Photoaffinity labeling of soluble chloroplast adenosine 5′-triphosphatase with 3′-O-(4-benzoyl)benzoyl ADP

3′-O-(4-benzoyl)benzoyl ADP (BzADP) acts as a reversible inhibitor of the chloroplast coupling factor 1 ATPase (CF₁) when incubated with the enzyme in the dark. The V_max of ATP hydrolysis is decreased and the kinetics of the reaction are altered from noncooperative to cooperative with respect to ATP. Photoactivation of the benzophenone group in BzADP by irradiation with ultraviolet light (366 nm) results in the covalent binding of BzADP to the enzyme and inactivation of its enzymic activity. Polyacrylamide gel electrophoresis of CF₁-ATPase in the presence of sodium dodecyl sulfate shows that the analog is bound primarily to the enzyme's β subunit. Complete inactivation of the activated CF₁-ATPase occurs upon covalent binding of 2.45 mol BzADP/mol CF₁. Binding of BzADP and inactivation of the ATPase are prevented if ADP, but not ATP, is present during the photoactivation step. The presence of Ca²⁺ during irradiation enhances the rate of BzADP covalent binding as well as the rate of inactivation of the enzyme.     

Studies on photophosphorylation utilizing methylene diphosphonate analogs of ADP and ATP

Spinach chloroplasts were able to photophosphorylate the ADP analog α,β-methylene adenosine 5′-diphosphate (AOPCP). Phosphorylation of AOPCP was catalyzed by chloroplasts that were washed or dialyzed to remove free endogenous nucleotides. In the presence of glucose, hexokinase, AOPCP and ³²P_i, the ³²P label was incorporated into α,β-methylene adenosine 5′-triphosphate (AOPCPOP).In contrast to photophosphorylation of AOPCP, the ATP analog AOPCPOP was a poor substrate for the ATP-P_i exchange reaction and its hydrolysis was neither stimulated by light and dithiothreitol nor inhibited by Dio-9.Photophosphorylation of AOPCP was inhibited by the α,β- and β,γ-substituted methylene analogs of ATP, while phosphorylation of ADP was unaffected by them. The ATP-P_i exchange was also unaffected by both ATP analogs, while the weak AOPCPOP-P_i exchange was inhibited by the β,γ-methylene analog of ATP.Direct interaction of methylene analogs with the chloroplast coupling factor ATPase was indicated by the enzymatic hydrolysis of AOPCPOP on polyacrylamide gels.     

Differential inhibition of Pi-ATP exchange in relation to ATP synthesis and hydrolysis by modification of chloroplast thylakoid membranes with glutaraldehyde

Limited modification of thylakoid membranes with glutaraldehyde inhibits the P_i-ATP exchange reaction much more than ATP synthesis or hydrolysis. More extensive modification of the membranes results in the inhibition of all activities of the ATP synthetase, but does not affect electron transport. Limited modification also does not have much effect on the tight binding of [³H]ADP or the ΔpH supported by ATP hydrolysis. The modification affects the catalytic process itself and not the activation of the latent enzyme. Cross-linking between thylakoid polypeptides is observed only after extensive treatment with glutaraldehyde, while limited modification does not result in cross-linking between polypeptides. The differential inhibition of the P_i-ATP exchange relative to ATP hydrolysis can be explained by the decrease in only one of the kinetic rate constants involved in these reactions. However, the relative insensitivity of photophosphorylation to the modification suggests that different enzyme conformations may participate in phosphorylation (light) and ATP hydrolysis or P_i-ATP exchange (dark).     

Formation of ATP by the adenosine triphosphatase complex from spinach chloroplasts reconstituted together with bacteriorhodopsin.

The energy-linked ATPase complex has been isolated from spinach chloroplasts. This protein complex contained all the subunits of the chloroplast coupling factor (CF1) as well as several hydrophobic compoenents. When the activated complex was reconstituted with added soybean phospholipids, it catalyzed the exchange of radioactive inorganic phosphate with ATP. Sonication of the complex into proteoliposomes together with bacteriorhodopsin yield vesicles that catalyzed light-dependent ATP formation. Both the 32Pi-ATP exchange reactions and ATP formation were sensitive to uncouplers such as 3-tert-butyl-5,2'-dichloro-4'-nitrosalicylanilide, bis-(hexafluoroacetonyl)acetone and carbonyl cyanide-p-trifluoromethoxyphenyl-hydrazone, that act to dissipate a proton gradient. The energy transfer inhibitors dicyclohexylcarbodiimide, triphenyltin chloride and 2-beta-D-glucopyranosyl-4,6'-dihydroxydihydrochalcone were also effective inhibitors of both reactions.     

