The primary acid product of DPNH

Analysis of the proton magnetic resonance spectra obtained at 220 MHz confirms the axial conformation of the C-6 hydroxyl in the model primary acid product 1-n-(2,6-dichlorobenzyl)-6-hydroxy-1,4,5,6-tetrahydronicotinamide. In the primary acid product of DPNH however the reaction occurs stereospecifically with the substitution at the C-6 position equatorial and on the B-side of the pyridine ring and the C-4A proton axial. A cyclic structure α,O^2′-6B cyclotetrahydronicotinamide is proposed for the primary acid product of DPNH, formed by epimerization of βDPNH to the α configuration followed by protonation at C-5 and subsequent attack of the ribose C-2′-OH on the C-6 position forming a new five membered ring.     

Absolute stereochemistry of methanopterin and 5,6,7,8-tetrahydromethanopterin

The configuration at the C-9 of methanopterin (MPT) has been determined by comparing the circular dichroism (CD) spectra of MPT and its hydrolytic fragment, 1-[4-[[1-(2-amino-7-methyl-4-hydroxy-6-pteridinyl)-ethyl]amino]phenyl]-1-deoxy-D -ribitol (HP-1), with the CD spectra of a series of model compounds of known stereochemistry. These compounds included (S)-6-[1-(4-carboxymethylanilino)ethyl]pterin, (S-6(1-hydroxyethyl)-7-methylpterin, (S-6-(1-hydroxyethyl)pterin, (R)-6-(1-phenoxyethyl)pterin, D (+)-neopterin, and L -biopterin. From this comparison it was concluded that MPT has the R configuration at C-9 and is thus configurationally related to D (+)-neopterin, which has the S configuration at C-1. From previous work establishing the relative stereochemistry at C-6, C-7, and C-9 of N⁵-N¹⁰-methenyl-5,6,7,8-tetrahydromethanopterin (N⁵-N¹⁰-methenyl-H₄MPT) as R, S, and R, respectively, it is clear that the remaining asymmetric carbons at C-6 and C-7 of H₄MPT have the S and S configuration, respectively. Comparison of these latter two positions to the equivalent carbons in 5,6,7,8-tetrahydrofolate (H₄folate) show that the steps involved in the biological reduction of MPT to H₄MPT occur with the same stereochemical outcome as those involved in the biological reduction of folate to H₄folate. © 1996 Wiley-Liss, Inc.     

Properties of metal-ion coordinated imidazoles: nmr and C-2 H Exchange in Co(III) Complexes

The ¹H and ¹³C nmr spectra of Co(NH₃)₅ImH³⁺ and the ¹H nmr spectra of αCotrien(ImH)₂³⁺ and βCotrien(ImH)₂³⁺ are reported. The pK_a values determined from the dependence of the chemical shift on pH are 10.0, 9.6, and 10.1, respectively. The range of the chemical shift between the acid and base forms is unusually small in the ¹H nmr, 0.5–0.7 ppm for the C-2 H and about 0.25 ppm for the C-4 H and C-5 H. In the ¹³C nmr, C-2 and C-4 have large shifts to low field and C-5 a small shift to high field on deprotonation. The C-2 proton is not exchanged with solvent ²H under acidic or basic conditions, in marked contrast to the corresponding proton in both imidazole and 1-methylimidazole. These spectroscopic and chemical properties should be useful for the direct identification of metal-ion coordinated histidines in proteins.     

Isotope effects in 3-dehydroquinate synthase and dehydratase. Mechanistic implications.

