The nicotinamide nucleotide specificity of glutamate dehydrogenase in intact RAT-liver mitochondria

1. The kinetics of oxidation of intramitochondrial reduced nicotinamide nucleotides by -oxoglutarate plus ammonia in intact rat-liver mitochondria have been reinvestigated. It is demonstrated that the preferential oxidation of NADPH observed on addition of ammonia to mitochondria, preincubated under energized conditions in the presence of -oxoglutarate, is due to a transhydrogenation catalysed by glutamate dehydrogenase rather than to an energy-dependent modification of the nicotinamide nucleotide specificity of the enzyme in intact mitochondria.

2. When mitochondria are preincubated at 25 °C under energized conditions in the presence of respiratory inhibitors with the substrates of glutamate dehydrogenase, an oxidation of NADPH, but not of NADH, is brought about by decreasing the reaction temperature. Both the rate of NADPH oxidation and the final steady-state mass-action ratio of nicotinamide nucleotides are dependent on the concentration of ammonia and on the final reaction temperature. A similar effect is observed when rhein is added to the reaction medium at 25 °C in order to inhibit the energy-linked transhydrogenase reaction.

3. In the presence of the substrates of glutamate dehydrogenase, intact ratliver mitochondria catalyse an ATPase reaction due to the simultaneous activity of the energy-linked transhydrogenase and the non-energy-linked transhydrogenation catalysed by glutamate dehydrogenase.

4. These findings are discussed in relation to the nicotinamide nucleotide specificity of glutamate dehydrogenase and to a possible compartmentation of nicotinamide nucleotides in intact rat-liver mitochondria.     

Apparent negative co-operativity and substrate inhibition in overexpressed glutamate dehydrogenase from Escherichia coli

The gene for Escherichia coli glutamate dehydrogenase (EcGDH) has been overexpressed, and a simplified purification procedure afforded greatly increased yields of c. 40 mg pure EcGDH L⁻¹ culture. EcGDH was unstable at a low concentration in plastic tubes, but stabilization measures allowed a robust kinetic characterization. Contrary to past reports, EcGDH deviates from Michaelis–Menten kinetics, exhibiting apparent mild negative co-operativity with both l -glutamate and NADP⁺, with Hill coefficients of 0.90 and 0.92, respectively. NADPH yielded simple Michaelis–Menten kinetics but both 2-oxoglutarate and NH₄⁺ showed substrate inhibition. pH optima were 9 for oxidative deamination and 8 for reductive amination.     

The chymotrypsin-catalysed activation of bovine liver glutamate dehydrogenase.

Rat heart cells and mitochondria were incubated with supernatants from eosinophils or neutrophils that had been stimulated with zymosan-C3b. Supernatants from eosinophils, but not neutrophils, were toxic to rat heart cells in a dose-dependent manner. This was associated with an increased O2 uptake, which was blocked by either 1 mM-cyanide or 100 microM-ouabain. Supernatants from eosinophils, but not neutrophils, caused a decrease in O2 uptake by rat heart mitochondria utilizing pyruvate (+ malate) but not other substrates. The activity of pyruvate dehydrogenase (EC 1.2.4.1) from rat heart was inhibited by Ca2+-free eosinophil supernatants. The activity of oxoglutarate dehydrogenase (EC 1.2.4.2) was also inhibited but not that of lipoamide dehydrogenase (EC 1.6.4.3). Prior incubation with heparin prevented these effects of eosinophil supernatants on heart cells, suggesting that they were caused by eosinophil cationic proteins. Other cationic proteins, including poly-L-lysine and poly-L-arginine were also toxic to rat heart cells, but these reduced O2 uptake. It was concluded that granulocyte secretion products containing eosinophil cationic proteins are toxic to isolated rat heart cells in vitro. This may be due to an initial increase in membrane permeability, which may lead to activation of (Na+ + K+)-dependent ATPase and increased O2 uptake. A second step may involve inhibition of pyruvate dehydrogenase by the same products, leading to a decreased O2 uptake. It is suggested that these mechanisms could contribute to the development of cardiac injury and myocardial disease in clinical situations where many degranulated eosinophils are present.     