Regulation of proton leakage from broken chloroplasts by CF0.

Measurements of proton translocation in CF₁-depleted, N, N′-dicyclohexylcarbodiimide-resealed broken chloroplasts were made under different light intensities. Kinetic analysis of the data shows that the outward leakage of accumulated protons through CF₀ is still dependent on light intensity with a first-order rate constant equal to mR₀, where R₀ is the initial rate of proton uptake which normally increases with light intensity and m is a characteristic constant which is independent of proton gradient and light intensity. Measurements of proton translocation in these modified chloroplasts cross-linked with glutaraldehyde under illumination and in the dark respectively suggest that the light-dependent proton leakage through CF₀ is regulated by conformation change in the membrane. It is proposed that the ovserved regulation of proton leakage through the CF₁.CF₀ complex in native chloroplasts is for optimizing the steady state synthesis of ATP under different light intensities.     

Adenosine triphosphate (ATP) hydrolysis promoted by cobalt(III).Participation of polynuclear metal complexes

Complex formation between ATP (adenosine 5′-triphosphate) and tn₂CO^III(aq) (tn = trimethylenediamine) and resulting hydrolysis of the ATP to ADP (adenosine 5′-diphosphate), AMP (adenosine 5′-monophosphate), PP_i (pyrophosphate), and P_i (orthophosphate) have been examined by means of ³¹P nmr. With ATP ～0.1 M and tn₂Co^III(aq) up to 0.3 M, complex formation was promoted by equilibrating solutions for a period at pH 4, after which hydrolysis was allowed to proceed at each of several pHs in the range 5 to 9 prior to quenching by addition of strong base. With ATP 0.01 M and tn₂Co^III(aq) up to 0.08 M, the above procedure was followed in some cases; in other experiments the pH of each ATP/tn₂Co^III(aq) solution was adjusted immediately to a value in the range 5 to 9 with the remainder of the procedure as before. In most cases the hydrolysis was at 25°C, but temperature dependence was also examined. The integrals for the β-phosphorus resonance have been used to analyze for ATP in the quenched solutions; independent measurements of ATP by an enzyme/spectrophotometric method (Bergmeyer) gave similar results. Cobalt to ATP molar ratios up to 1 produce tn₂Co^IIIATP as the predominant ATP complex; this 1:1 complex shows no detectable acceleration in hydrolysis compared to free ATP. Cobalt to ATP molar ratios of ?1 lead to complexes of type (tn₂Co^III)₂ATP and (tn₂Co^III)₃ATP, which exhibit greatly enhanced reactivity towards ATP hydrolysis. At a 2:1 molar ratio (0.1 or 0.01 M ATP), the enhancement is rate is ～10⁵ at pH 7 where the rate is a maximum (comparison for 25°C); at higher molar ratios the rate enhancements are even greater. The results support the view that effective metal ion catalysis of ATP hydrolysis requires formation of reactive species involving more than one metal ion per ATP.     

Assay of RNA-linked nascent DNA pieces with polynucleotide kinase.

The 5′-OH end of DNA created upon alkaline hydrolysis of the RNA-linked nascent DNA pieces can be labeled with [γ-³²P]ATP using T4 polynucleotide kinase. However, it is difficult to use this method for the assay of these molecules in the presence of RNA-free DNA pieces because of the exchange reaction between the γ-phosphate of ATP and the 5′-phosphate of DNA catalyzed by the kinase. This difficulty can be circumvented by performing the polynucleotide kinase reaction at 0°C, where little exchange reaction occurs. Using these conditions, $\text{E. coli pol}$Aexl, a mutant defective in the 5′ → 3′ exonuclease activity of DNA polymerase I, is shown to contain several times as many RNA-linked DNA pieces as the wild type.     

