Electron paramagnetic resonance studies on nitrogenase. II. Interaction of adenosine 5′-triphosphate with azoferredoxin

The interaction of ATP with both iron-sulfur proteins of nitrogenase from Clostridium pasteurianum, azoferredoxin and molybdoferredoxin, has been studied by low-temperature EPR spectroscopy. ATP in the presence of Mg²⁺ changes the rhombic EPR signal of azoferredoxin with g-values of 2.06, 1.94 and 1.87 to an axial signal, with g values of 2.04 and 1.93. The binding of two molecules of ATP per azoferredoxin dimer (mol. wt 55 000) is suggested. Comparative data with other purine and pyrimidine nucleotides and ATP analogues demonstrate the involvement of structural elements of the substrate in the conversion of the EPR signal of azoferredoxin. A similar effect is induced by 5 M urea, which suggests that ATP causes a conformation change of the protein. In contrast, no effect of ATP was observed on the EPR signal of molybdoferredoxin.     

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.     

Regulation of the in vitro synthesis of the alpha-peptide of beta-galactosidase directed by a restriction fragment of the lactose operon.

The regulation of the $\text{in vitro}$ synthesis of the N-terminal portion of the β-galactosidase molecule (α-peptide) has been investigated using DNA fragments of the lactose operon as template. DNA fragments of about 789 base pairs were isolated after endonuclease (Hin II) digestion of either λplac5, λh80dlacp^s or λh80dlacUV5 phage DNA or DNA from the recombinant plasmid PMC3. The regulation of the expression of these fragments is similar to that observed for the synthesis of β-galactosidase using total phage or plasmid DNA as template, indicating that the regulatory regions on the fragments are intact and functional. Thus, the synthesis of the α-peptide required an inducer due to the presence of $\text{lac}$ repressor in the $\text{E. coli}$ S-30 extract used. In addition a dependency on adenosine 3′,5′-cyclic monophosphate (cAMP)¹ for α-peptide synthesis was obtained with the fragments isolated from λplac5 and λh80dlacp^s DNAs, whereas little effect of cAMP was seen with the fragment isolated from λh80dlacUV5 phage DNA or PMC3 plasmid DNA containing a UV5 promotor region. However, a significant difference in the effect of guanosine-3′-diphosphate-5′-diphosphate (ppGpp) was observed. With the total phage DNA as template, ppGpp resulted in a 2–4 fold stimulation whereas with the fragment, or PMC3 plasmid DNA, directed synthesis of the α-peptide no significant stimulation by ppGpp was seen.     

Synthetic polynucleotides as model substrates for ribosomal RNA processing

A nuclear exoribonuclease from Novikoff ascites cells was used to study the hydrolysis of single-stranded heteropolymers containing [¹⁴C]adenylic acid and either uridylic acid or cytidylic acid and heteropolymers of [¹⁴C]adenylic acid and one of the corresponding 2′-$\text{O}$-methylated nucleotides. The results of these studies indicate that both the rate and extent of hydrolysis are greatly inhibited by the presence of 2′-$\text{O}$-methylated nucleotides. Restriction of exonuclease activity by 2′-$\text{O}$-methylated nucleotides provides a possible mechanism for rRNA processing.     

Interaction of the low molecular weight form of elongation factor 1 with guanine nucleotides and aminoacyl-tRNA.

