Ionization-linked cooperative interactions in the active site of horse liver alcohol dehydrogenase

Affinity labeling of horse liver alcohol dehydrogenase with iodoacetate in the presence of the activator imidazole has been studied from pH 6.1 to 10.5. The pH profiles for the dissociation constants of iodoacetate from the free enzyme and the enzyme-imidazole complex and of imidazole from the free enzyme and the binary enzyme-iodoacetate complex were determined. The variation with pH of the dissociation constants of iodoacetate (KI) and imidazole (KL) have in common a pKa of 8.6 assigned to the zinc-water ionization, and a pKa near 10. Lysine modification by ethyl acetimidate results in a higher affinity of iodoacetate to the enzyme at high pH as the pKa values of the lysine residues are increased. The binding of iodoacetate and imidazole at each enzyme subunit shows negative cooperativity at pH less than 9, with an interaction constant of 4.8 at pH 6.1. Positive cooperativity is observed at pH greater than 9, with an interaction constant of 0.5 at pH 10.5. The pH-dependent change in cooperativity results from the removal of the zinc-water ionization when imidazole becomes coordinated to the catalytic zinc ion. When iodoacetate binds at the anion binding site, a large perturbation of the zinc-water ionization is observed. Unlike imidazole, the binding of 1,10-orthophenanthroline and iodoacetate shows positive cooperativity at both pH 8.2 and 10.0 with an interaction constant as low as 0.06 at pH 10.0.     

Mapping of the active site of alcohol dehydrogenase with low-molecular ligands

In search of an active alcohol dehydrogenase inhibitor, the structure of which may serve as the basis for a potential drug design, the active site of alcohol dehydrogenase containing NAD and Zn²⁺ ions was mapped using the method of molecular mechanics. Molecular docking was performed using a number of ligands containing characteristic functional groups: formate ion, ammonia, ammonium ion, methanol, and methylamine. Sites of preferable binding were revealed for each ligand and arranged in order of decreasing energy of binding to the enzyme. A comparison of the predicted ligand-binding sites and the experimental data on the location of water and inhibitor binding sites in the known structures of corresponding alcohol dehydrogenase complexes indicated a coincidence of the complex formation sites, which confirms the validity of the method and provides the requirements for a highly effective inhibitor (the pharmacophore model).     

Mapping of active site of alcohol dehydrogenase with low-molecular ligands

In search of an active alcohol dehydrogenase inhibitor, the structure of which may serve as the basis for a potential drug design, the active site of alcohol dehydrogenase containing NAD and Zn2+ ions was mapped using the method of molecular mechanics. Molecular docking was performed using a number of ligands containing characteristic functional groups: formate ion, ammonia, ammonium ion, methanol, and methylamine. Sites of preferable binding were revealed for each ligand and arranged in order of decreasing energy of binding to the enzyme. A comparison of the predicted ligand-binding sites and the experimental data on the location of water and inhibitor binding sites in the known structures of corresponding alcohol dehydrogenase complexes indicated a coincidence of the complex formation sites, which confirms the validity of the method and provides the requirements for a highly effective inhibitor (the pharmacophore model).     

Kinetic equivalence of the active sites of alcohol dehydrogenase from horse liver.

The reduction, catalysed by liver alcohol dehydrogenase, of benzaldehyde in the presence and absence of pyrazole, and the oxidation of benzyl alcohol and cyclohexanol in the presence of isobutyramide, has been measured by the stopped-flow technique. In performing these experiments particular care was taken to purify the enzyme, coenzymes, substrates and inhibitors, and to minimise as much as possible the effects of a blank substrate reaction. The calculation of the amount of substrate converted to product during the various phases of the transient process was based on the absorption coefficients for the enzyme-coenzyme and enzyme-coenzyme-inhibitor complexes determined in the absence of substrate. The results show that the two active sites of liver alcohol dehydrogenase are kinetically equivalent and that the enzyme does not exhibit half-of-the-sites reactivity.     

Dissociation of outer-sphere water is rate-limiting for the binding of ligands in the active site of horse liver alcohol dehydrogenase

The association of imidazole and auramine O to native horse-liver alcohol dehydrogenase [Zn(II)LADH] and active-site specifically cobalt(II)-substituted horse-liver alcohol dehydrogenase [Co(II)LADH], respectively, has been investigated. In all cases [except imidazole binding to Zn(II)LADH in the presence of auramine O] the association rates approached an upper limit (kmax). The kmax values were compared for the metal ligands imidazole (monodentate), 1,10-phenanthroline and 2,2'-bipyridine (bidentate; see also the preceding paper), and for auramine O which does not coordinate to the catalytic metal ion. Independent of the large differences in their structure and metal-bonding capability, all these compounds exhibit common, maximum, limiting rate constants of about 60 s-1 and 200 s-1 for Co(II)LADH and Zn(II)LADH, respectively. These results demonstrate that kmax is strongly dependent on the catalytic metal ion but not on the ligand. The absence of spectral changes in the d-d transitions of the catalytic Co(II) ion upon auramine O binding to Co(II)LADH indicates that the rate-limiting step is not accompanied by a major conformational change. Finally, it is concluded that reactions in the inner coordination sphere of the catalytic metal ion (i.e. the metal-bound water molecule) are not responsible for the step characterized by kmax. We propose the rate-limiting step to consist of the dissociation of one or several water molecules from the second coordination sphere of the catalytic metal ion in the active site of LADH in its open conformation.     