On the mechanism of H+ translocation by mitochondrial H+-ATPase. Studies with chemical modifier of tyrosine residues

In this paper a detailed study of the effect of nitration of tyrosine residues by tetranitromethane on H⁺ conduction and other reactions catalyzed by the H⁺-ATPase complex in phosphorylating submitochondrial particles, uncoupled particles, and the purified complex is presented. Tetranitromethane treatment of submitochondrial particles results in marked inhibition of ATP hydrolysis, ATP-³³P_i exchange, and proton conduction by the H⁺-ATPase complex. These effects are caused by nitration of tyrosine residues of H⁺-ATPase complex as shown by the appearance of the absorption peak at 360 nm (specific for nitrotyrosine formation) and inhibition of ATP hydrolysis and ATP-³³P_i exchange in the complex purified from tetranitromethane-treated particles. H⁺ conduction in phospholipid vesicles inlaid with F₀ is also inhibited by tetranitromethane treatment. These observations indicate that tyrosine residue(s) of F₀ are critically involved in energy-linked proton translocation in the ATP-ase complex.     

Effect of methanol on spinach thylakoid ATPase

Methanol at 35% ($\text{v}\text{v}$) overcomes the latency of spinach thylakoid ATPase. Activation is immediate and reversible involving changes in the V_max, not the K_m of the enzyme, MgATP is a much better substrate than CaATP; free Mg²⁺ noncompetitively inhibits activity. This inhibition can be overcome by the addition of Na₂SO₃. While both MgATP and MgGTP act as substrates, free ATP and GTP both inhibit activity. ADP and MgADP are also inhibitory. Insensitivity to certain inhibitors indicates that methanol neither induces the same conformational changes in CF₁ as illumination does, nor does it lead to coupling between H⁺ movement through CF₀ and ATP hydrolysis. Methanol activation provides a much improved method for assaying thylakoid ATPase.     

Synthesis of modified tryptophanyl-adenylates and of modified adenosine-triphosphates and their use as tools for elucidation of the mechanism of tryptophanyl-tRNA synthetase from yeast

Six analogs of tryptophanyl-adenylate, which is an important intermediate in the enzymatic synthesis of Trp-tRNA^Trp, have been prepared. Four compounds, tryptophanyl-8-bromoadenylate, tryptophanyl-2-chloroadenylate, tryptophanyl-7-deazaadenylate and tryptophanyl-(N⁶-methyl)adenylate, contain modifications in the nucleobase moiety, while tryptophanyl-2′ deoxyadenylate and tryptophanyl-3′-deoxyadenylate were modified in the carbohydrate part of the molecule. Three of these analogs (2-chloro, 7-deaza, 2′-deoxy analogs) as well as ATP analogs with the same modifications were substrates in the aminoacylation reaction; three analogs (8-bromo, N⁶-methyl, 3′-deoxy analogs) were inactive as well as the corresponding ATP analogs. In contrast, in the $\text{ATP}\text{PP}{}_{\mathrm{<mtext>i</mtext>}}$ pyrophosphate exchange in the absence of tRNA all ATP analogs except 8-bromo-ATP were substrates. However, the presence of tRNA reduced the number of ATP analogs being substrates to that number of substrates observed in the aminoacylation. Therefore, it can be concluded that the presence of tRNA is responsible for an increase of specificity. The diastereomers of adenosine 5′-O-(3-thiotriphosphate) (ATPαS), adenosine 5′-O-(2-thiotriphosphate) (ATPβS), and adenosine 5′-O-(3-thiotriphosphate) (ATPγS) were tested with various divalent metals as substrates in the pyrophosphate exchange reaction. The S_p diastereomer of ATPαS is a substrate with Mg²⁺, whereas the R_p diastereomer is inactive. Both diastereomers are inactive in the presence of Zn²⁺. Since Zn²⁺ binds preferentially to the sulfur atom, an explanation of these results is that the Mg²⁺ ion is not bound to the α-phosphate. Only the S_p isomer of the diastereomers of ATPβS acts as substrate in the presence of Mg²⁺. The stereospecificity becomes reversed in the presence of Zn²⁺. ATPγS acts as substrate with both Mg²⁺ and Zn²⁺. These results suggest that the Δ isomer of the β,γ-bidentate ATP-Mg²⁺ complex is the substrate for this enzyme. From these results a molecular model of the ATP-Mg²⁺ complex in the active site can be derived in which the nucleotide is attached to the enzyme by interactions in which the 3′-OH and 6-NH₂ group, one oxygen atom of the α-phosphorus atom, and the coordinated magnesium cation are all involved.     