A low molecular weight form of the eukaryotic polypeptide chain elongation factor 1 (EF-1α) has been extensively purified from pig liver to give an apparently homogeneous preparation, which seemed to be analogous to the bacterial elongation factor, EF-Tu (Iwasaki, K., Nagata, S., Mizumoto, K., and Kaziro, Y. (1974) J. Biol. Chem. 249, 5008). Thus, the interaction of the purified EF-1α with guanine nucleotides as well as aminoacyl-tRNA has been investigated and the following results have been obtained. (1) EF-1α when kept in the absence of glycerol lost its activity to promote the binding of aminoacylt-RNA to ribosomes though it retained the ability to bind guanine nucleotides. However, the former activity could be stabilized by the addition of 25% ($\text{v}\text{v}$) glycerol to the solution. (2) EF-1α formed a binary complex with guanine nucleotides such as GTP, GDP, 5′-guanylyl methylenediphosphonate or 5′-guanylyl imidodiphosphate. The molar ratio of EF-1α to GTP or GDP in the binary complex was shown to be 1. (3) The presence of a ternary complex containing EF-1α, GTP and aminoacyl-tRNA was demonstrated by several methods, i.e., (i) an increased heat stability of EF-1α in the presence of GTP and Phe-tRNA, (ii) a decrease in the amount of the EF-1α·GTP complex in the presence of aminoacyl-tRNA, (iii) a protection of the ester linkage of Phe-tRNA from hydrolysis at alkaline pH by the presence of both EF-1α and GTP, and (iv) the isolation of the complex by gel filtration.     

Effect of specific inhibitors on mitochondrial DNA replication in HeLa cells

The crystal structure of an orthorhombic form of 2′-0-methyl cytidine was determined from three dimensional X-ray diffraction data. The two molecules in each asymmetric unit have C2-$\text{endo}$ C3-$\text{exo}$ puckered furanose rings. This differs from the C3-$\text{endo}$ puckering observed for cytidine (1) and it may have some relevance to the kinks that appear at the two 2′-0-methylated nucleotides in the anticodon phosphate ester backbone of the phe tRNA structure (2). This work and other studies (3,4) show that the presence of a 2′-0-methyl group does not prevent the furanose moiety from adopting its most commonly observed configurations. 2′-0-methyl nucleotides make up a small percentage of the residues in HnRNA, rRNA, tRNA and mRNA and therefore their conformational nuances are of interest.     

Concerning the specificity of heme oxygenase: the enzymatic oxidation of synthetic hemins.

Hemin XIII $\text{4}\text{～}$, hemin III $\text{5}\text{～}$, and iron $\text{1,4-di(β-hydroxyethyl)porphyrin}\text{6}\text{～}$ were enzymatically oxidized by a microsomal heme oxygenase preparation from rat liver. These are all better substrates of the oxygenase than the natural substrate, hemin IX $\text{1}\text{～}$. The enzymatic oxidation was selective for the α-methine bridge and in every case only the α-biliverdins were obtained. The latter were readily reduced by biliverdin reductase to the corresponding α-bilirubins. The absence of isomers in addition to the α-bilirubins was established by preparing the derived azopigments and by using [α-¹⁴C]$\text{6}\text{～}$ and [α-¹⁴C]$\text{4}\text{～}$ as substrates. The chemical oxidation of $\text{4}\text{～}$, $\text{5}\text{～}$, and $\text{6}\text{～}$ gave the expected mixture of biliverdins. It is concluded that heme oxygenase is not specific for hemin IX. On the other hand, the enzyme is highly selective for the α-methine bridge, defined as the methine opposed to that flanked by the 6,7-propionic acid residues.     

The biosynthesis of blood group B determinants by the blood group A gene-specified alpha-3-N-acetyl-D-galactosaminyltransferase

The blood group $\text{A}{}^1$ gene-specified α-3-N-acetyl-D-galactosaminyl-transferase in human plasma, when concentrated by adsorption onto group O red cell ghosts or Sepharose 4B, catalyses the transfer of D-galactose in α-linkage to low-molecular-weight H-active acceptors. The product synthesised with 2′-fucosyllactose is chromatographically indistinguishable from the blood group B-active tetrasaccharide, Galα1→3[Fucα1→2]Galβ1→4Glc. The optimum pH for the transfer of D-galactose by the $\text{A}{}^1$-transferase is 7. At this pH the V_max for the transfer of N-acetyl-D-galactosamine is about 300 times higher than that for the transfer of D-galactose. These results indicate that an $\text{A}{}^1$-transferase can, under centain conditions, synthesise B determinant structures.     