The mechanism of 3-dehydroquinate synthase was explored by incubating partially purified enzyme with mixtures of [1-14C]3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) and one of the specifically tritiated substrates [4-3H]DAHP, [5-3H]DAHP, [6-3H]DAHP, (7RS)-[7-3H]DAHP, (7R)-[7-3H]DAHP, or (7S)-[7-3H]DAHP. Kinetic and secondary 3H isotope effects were calculated from 3H:14C ratios obtained in unreacted DAHP, 3-dehydroquinate, and 3-dehydroshikimate. 3H was not incorporated from the medium into 3-dehydroquinate, indicating that a carbanion (or methyl group) at C-7 is not formed. A kinetic isotope effect kH/k3H of 1.7 was observed at C-5, and afforded support for a mechanism involving oxidation of C-5 with NAD. A similar kinetic isotope effect was found at C-6 owing to removal of a proton in elimination of phosphate, which is reasonably assumed to be the next step in 3-dehydroquinate synthase. Hydrogen at C-7 of DAHP was not lost in the cyclization step of the reaction, indicating that the enol formed in phosphate elimination participated directly in an aldolase-type reaction with the carbonyl at C-2. In the dehydration of 3-dehydroquinate to 3-dehydroshikimate the (7R) proton from (7RS)- or (7R)-[7-3H]DAHP is lost, indicating that the 7R proton occupies the 2R position in dehydroquinate. Hence the cyclization step occurs with inversion of configuration at C-7. A kinetic isotope effect kH/k3H = 2.3 was observed in the conversion of (2R)-[2-3H]dehydroquinate to dehydroshikimate. Hence loss of a proton from the enzyme-dehydroquinate imine contributed to rate limitation in the reaction.     

A radiometric technique for the measurement of adenylosuccinate lyase

When radioactive adenylsuccinic acid (AMP-S) is metabolized to AMP and fumaric acid by the enzyme adenylsuccinate lyase (EC 4.3.2.2), a proton is released to the solvent as ³H₂O. This removal is believed to be stereospecifically identical to that catalyzed by the enzyme, l-aspartase [1–5], and therefore entails the loss of a proton from C-3 of the dicarboxylic acid moiety of the nucleotide. Advantage has been taken of this fact in the design of a facile assay for this enzyme. Adenylosuccinic acid, tritiated on C-2 and C-3 of the l-aspartase moiety, is prepared by chemical synthesis. This product is purified, lyophilized to dryness and reconstituted in a solution of unlabelled AMP-S, bringing the final concentration to 5·10^?3 M, and the final specific activity to 8.0 μCi/mol. 5-μl aliquots of this substrate are then incubated at 37°C with 5-μl aliquots of tissue extract; after an appropriate period, any tritium released to the solvent water is distilled at room temperature overnight into a 5 μl droplet of saturated aqueous KOH adherent to the lid of the sealed reaction vessel. The lid is removed and tritium thereon is measured by scintillation spectrometry. The assay, performed as prescribed, is facile, in that it permits the simultaneous estimation of the lyase activity in a large battery of samples, is not interfered with by opalescent or proteinaceous suspensions, is accurate and outstandingly sensitive.     

Dihydrofolate reductase from a methotrexate-resistant Escherichia coli: Proton magnetic resonance studies of complexes with folate and methotrexate

Proton magnetic resonance studies of 1:1 complexes of E. coli dihydrofolate reductase with folate and methotrexate were performed. A resonance at 1850 Hz in 1:1 enzyme-folate was assigned as the C-7 proton of bound folate by comparison with the spectra of enzyme complexed with folate specifically deuterated at C-7. The first order rate constant for folate dissociation was calculated to be less than 110 sec^?1. Four of the five histidine residues exhibited the same pK's and chemical shifts in the two complexes with pK values of 8.0, 7.3, 6.5 and ～5. However, one histidine increased its pK by 0.7 units (6.25→6.95) and its C-2 proton resonance shifted upfield 50 Hz when folate was substituted for methotrexate. Comparison of these results with those of chemical modification and ultraviolet difference spectroscopy experiments suggests that this histidine may be in the folate binding site — possibly near the pteridine portion of that site.     