Purification and reconstitution of the 32Pi-ATP exchange activity of bovine chromaffin granule membrane

Ghosts derived from bovine chromaffin granules have a ³²P_i-ATP exchange activity which is associated with the H⁺ pump of that membrane. This activity was low when compared to bacteria, chloroplasts or submitochondrial particles, but had similar properties (K_m for ATP and P_i, ATP/Mg²⁺ ratio, pH profile, inhibition by dicyclohexylcarbodiimide and tributyltin) to the ATPase from above membranes. The ³²P_i-ATP exchange activity was solubilized by cholate/octylglucoside mixtures. The soluble extract was lipid depleted by ammonium sulfate fractionation and partially purified by sucrose gradient centrifugation. The purified preparation was reconstituted with phospholipids by freeze-thawing. The reconstituted vesicles had a ³²P_i-ATP exchange sensitive to dicyclohexylcarbodiimide and trybutyltin and an ATPase with a sensitivity to the inhibitors which varied with the reconstitution conditions. The α- and β-subunits of F₁-ATPase were major components of the preparation.     

Involvement of phosphate-modified ATP analogs in the reactions of oxidative phosphorylation

Various analogs of adenosine 5′-triphosphate with a modified terminal phosphate group have been tested in energy-requiring reactions with intact mitochondria and submitochondrial particles.It is shown that the fluorophosphate analog ATP(γF) is a strong inhibitor of mitochondrial respiration and of energy requiring reactions which involve the participation of high energy intermediates, generated aerobically by the respiratory chain. On the other hand, ATP(γF) does not affect the ATPase activity of intact or disrupted mitochondria and is less effective in inhibiting ATP-driven reactions.The imidophosphate analog AMP-P(NH)P also inhibits the partial reactions of oxidative phosphorylation, but does not affect ATP synthesis from ADP and P_i. In contrast to ATP(γF), it is a strong inhibitor of both soluble and membrane-bound mitochondrial ATPases.The biological implication of the complementary effects of ATP(γF) and AMP-P(NH)P on mitochondria-catalysed reactions is discussed while suggesting the use of such nucleotide analogs as specific tools for the study of ATP-forming and ATP-utilizing reactions in mitochondria.     

Calorimetric determination of thermodynamic parameters of 2′-dUMP binding to Leishmania major dUTPase

We have investigated the binding of 2′-deoxyuridine 5′-monophosphate (2′-dUMP) to Leishmania major deoxyuridine 5′-triphosphate nucleotide hydrolase (dUTPase) by isothermal titration microcalorimetry under different experimental conditions. Binding to dimeric L. major dUTPase is a non-cooperative process, with a stoichiometry of 1 molecule of 2′-dUMP per subunit. The utilization of buffers with different ionization enthalpies has allowed us to conclude that the formation of the 2′-dUMP–dUTPase complex, at pH 7.5 and 30 °C, is accompanied by the uptake of 0.33±0.05 protons per dUTPase subunit from the buffer media. Moreover, 2′-dUMP shows a moderate affinity for the enzyme, and binding is enthalpically driven across the temperature range studied. Besides, whereas ΔG° remains practically invariant as a function of temperature, both ΔH and ΔS° decrease with increasing temperature. The T_S and T_H were 23.4 and 13.6 °C, respectively. The temperature dependence of the enthalpy change yields a heat capacity change of ΔC_p°=?618.1±126.4 cal·mol^?1·K^?1, a value low enough to discard major conformational changes, in agreement with the fitting model. An interpretation of this value in terms of solvent-accessible surface areas is provided.     

Occurrence of a 3′-phosphoadenosine 5′-Phosphosulphate synthesizing system In two Ochromonas species

The presence of an enzyme capable of incorporating ³⁵SO₄^2? into 3′-phosphoadenosine 5′-phosphosulphate has been demonstrated,in Ochromonas danica and O. malhamensis. This system probably includes the enzymes ATP:sulphate adenyltransferase. E.C. 2.7.7.4 and ATP:adenylsulphate 3′-phosphotransferase, E.C. 2.7.1.25.     