Stopped-flow determination of the active form of acetaldehyde in the liver alcohol dehydrogenase catalyzed reaction.

A stopped-flow spectrophotometer was modified so that the volumes to be mixed were in a ratio of 1:50. Using this instrument, we have shown that the effective substrate in the reduction of acetaldehyde catalyzed by horse liver alcohol dehydrogenase was the carbonyl form of acetaldehyde and that the enzyme does not catalyze the dehydration of the hydrated form of acetaldehyde. Unlike trifluoroacetaldehyde hydrate, which is a competitive inhibitor with respect to ethanol, acetaldehyde hydrate did not inhibit the enzymatic reaction at concentrations as high as 60 mM.     

Esterase activity of liver alcohol dehydrogenase.

Liver alcohol dehydrogenase is found to possess, in addition to its dehydrogenase and dismutase activities, the ability to hydrolyze octanoate esters at a rate approximately $\text{1}\text{500}\text{–}\text{1}\text{1000}$ of that of the dehydrogenase reaction. The esterase and dehydrogenase activities exhibit an identical isozyme pattern indicating that the same protein catalyzes both reactions. Inhibition studies suggest that the esterase activity presumably shares the catalytic domain with the dehydrogenase activity.     

Chemical and computer graphics studies on the topography of the ribonuclease A active site cleft. A model of the enzyme-pentanucleotide substrate complex

The affinity labelling of bovine pancreatic ribonuclease A with 6-chloropurine 5' ribonucleotide allowed us to postulate the existence of a new phosphate-binding subsite, P2, adjacent to the main purine-binding subsite. The study of this reaction in greater detail together with the study of a complex of the enzyme with the pentanucleotide pApUpApApG by means of model building and computer graphics indicate that at least five phosphate groups of the RNA molecule can interact with five positive regions of the enzyme. In each one a lysine residue is present: Lys-104, -66, -41, -7 and -37 appear sequentially in the 5'----3' direction. The distance between each lysine is 0.7-0.8 nm, the same distance as that found between the phosphate groups on the RNA molecule. The study also enabled many amino acid residues of the enzyme to be described as forming part of, or being near, the different binding subsites.     

Multifunctionality of liver alcohol dehydrogenase. Studies of aldehyde dehydrogenase activity

Kinetic studies of the liver alcohol dehydrogenase catalyzed dehydrogenation of aldehydes were carried out over a wide range of octanal concentrations. The effect of specific inhibitors of liver alcohol dehydrogenase on aldehyde dehydrogenase activity was examined. The results were consistent with a steady-state random mechanism with the formation of the ternary E · NADH octanal complex at low temperatures. This ternary complex becomes inconspicuous at high temperatures. The aldehyde dehydrogenase activity was found to associate with all ethanol-active isozymes. The dual dehydrogenase reactions are catalyzed by the same molecule, presumably in the region of the same domain. However, the two activities respond differently to structural changes.     

Self-association of lyophilized horse liver alcohol dehydrogenase.

The molecular weights of lyophilized and non-lyophilized horse liver alcohol dehydrogenase have been compared by quasi-elastic light scattering, and ultracentrifugation. Whereas the non-lyophilized enzyme has the expected molecular weight of 78 000, the lyophilized enz)me has an initial molecular weight of about 10(6) which increases with time by an endothermic process. This result shows that any physical measurement using lyophilized liver alcohol dehydrogenase to investigate the enzyme mechanism, which relies upon the molecular size, will be invalid.     

Rat liver alcohol dehydrogenase. I. Purification and characterization

Alcohol dehydrogenase was purified in 14 h from male Fischer-344 rat livers by differential centrifugation, (NH4)2SO4 precipitation, and chromatography over DEAE-Affi-Gel Blue, Affi-Gel Blue, and AMP-agarose. Following HPLC more than 240-fold purification was obtained. Under denaturing conditions, the enzyme migrated as a single protein band (Mr congruent to 40,000) on 10% sodium dodecyl sulfate-polyacrylamide gels. Under nondenaturing conditions, the protein eluted from an HPLC I-125 column as a symmetrical peak with a constant enzyme specific activity. When examined by analytical isoelectric focusing, two protein and two enzyme activity bands comigrated closely together (broad band) between pH 8.8 and 8.9. The pure enzyme showed pH optima for activity between 8.3 and 8.8 in buffers of 0.5 M Tris-HCl, 50 mM 2-(N-cyclohexylamino)ethanesulfonic acid (CHES), and 50 mM 3-(cyclohexylamino)-1-propanesulfonic acid (CAPS), and above pH 9.0 in 50 mM glycyl-glycine. Kinetic studies with the pure enzyme, in 0.5 M Tris-HCl under varying pH conditions, revealed three characteristic ionization constants for activity: 7.4 (pK1); 8.0-8.1 (pK2), and 9.1 (pK3). The latter two probably represent functional groups in the free enzyme; pK1 may represent a functional group in the enzyme-NAD+ complex. Pure enzyme also was used to determine kinetic constants at 37 degrees C in 0.5 M Tris-HCl buffer, pH 7.4 (I = 0.2). The values obtained were Vmax = 2.21 microM/min/mg enzyme, Km for ethanol = 0.156 mM, Km for NAD+ = 0.176 mM, and a dissociation constant for NAD+ = 0.306 mM. These values were used to extrapolate the forward rate of ethanol oxidation by alcohol dehydrogenase in vivo. At pH 7.4 and 10 mM ethanol, the rate was calculated to be 2.4 microM/min/g liver.