Stereochemistry of the biosynthesis of presqualene alcohol

Current hypotheses of the biosynthesis of presqualene pyrophosphate were tested by the examination of presqualene alcohol biosynthesized from [1R,5R,9R-1,5,9-D₃]farnesyl pyrophosphate and from [1-¹⁸O]farnesyl pyrophosphate. Nuclear magnetic resonance spectrometry showed that the octet of the two cyclopropylcarbinyl protons seen in the spectrum of protio-presqualene alcohol, centered at τ 6.35, was replaced by a broad doublet of one proton (τ, 6.23; J, 6.2 Hz), which became sharpened after deuterium decoupling and was reduced to a singlet after deuterium and proton decoupling. Also the doublet of a single olefinic proton adjacent to the cyclopropane ring, seen in the spectrum of protio-presqualene alcohol at τ 5.08 (J, 8.5 Hz), was reduced to a broad singlet. The presqualene alcohol biosynthesized from the [1-¹⁸O]farnesyl pyrophosphate contained the same isotopic concentration as its precursor. The observations, taken together with previous results, are interpreted to mean that the pyrophosphate-bearing group of one farnesyl pyrophosphate molecule appears without chhnge of configuration, and without previous cleavage of the CO bond of farnesyl pyrophosphate, in presqualene pyrophosphate and that the pro-R hydrogen atom at C-1 of the second farnesyl pyrophosphate molecule appears at C-3 of the cyclopropane ring anti to the vinylic substituent. The observations support the view that presqualene pyrophosphate is not an artifact, but a true intermediate in the biosynthesis of squalene.     

Biosynthesis of dioscorine : Incorporation of nicotinic acid into the isoquinuclidine moiety

The administration of nicotinic-[2-¹⁴C] acid to Dioscorea hispida plants afforded radioactive dioscorine (1.9% absolute incorporation) and a systematic degradation of the alkaloid indicated that essentially all the activity was located at C-3. Dioscorine derived from nicotinic-[5,6-¹⁴C, ¹³C₂] acid was also labelled. Its proton noise decoupled ¹³C NMR spectrum contained satellites at C-1 and C-7 due to spin-spin coupling of contiguous ¹³C atoms arising from direct incorporation of the labelled nicotinic acid. A biosynthetic scheme representing a novel utilization of nicotinic acid is proposed.     

The interactions between nucleic acids and polyamines: I. High resolution carbon-13 and hydrogen-1 nuclear magnetic resonance studies of spermidine and 5'-AMP

In 0.5 M solution at pH 7.6, interaction of spermidine and 5'-AMP is demonstrated by downfield proton NMR shifts. Shifts of ribose and adenine protons support a model in which triprotonated spermidine engages the phosphate, anion with the C-3 diamine segment in a conformation to maximize interaction and the C-4 ammo segment extended to interact with adenine N-7 (base anti, 2'endo, g'g' and gg nucleoside conformation). Changes in carbon-13 chemical shifts for ribose C-5' (downfield), C-2' C-3', and C-4' (upfield) and for adenine C-6 and C-8 (upfield) support this model. In 0.006 M solution no significant changes in proton shifts and therefore no evidence for interaction was found. Spermidine and 5'-UMP (0.006 M) showed interaction at pH 10.5 (small upfield shifts in the proton nmr) interpreted as changing conformation by solvent interaction. In 0.006 M 3'-UMP at pH 10.5 small downfield proton shifts induced by spennidine are attributed to interactions with phosphate anion.     

Mechanistic studies on PseB of pseudaminic acid biosynthesis: a UDP-N-acetylglucosamine 5-inverting 4,6-dehydratase

UDP-N-acetylglucosamine 5-inverting 4,6-dehydratase (PseB) is a unique sugar nucleotide dehydratase that inverts the C-5″ stereocentre during conversion of UDP-N-acetylglucosamine to UDP-2-acetamido-2,6-dideoxy-β-l-arabino-hexos-4-ulose. PseB catalyzes the first step in the biosynthesis of pseudaminic acid, which is found as a post-translational modification on the flagellin of Campylobacter jejuni and Helicobacter pylori. PseB is proposed to use its tightly bound NADP⁺ to oxidize UDP-GlcNAc at C-4″, enabling dehydration. The α,β unsaturated ketone intermediate is then reduced by delivery of the hydride to C-6″ and a proton to C-5″. Consistent with this, PseB from C. jejuni has been found to incorporate deuterium into the C-5″ position of product during catalysis in D₂O. Likewise, PseB catalyzes solvent isotope exchange into the H-5″ position of product, and eliminates HF from the alternate substrate, UDP-6-deoxy-6-fluoro-GlcNAc. Mutants of the putative catalytic residues aspartate 126, lysine 127 and tyrosine 135 have severely compromised dehydratase, solvent isotope exchange, and HF elimination activities.     