Identification of the Cl− transport site of human red blood cells by a kinetic analysis of the inhibitory effects of a chemical probe

H₂DIDS, the dihydro analog of DIDS (4,4′-diisothiocyanostilbene-2,2′-disulfonic acid) can interact covalently with membrane sites, resulting in an irreversible inhibition of anion exchange. At low temperatures (0°C) and for relatively short times, however, its interaction is largely reversible, so that a kinetic analysis of the nature of its inhibitory effect on Cl^? self exchange can be performed. The effects of variations in the chloride concentration on the inhibitory potency of H₂DIDS are consistent with the concept that Cl^? and H₂DIDS compete for the transport site of the anion exchange system. The value of K_i for H₂DIDS is 0.046 μM, indicating that H₂DIDS has a higher affinity for the transport system than any other inhibitor so far examined. If, as seems probable, the covalent labelling of H₂DIDS occurs at the same site as the reversible binding, H₂DIDS can be used as a covalent label for the transport site. The specific localization of H₂DIDS in the band-3 protein thus indicates that this protein participates directly in anion exchange.     

Isolation,characterization, and reconstitution of a solubilized fraction containing the hydrophobic sector of the mitochondrial proton pump

The hydrophobic sector of the mitochondrial ATPase complex was purified by sequential extraction with cholate and octylglucoside, by further differential solubilization with guanidine and cholate in the presence of phosphatidylcholine, and by fractionation with ammonium sulfate. A polypeptide with a mass of 28,000 dalton was present in the purified hydrophobic section which was cleaved by trypsin, resulting in loss of reconstitution activity. In contrast, dicyclohexylcarbodiimide-binding proteolipid remained unimpaired after exposure to trypsin. The³²P_i-ATP exchange activity of the reconstituted ATPase complex was inhibited byp-hydroxymercuribenzoate, which reacted primarily with the 28,000-dalton protein, as monitored by acrylamide gel electrophoresis with¹⁴C-labeled inhibitor. The function of a 22,000-dalton polypeptide and of some minor components in the region of the proteolipid remains unknown. An examination of the phospholipid requirements for reconstitution of an active complex revealed an unexpected discrepancy. With an excess of phosphatidylethanolamine, optimal reconstitution of³²P_i-ATP exchange and ATP synthesis in the presence of bacteriorhodopsin and light was achieved; at a high phosphatidylcholine:phosphatidylethanolamine ratio, the rate of ATP synthesis remained high, but the rate of³²P_i-ATP exchange dropped precipitously. A new procedure is described for the reconstitution of the ATPase complex with purified phospholipids which is stable for at least 15 days.Abbreviations DCCD N,N-dicyclohexylcarbodiimide - STE-DTT buffer sucrose (250 mM), Tricine-KOH (50 mM), EDTA (5 mM), DTT (5 mM), pH 8.0 - F _o a membranous preparation from mitochondria conferring oligomycin (or rutamycin) sensitivity to F₁ - F₁F₆ coupling factors 1 (ATPase) and 6 - OSCP oligomycin-sensitivity-conferring protein - BSA bovine serum albumin - SDS sodium dodecyl sulfate - DTT dithiothreitol - STE buffer sucrose (250 mM), Tricine-KOH (50 mM), EDTA (5 mM) - TUA particles submitochondrial particles prepared by stepwise exposure of light-layer submitochondrial particles to trypsin and urea, then sonic oscillation in the presence of dilute ammonia (pH 10.4) - OG-cholate buffer glycerol (20%), Tricine (50 mM), MgSO₄ (5 mM), DTT (5mM), cholate (0.5%), octylglucoside (0.5%), pH 8.0 - p-HMB p-hydroxymercuribenzoate     

Formation of pyrophosphate by soluble guanylate cyclase from rat lung.