Theoretical analysis of the consequences of cyclic nucleotide phosphodiesterase negative co-operativity. Amplification and positive co-operativity of cyclic AMP accumulation.

Most tissues contain multiple forms of cyclic nucleotide phosphodiesterases (3':5'-cyclic-nucleotide 5' nucleotidohydrolase, EC 3.1.4.17). Consequently, in most, if not in all, tissues, substrate-velocity curves deviate from Michaelian kinetics and exhibit an apparent negative co-operativity. We have studied the possible theoretical consequences of this property on the quantitative features of cyclic AMP accumulation in response to activation of adenylate cyclase. Negative co-operativity of phosphodiesterases tends to generate a "positively co-operative" cyclic AMP accumulation curve. It amplifies the stimulation of cyclic AMP accumulation as compared with the stimulation of cyclic AMP synthesis. It enhances the sensitivity of cyclic AMP accumulation to slight variation of phosphodiesterase maximal velocity. It tends to shift the cyclic AMP accumulation curve to higher concentrations of stimulator as compared with the adenylate cyclase activation curve. This accounts for much of the data in the literature of hormonal effects on phosphodiesterase activity. It shows that the characteristics of cyclic nucleotide phosphodiesterases are as important as those of adenylate cyclase in determining the response of the system.     

The role of the nicotinamide and adenine subsites in the negative co-operativity of coenzyme binding to glyceraldehyde-3-phosphate dehydrogenase.

The interaction of 3-aminopyridine-adenine dinucleotide, an NAD ⁺ 2 analogue which is fluorescent at the pyridine end of the molecule, with rabbit muscle glyceraldehyde-3-phosphate dehydrogenase was investigated. The fluorescence properties of the AAD⁺ molecule were used to monitor the nicotinamide subsites ou the GPDHase tetramer, the fluorescent aminopyridine moiety of the molecule serving as an intrinsic probe. Although the binding of AAD⁺ wag found to be negatively co-operative, no conformational changes induced at the nicotinamide subsite upon coenzyme binding were found to be transmitted to neighboring subunits. These findings, in conjunction with our earlier findings and with the observation that different NAD⁺ analogues which differ in the chemistry of the pyridine moiety bind with different extents of co-operativity, enable us to offer specific roles for the nicotinamide and the adenine subsites in generating the negative co-operativity.It is suggested that the structure of the pyridine moiety of the coenzyme controls the mode of binding of the pyridine moiety to the nicotinamide subsite. This, in turn, controls the orientation of the adenine moiety with respect to its subsite, thereby determining the mode of the interactions between the adenine and its binding domain. As the propagation of conformational changes caused by these interactions to neighboring subunits is believed to be the cause of the negative co-operativity exhibited by this enzyme towards coenzyme binding, the structure of the pyridine moiety controls this phenomenon.     

Heat denaturation of bovine liver glutamate dehydrogenase.

Heat denaturation of bovine liver glutamate dehydrogenase occurred at 47 degrees with loss of enzyme activity and formation of inactive, insoluble protein. Fractional loss of catalytic activity coincided with alteration in protein fluorescence and solubility for a corresponding percentage of protein molecules. Operationally, at 50% denaturation, one-half of the total population of enzyme molecules is fully active catalytically and soluble and the other half of the protein molecule population is completely inactive catalytically and insoluble.     

Negative co-operativity in glutamate dehydrogenase. Involvement of the 2-position in glutamate in the induction of conformational changes.