Novel Types of N6,2′-Cyclonucleosides

Abstract

Upon oxidation followed by treatment with hydroxylamine, the 3′,5′-diblocked uridine 1 gave the expected oxime 2 together with the N⁶,2′.cyclonucleoside 3 formed by nucleophilic attack of hydroxylamine at both C-6 and C-2′ positions. Reduction of 2 took place predominantly from the α face and the major D-arabino compound obtained gave the cyclonucleosides, 7 via Michael type addition. The structures of the novel cyclonucleosides, particularly their configuration at C-6 were established by X-ray diffraction.     

A divalent-ion binding site on the 16-kDa proton channel from Nephrops norvegicus—revealed by EPR spectroscopy

As purified from the hepatopancreas of Nephrops norvegicus, the 16-kDa proton channel proteolipid is found to contain an endogenous divalent ion binding site that is occupied by Cu²⁺. The EPR spectrum has g-values and hyperfine splittings that are characteristic of type 2 Cu²⁺. The copper may be removed by extensive washing with EDTA. Titration with Ni²⁺ then induces spin-spin interactions with nitroxyl spin labels that are attached either to the unique Cys⁵⁴, or to fatty acids intercalated in the membrane. Paramagnetic relaxation enhancement by the fast-relaxing Ni²⁺ is used to characterise the binding and to estimate distances from the dipolar interactions. The Ni²⁺-binding site on the protein is situated around 14-18 Å from the spin label on Cys⁵⁴, and is at a similar distance from a lipid chain spin-labelled on the 5 C-atom, but is more remote from the C-9 and C-14 positions of the lipid chains.     

X-ray crystal,and molecular,structure of 1,2,3-tri-O-acetyl-4,5-dideoxy-4-C-[(R)-phenylphosphinyl]-α-l-lyxofuranose: The first x-ray analysis of a pentofuranose having phosphorus in the hemiacetal ring

X-Ray crystallographic analysis was performed on the compound to which had been assigned the structure of 1,2,3-tri-O-acetyl-4,5-dideoxy-4-C-[(R)-phenylphosphinyl]-α-l-lyxofuranose. The results showed that the compound has the proposed configuration, the five-membered ring is in the E₃ conformation, with a tendency towards the ³T₂ form, the substituents at P-5 and C-5 are linked bisectionally, the acetoxyl group at C-2 and the methyl group at C-4 are linked quasiequatorially, and the acetoxyl group at C-3 is linked axially.     

Der einfluss des anomeren effektes auf furanosekonformationen. Röntgenstrukturanalyse fünf isomerer methyl-3,6-anhydrohexofuranoside

X-Ray crystallographic analysis of five isomeric methyl 3,6-anhydrohexofuranosides, methyl 3,6-anhydro-β-d-glucofuranoside (1), methyl 3,6-anhydro-α-l-idofuranoside (2), methyl 3,6-anhydro-β-d-mannofuranoside (3), methyl 3,6-anhydro-α-d-glucofuranoside (5), and methyl 3,6-anhydro-α-d-mannofuranoside (7), showed that the anomeric effect determines the conformation of the furanoid ring, which resulted in the quasi-axial orientation of the aglycon in all cases. Thus, 2 adopts an almost ideal E₂ conformation, whereas 1 and 3 having the same R configuration at the anomeric center showed conformations of the furanoid ring intermediate between E₂ and ¹T₂. Of the anomers 5 and 7 having an S configuration at C-1, 7 showed a related but opposite geometry, intermediate between ²E and ²T₁, and 5 had a ^oT₁ conformation, slightly distorted into ^oE. The anhydroring of all compounds showed a C-6 endo orientation, with the exception of 7, in which C-6 is exo oriented. These results from compounds in the solid state were compared with the conformations of the same compounds in solution, as deduced by ¹H-n.m.r. spectroscopy.     