The guanylate cyclase reaction was studied to determine the identity of the product(s) formed other than guanosine-3′,5′-monophosphate (cyclic GMP). Partially purified guanylate cyclase preparations from rat lung catalyzed the formation of nearly equal amounts of PP₁ and of cyclic GMP from GTP. Column chromatography of the enzyme preparation on DEAE-Sephadex or Bio-Gel A-5m failed to separate the enzyme(s) involved in formation of cyclic GMP and of PP₁. Nucleotide inhibitors of cyclic GMP formation also inhibited PP₁ formation, and Ca²⁺, a stimulant of cyclic GMP formation in the presence of Mn²⁺, also stimulated PP₁ formation. Detectable PP₁ formation was not observed when ATP was present instead of GTP.The results show that guanylate cyclase, in vitro, catalyzes the formation of pyrophosphate from GTP concomitant with the synthesis of cyclic GMP.     

Stereochemistry of binding of thiophosphate analogs of ATP and ADP to carbamate kinase, glutamine synthetase, and carbamoyl-phosphate synthetase

Thiophosphate analogs of adenine nucleotides were used to establish the absolute stereochemistry of nucleotide substrates in the reactions of carbamate kinase (Streptococcus faecalis), unadenylylated glutamine synthetase (Escherichia coli), and carbamoyl-phosphate synthetase (E. coli). ³¹P NMR was used to determine that carbamate kinase uses the B isomer of Ado-5′-(2-thioPPP) in the presence of Mg²⁺. The stereospecificity of the reaction with carbamate kinase was not reversed by Cd²⁺ suggesting that the metal ion does not bind to the β-phosphoryl group or that both Mg²⁺ and Cd²⁺ bind to the sulfur atom. Carbamate kinase uses both A and B isomers of Ado-5′-(1-thioPP) with Mg²⁺ and Cd²⁺. We have previously reported that carbamoyl-phosphate synthetase uses the A isomer of Ado-5′-(2-thioPPP) at both ATP sites with Mg²⁺ (Raushel et al., 1978J. Biol. Chem.253, 6627). Current experiments show that the stereospecificity is reversed by Cd^2? and that both A and B isomers are used when Zn²⁺ is present. With Ado-5′-(1-thioPPP), the B isomer is used with Mg²⁺, the A isomer with Cd²⁺, and both isomers with Zn²⁺. Neither carbamate kinase nor carbamoyl-phosphate synthetase utilized Co(III)(NH₃)₄ATP as a substrate and thus we can only speculate that the Δ chelate ring configuration is the chelate structure utilized by carbamoyl-phosphate synthetase (based on the analogy between thiophosphate-ATP analogs and Co³⁺-ATP analogs utilized by hexokinase (E. K. Jaffe, and M. Cohn, 1978Biochemistry17, 652). If the sulfur of the β-phosphoryl of Ado-5′-(2-thioPPP) binds to the metal ion with carbamate kinase, then the Δ chelate ring is also used in this enzyme that catalyzes one of the steps in the overall reaction catalyzed by carbamoyl-phosphate synthetase. Glutamine synthetase reacts with the B isomer of both Ado-5′-(2-thioPPP) and Ado-5′-(1-thioPPP) in the presence of Mg²⁺. When Co²⁺ is used with this enzyme the A and B isomers of both thio-ATP compounds are substrates. Co(III)(NH₃)₄ATP is not a substrate for glutamine synthetase. Glutamine synthetase is therefore different from the two previously mentioned enzymes in that it used the opposite A ring configuration for the metal-ATP chelate.     

Energy-linked reactions in photosynthetic bacteria: Pi in equilibrium with HOH oxygen exchange catalyzed by the membrane-bound inorganic pyrophosphatase of Rhodospirillum rubrum

The inorganic phosphate-water oxygen exchange reaction has been studied in chromatophores of Rhodospirillum rubrum. Under appropriate conditions, chromatophores catalyzed this exchange at a rate of up to 150 μatom oxygen/h/mg bacteriochlorophyll. The reaction is largely inhibited by inhibitors of the membrane-bound inorganic pyrophosphatase, fluoride and methylene diphosphonate, and is not inhibited by oligomycin. These results indicate that the P_i ? HOH oxygen exchange is almost entirely due to the pyrophosphatase. In the presence of ADP, the exchange reaction was stimulated by about 40% and this portion of the exchange was sensitive to oligomycin, but not to fluoride or methylene diphosphonate. Thus this portion of the exchange can be attributed to the ATP synthese complex. The rates of the oxygen exchange reaction and other chromatophore-catyalyzed reactions are compared.