The 2-position substituent on substrates or substrate analogues for glutamate dehydrogenase is shown to be intimately involved in the induction of conformational changes between subunits in the hexamer by coenzyme. These conformational changes are associated with the negative co-operativity exhibited by this enzyme. 2-Oxoglutarate and L-2-hydroxyglutarate induce indications of co-operativity similar to those induced by the substrate of oxidative deamination, glutamate, in kinetic studies. Glutarate (2-position CH2) does not. A comparison of the effects of L-2-hydroxyglutarate and D-2-hydroxyglutarate or D-glutamate indicates that the 2-position substituent must be in the L-configuration for these conformational changes to be triggered. In addition, glutarate and L-glutamate in ternary enzyme-NAD(P)H-substrate complexes induce very different coenzyme fluorescence properties, showing that glutamate induces a different conformation of the enzyme-coenzyme complex from that induced by glutarate. Although glutamate and glutarate both tighten the binding of reduced coenzyme to the active site, the effect is much greater with glutamate, and the binding is described by two dissociation constants when glutamate is present. The data suggest that the two carboxy groups on the substrate are required to allow synergistic binding of coenzyme and substrate to the active site, but that interactions between the 2-position on the substrate and the enzyme trigger the conformational changes that result in subunit-subunit interactions and in the catalytic co-operativity exhibited by this enzyme.     

A product-inhibition study of bovine liver glutamate dehydrogenase.

1. Initial rates of oxidative deamination of L-glutamate with NAD+ as coenzyme, and of reductive aminiation of 2-oxoglutarate with NADH as coenzyme, catalysed by bovine liver glutamate dehydrogenase were measured in 0.111 M-sodium phosphate buffer, pH 7, at 25 degrees C, in the absence and presence of product inhibitors. All 12 possible combinations of variable substrate and product inhibitor were used. 2. Strict competition was observed between NAD+ and NADH, and between glutamate and 2-oxoglutarate. All other inhibition patterns were clearly non-competitive, except for inhibition by NH4+ with NAD+ as variable substrate. Here the extrapolation did not permit a clear distinction between competitive and non-competitive inhibition. 3. Mutually non-competitive behaviour between glutamate and NH4+ indicates that these substrates can be bound at the active site simultaneously. 4. Primary Lineweaver-Burk plots and derived secondary plots of slopes and intercepts against inhibitor concentration were linear, with one exception: with 2-oxoglutarate as variable substrate, the replot of primary intercepts against inhibitory NAD+ concentration was curved. 5. Separate Ki values were evaluated for the effect of each product inhibitor on the individual terms in the reciprocal initial-rate equations. With this information it is possible to calculate rates for any combination of substrate concentrations within the experimental range with any concentration of a single product inhibitor. 6. The inhibition patterns are consistent with neither a simple compulsory-order mechanism nor a rapid-equilibrium random-order mechanism without modification. They can, however, be reconciled with either type of mechanism by postulating appropirate abortive complexes. Of the two compulsory sequences that have been proposed, one, that in which the order of binding is NADH, NH4+, 2-oxoglutarate, requires an implausible pattern of abortive complex-formation to account for the results. 7. On the basis of a rapid-equilibrium random-order mechanism, dissociation constants can be calculated from the Ki values. Where these can be compared with independent estimates from the kinetics of the uninhibited reaction or from direct measurements of substrate binding, the agreement is reasonable good. On balance, therefore, the results provide further support for the rapid-equilibrium random-order mechanism under these conditions.     

Molecular basis of negative co-operativity in rabbit muscle glyceraldehyde-3-phosphate dehydrogenase