Carbon-13 as a tool for the study of carbohydrate structures,conformations and interactions

The application of ¹³C-NMR spectroscopy to problems involving the structures and interactions of carbohydrates is described. Both ¹³C-enriched and natural abundance compounds were used and some advantages of the use of the stable isotope are described. Carbon-carbon and carbon-proton coupling constants obtained from 1-¹³ C enriched carbohydrates were employed in the assignment of their chemical shifts and to establish solution conformation. In all cases studied thus far, C-3 couples to C-1 only in the β-anomers while C-5 couples to C-1 only in the α-anomers. C-6 and C-2 always couple to C-1 in both anomeric species. The alkaline degradation of glucose [1-¹³ C] to saccharinic acids was followed by ¹³C-NMR. The conversion of glucose [1-¹³ C] to fructose-1,6-bisphosphate [1,6-¹³ C] by enzymes of the glycolytic pathway was shown as an example of the use of ¹³C-enriched carbohydrates to elucidate biochemical pathways. In a large number of glycosyl phosphates the ³¹P to H-1 and ³¹P to C-2 coupling constants demonstrate that in the preferred conformation the phosphate group lies between the O-5 and the H-1 of the pyranose ring. The influence of paramagnetic Mn²⁺ ions on the proton decoupled ¹³C-NMR spectra of uridine diphosphate N-acetylglucosamine indicates that the Mn²⁺ interacts strongly with the pyrophosphate moiety and with the carbonyl groups of the uracil and N-acetyl groups.     

Stereochemistry of reactions catalysed by mammalian-brain L-glutamate 1-carboxy-lyase and 4-aminobutyrate: 2-oxoglutarate aminotransferase.

Deamination of 4-aminobutyrate by mammalian or bacterial 4-aminobutyrate aminotransferases involves the abstraction of the pro-S hydrogen on C-4 of 4-aminobutyrate. Decarboxylation of L-glutamate by rat brain glutamate decarboxylase occurs with retention of configuration. Inhibition of this enzyme by (S)-4-aminohex-5-ynoic acid involves the abstraction of the proton at C-4 of the inhibitor. On the basis of this finding, we postulate the existence of an abnormal reaction of glutamate decarboxylase in which the proton at C-4 of (S)-4-aminohex-5-ynoic acid is removed in a manner similar to the one which normally occurs in enzymatic transaminations of L-amino acids. This reaction is presumably facilitated by the acetylenic group adjacent to the eliminated proton.     

Hydroxylation of steroids by <Emphasis Type="Italic">Curvularia lunata</Emphasis> mycelium in the presence of methyl-β-cyclodextrine

Transformation of 16 Δ⁵-3β-hydroxy- and Δ⁴-3-ketosteroids of androstane and pregnane classes was carried out using Curvularia lunata mycelium suspended in phosphate buffer with methyl-β-cyclodextrine (MCD). As the result, 20 monohydroxy- and dihydroxy-metabolites, whose structure was determined using spectra of proton magnetic resonance and mass-spectra, have been isolated. Hydroxylation of Δ⁵-3β-hydroxy-steroids occurred mostly in the C-7α position whereas hydroxylation of Δ⁴-3-ketosteroids was in the C-11β position. Only androst-4-en-3,17-dione, 9α-hydroxy-androstenedione, and androsta-1,4-diene-3,17-dione were hydroxylated at C-14α position. Besides main 11β-derivatives, the 6β- and 7β-hydroxy-derivatives with yield 10 and 30%, respectively, were isolated during transformation of progesterone and hydroxymethyl pregnadienone. The ratio of MCD to transforming steroid was 1: 1 (mol/mol). Hydrocortisone and 7α-hydroxyandrostenolone with the yield 55 and 77%, respectively, were obtained at the maximal concentrations of cortexolone 20 g/l and androstenolone acetate 10 g/l in the presence of MCD. Absorption of steroids on mycelium, lower speed of their transformation, low concentrations of modifying substrates, and low yield of hydroxyderivatives have been observed in the absence of MCD.     