Guanine nucleotides modulate cell surface cAMP-binding sites in membranes from Dictyostelium discoideum

D. discoideum contains kinetically distinguishable cell surface cAMP binding sites. One class, S, is slowly dissociating and has high affinity for cAMP (K_d = 15 nM, $\text{t}\text{1}\text{2}\text{= 15 s}$). A second class is fast dissociating ($\text{t}\text{1}\text{2}$ about 1 s) and is composed of high affinity binding sites H (K_d ≈ 60 nM), and low affinity binding sites L (K_d = ≈ 450 nM) which interconvert during the binding reaction. Guanine nucleotides affect these three binding types in membranes prepared by shearing D.discoideum cells through Nucleopore filters. The affinity of S for cAMP is reduced by guanine nucleotides from 13 nM to 25 nM, and the number of S-sites is reduced about 50%. The number of fast dissociating sites is not altered by guanine nucleotides, but these sites are mainly in the low affinity state. Half-maximal effects are obtained at about 1 μM GTP, 2 μM GDP and 10 μM Gpp(NH)p(guanyl-5′-yl-imidodiphosphate); ATP and ADP are without effect up to 1 mM. These results indicate that D.discoideum cells have a functionally active guanine nucleotide binding protein involved in the transduction of extracellular cAMP signals via cell surface cAMP receptors.     

Mn++-specific reactivation of EDTA inactivated alpha-isopropylmalate synthase from Alcaligenes eutrophus H 16.

The α-isopropylmalate synthase (EC 4.1.3.12) from $\text{Alcaligenes}\text{eutrophus}\text{H 16}$ was inactivated by EDTA in a time-dependent reaction. Only the addition of Mn⁺⁺ plus dithiothreitol could restore the activity. The substrate, α-ketoisovalerate, prevented the inactivation; the feedback inhibitor, leucine, and it's antagonist, valine, increased the rate of inactivation. Except for α,α′-bipyridyl, chelating reagents, other than EDTA had no effect on the enzyme stability. It is suggested that the α-isopropylmalate synthase is a metallo enzyme - the evidence points to Mn⁺⁺ as the metal ion - and that this enzyme uses a mechanism of catalysis which differs from that of the analogous malate synthase (EC 4.1.3.2) and citrate synthase (EC 4.1.3.4).     

Aryl alpha-haloalkyl ketoximes as enzyme modifying agents. The reaction of alpha-haloacetophenone oximes with the active site of papain

$\text{Syn}$-α-chloroacetophenone oxime has been found to inactivate papain rapidly at pH 7 and 25.0^O in a 1:1 stoichiometric fashion as measured by rate assays with $\text{p}$-nitrophenyl $\text{N}$-benzyloxycarbonylglycinate and sulfhydryl group titrations with 5,5′-dithiobis-(2-nitrobenzoic acid). By the use of a ¹⁴C label in the halomethyl function a similar stoichiometric reaction with papain could be demonstrated for $\text{syn}$-α-bromoacetophenone oxime despite the rapidity of the competitive nonenzymatic solvolysis of the latter compound under the conditions employed. These results indicate that a new class of reactive modifying agents, α-haloalkyl oximes, can be used for the selective alkylation of catalytically essential functional groups in enzyme active sites.     

Stimulatory effect of prostaglandin E1 on thyroliberin-induced α-melanotropin release from perifused neuro-intermediate lobes of frog pituitary gland

A possible direct effect of prostaglandins on α-melanotropin (α-MSH) release at the level of the intermediate lobe of the frog pituitary was investigated $\text{in vitro}$ using a perifusion system technique. The effect of prostaglandins was studied on both spontaneous and TRH-stimulated α-MSH secretion. No significant effect of PGE₁, PGE₂, PGF_1α or PGF_2α on basal release of α-MSH could be detected. Indomethacin did not alter the α-MSH release induced by TRH. Conversely a significant increase in TRH-induced α-MSH secretion was observed in the presence of 1 x 10^?6M PGE₁. This magnifying effect was directly related to the concentration of TRH for doses ranging from 1 x 10^?8M to 1 x 10^?6M.     