The interactions of rabbit muscle glyceraldehyde-3-phosphate dehydrogenase with NAD⁺ and with its fluorescent derivative 1, N⁶-etheno-adenine dinucleotide were investigated using a variety of spectroscopic methods. These techniques included: difference spectroscopy, circular dichroism, fluorescence and circular polarized luminescence. It was found that the greatest structural change in the protein tetramer occurs upon binding of the first mole of coenzyme. We have also demonstrated that progressive structural changes occur at the adenine subsite in the NAD⁺ binding site as a function of coenzyme saturation. These conformational changes are probably responsible for the progressive decrease in the affinity towards the coenzyme. It was also found that every NAD⁺ molecule induces the same conformational change of the nicotinamide subsite. These results offer a molecular explanation for the negative co-operativity in the binding of the coenzyme, without a change in the catalytic power of the NAD⁺ site as a function of coenzyme saturation. These results also offer a new explanation for the fact that enzyme exhibits half-of-the-sites reactivity towards certain ligands and full-site reactivity towards others. It is suggested that those ligands interacting at the adenine subsite of the NAD⁺ binding site induce the half-of-the-sites reactivity.Our results support the view that both the negative co-operativity in coenzyme binding and half-of-the-sites reactivity are due to ligand-induced conformational changes on an a priori symmetric glyceraldehyde-3-phosphate dehydrogenase molecule.     

The reaction of bovine glutamate dehydrogenase with periodate-oxidised ADP

1. The reactive analogue oADP produced by periodate oxidation of ADP has been studied as a potential affinity label for the enzyme bovine glutamate dehydrogenase, using circular dichroism (CD) difference spectroscopy to monitor specific binding. 2. The analogue binds stoichiometrically, rapidly and reversibly to the adenine nucleotide binding site with Kd approximately equal to 12 microM (20 degrees C, pH 7) with characteristic intensification of the adenine nucleotide CD at 260 nm. 3. This complex is unstable and decays with a half-life of about 1.5 h; the analogue then becomes attached as a Schiff base to a number of subsidiary sites, including the enzyme active site, with partial inactivation of the enzyme. 4. Depending upon initial concentration of oADP, the enzyme activity is progressively lost during the slow reaction; following borohydride reduction, up to four molecules of analogue are bound/subunit. 5. Protection against loss of enzyme activity is afforded by the coenzyme NAD+ plus glutarate or L-hydroxyglutarate (an effective inhibitor), or by glutarate alone, but not by NAD+ alone. 6. Spectroscopic and protection studies indicate that after the decay of the specific CD signal, the enzyme retains the capacity to bind ADP, but that this is progressively lost in parallel with decay of enzymic activity. 7. The results are consistent with proximity or functional interaction between the adenine nucleotide site and the coenzyme binding portion of the active site. 8. Thus oADP does not act as a true affinity label for the adenine nucleotide binding site, but the reaction subsequent to binding at that site shows some specificity directed towards the active site.     

Analysis of negative cooperativity for glutamate dehydrogenase

The empirical equation, which describes negative cooperativity in the enzyme kinetics, has been proposed. The equation is obtained from the Michaelis-Menten equation where the Michaelis constant is replaced by the effective Michaelis constant, which is a linear function of the v/Vmax ratio (v is the rate of the enzymatic reaction and Vmax is the limiting value of v at saturating concentrations of substrate). The equation allows the limiting values of the Michaelis constant at v/Vmax --> 0 and V/Vmax --> 1 to be estimated, K0 and Klim, respectively. The Klim/K0 ratio is considered as a quantitative characteristic of negative cooperativity. The applicability of the equation has been demonstrated for the kinetic data obtained for glutamate dehydrogenases from various sources (negative kinetic cooperativity for coenzyme). The negative cooperativity for the functions of saturation of protein by ligand is also analyzed. The data on binding of spin-labeled NAD, NADH, and NADPH by beef liver glutamate dehydrogenase are used as examples.     

Substrate specificity via ternary complex formation with glutamate dehydrogenase.

Very littly discrimination is observed in the binary binding of dicarboxylic acid substrate analogues to glutamate dehydrogenase as monitored by proton nuclear magnetic resonance. Variation in length, charge, bulkiness and conformational rigidity resulted in only a factor of five variation in KD and apparent relaxation time, T2. Upon titration of the binary enzyme-ligand complex with coenzyme to form the ternary enzyme-ligand-coenzyme complex strong discrimination is observed. Coenzyme binds tightly only when the correct substrate is present, otherwise it binds 10 to 150 times more weakly.