed by alanine race-mase, the enhanced nuclear quantum effects in nitroalkane oxidase catalysis, and the temperature (in)dependence of the wild-type and the M42W/G121V double mutant of dihydrofolate dehydrogenase. These examples show that incorporation of quantum mechanical effects is essential for enzyme kinetics simulations and that the methods discussed in this chapter offer a great opportunity to more accurately model the mechanism and free energies of enzymatic reactions. 

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