Analysis of Ca2+ Signaling Motifs That Regulate Proton Signaling through the Na+/H+ Exchanger NHX-7 during a Rhythmic Behavior in Caenorhabditis elegans

Membrane proton transporters contribute to pH homeostasis but have also been shown to transmit information between cells in close proximity through regulated proton secretion. For example, the nematode intestinal Na⁺/H⁺ exchanger NHX-7 causes adjacent muscle cells to contract by transiently acidifying the extracellular space between the intestine and muscle. NHX-7 operates during a Ca²⁺-dependent rhythmic behavior and contains several conserved motifs for regulation by Ca²⁺ input, including motifs for calmodulin and phosphatidylinositol 4,5-bisphosphate binding, protein kinase C- and calmodulin-dependent protein kinase type II phosphorylation, and a binding site for calcineurin homologous protein. Here, we tested the idea that Ca²⁺ input differentiates proton signaling from pH housekeeping activity. Each of these motifs was mutated, and their contribution to NHX-7 function was assessed. These functions included pH recovery from acidification in cells in culture expressing recombinant NHX-7, extracellular acidification measured during behavior in live moving worms, and muscle contraction strength as a result of this acidification. Our data suggest that multiple levels of Ca²⁺ input regulate NHX-7, whose transport capacity normally exceeds the minimum necessary to cause muscle contraction. Furthermore, extracellular acidification limits NHX-7 proton transport through feedback inhibition, likely to prevent metabolic acidosis from occurring. Our findings are consistent with an integrated network whereby both Ca²⁺ and pH contribute to proton signaling. Finally, our results obtained by expressing rat NHE1 in Caenorhabditis elegans suggest that a conserved mechanism of regulation may contribute to cell-cell communication or proton signaling by Na⁺/H⁺ exchangers in mammals.     

A method for the degradation of radioactive nicotinic acid

A chemical degradation scheme is reported, which permits the measurement of the radioactivity of each carbon atom of nicotinic acid. Nicotinic acid is decarboxylated by heating with copper chromite to give carbon dioxide (C-7) and pyridine. The pyridine is converted into 4-nitropyridine 1-oxide, which is heated with aqueous calcium hypobromite to give tribromonitromethane. Combustion of the latter gives carbon dioxide derived from C-4 of the nicotinic acid. Nicotinic acid is also reduced to nipecotic acid, which is oxidized to succinic acid by acidic potassium permanganate. Stepwise degradation of the succinic acid by standard procedures gives two samples of carbon dioxide, which correspond to C-3, C-6 and C-4, C-5 of the nicotinic acid. Benzoylation of the nipecotic acid, followed by oxidation with permanganate at pH7, gives 5-amino-4-carboxyvaleric acid; this is converted into 2-methyleneglutaric acid by the action of nitrous acid. Hydrogenation of the 2-methyleneglutaric acid over rhodium in methanol gives 2-methylglutaric acid, which is oxidized with dilute chromic acid to acetic acid. Stepwise degradation of the acetic acid by standard procedures gives two samples of carbon dioxide, which correspond to C-2 and C-3 of the nicotinic acid. Thus the radioactivities of C-2, C-3, C-4 and C-7 are determined directly and those of C-5 and C-6 by difference. The method was shown to be isotopically valid for [2,3,7-¹⁴C]-, [4,6-¹⁴C₂]- and [5-¹⁴C]-nicotinic acid.     

X-ray crystal, and molecular, structure of 1,2,3-tri-O-acetyl-4,5-dideoxy-4-C-[(R)-phenylphosphinyl]-α- -lyxofuranose: The first x-ray analysis of a pentofuranose having phosphorus in the hemiacetal ring

X-Ray crystallographic analysis was performed on the compound to which had been assigned the structure of 1,2,3-tri-O-acetyl-4,5-dideoxy-4-C-[(R)-phenylphosphinyl]-α- -lyxofuranose. The results showed that the compound has the proposed configuration, the five-membered ring is in the E₃ conformation, with a tendency towards the ³T₂ form, the substituents at P-5 and C-5 are linked bisectionally, the acetoxyl group at C-2 and the methyl group at C-4 are linked quasiequatorially, and the acetoxyl group at C-3 is linked axially.