The stereochemical course of thiophosphoryl group transfer catalyzed by adenosine kinase

Adenosine kinase was partially purified form beef liver and used to catalyze the conversion of (γR)ATPγS,γ¹⁸O and adenosine to ADP and AMPαS,α¹⁸O. The configuration at phosphorus in AMPαS,α¹⁸O was established by subjecting it to stereospecific phosphorylation to (αS)ATPαS,α¹⁸O and showing that only the nonbridging oxygen bonded to the α-P was enriched with ¹⁸O. The configuration at α-P in AMPαS,α¹⁸O was therefore S, and the transfer of the [¹⁸O]thiophosphoryl group occurred with $\text{inversion}$ of configuration.     

Synergistic inhibition of ATP phosphoribosyltransferase by guanosine tetraphosphate and histidine.

In the presence of partially inhibiting concentrations of the feedback inhibitor histidine guanosine-5′-diphosphate-3′-diphosphate becomes a potent inhibitor of the residual activity of ATP phosphoribosyltransferase from $\text{Salmonella typhimurium}$. Inhibition by guanosine tetraphosphate is higher order and slowly reversible. Inhibition does not occur in the absence of histidine. This effect constitutes an important control on the rate of histidine biosynthesis in response to the general aminoacid nutritional state of the cell.     

Effects of hormones and nucleotides on ciliary beating in frog esophagus and guinea pig trachea

The $\text{in vivo}$ effects of various hormones, nucleotides and related substances on the rate of ciliary beating in frog esophagus and guinea pig trachea were studied using both particle transport and photoelectric methods. Frog esophageal ciliary beating $\text{in vitro}$ was greatly accelerated by acetycholine, eserine, prostaglandin A₁ and E₂, N⁶- 2′-0-dibutyryl-adenosine--3′,5′-cyclic monophosphate, all tri- and di-phosphonucleotides (ATP, ADP, UTP, UDP, etc.), EDTA, EGTA, and calcium-free medium. Adenosine monophosphate, epinephrine, serotonin at low concentrations, 3,3′5-L-triiodothyronine, creative phosphate, and phosphoenolpyruvate were inactive or only minimally stimulatory in the frog. All substances tested, including those trachea. Furthermore, guinea pig ciliary activity was unaffected by hyperthyroidism or hypothyroidism induced in the intact animal before testing.     

Evidence for allosteric NADH regulation of Acinetobacter alpha-oxoglutarate dehydrogenase from multiple-inhibition studies.

Previous studies have suggested that the E1 component (α-oxoglutarate dehydrogenase) of the α-oxoglutarate dehydrogenase enzyme complex from $\text{Acinetobacter lwoffi}$ is inhibited by the end-product NADH. We have now carried out multiple-inhibition studies in the simultaneous presence of NADH and α-oxoadipate, both competitive inhibitors with respect to α-oxoglutarate. The results indicate that NADH acts at an allosteric site within the multi-enzyme complex.     

The collagen of chick embryonic notochord

Notochords, isolated from 2 $\text{1}\text{2}$ day chick embryos, were cultured in the presence of ³H proline and the labeled proteins co-purified with chick skin carrier collagen. The purified material, most of which eluted from CM-cellulose as a single peak in the region of the carrier collagen α1 chain, contained 41% of the incorporated proline as hydroxyproline and from gel filtration measurements had a molecular weight of approximately 100,000 daltons. When the material was chromatographed on DEAE-cellulose with carrier α1 chains from both skin [α1 (I)] and cartilage [α1 (II)], it eluted predominantly with the cartilage chains.     

Modulation of 3-hydroxy-3-methylglutaryl coenzyme A reductase activity with cAMP and wth protein fractions of rat liver cytosol

3-Hydroxy-3-methylglutaryl coenzyme A reductase activity is diminished in several $\text{in vitro}$ liver systems preincubated in the presence of cAMP. Reductase activity in isolated, washed liver microsomes is inactivated by ATP, Mg⁺⁺, and a protein fraction separated from the liver cytosol. This effect is augmented by 3′–5′ cyclic AMP. Reductase activity in previously inactivated microsomes can be partially restored by incubation with a second protein fraction of the cytosol.