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A Bacher

Publications and source records attributed to A Bacher.

At least 91 records · Page 5Linked to original sources
PubMed1999

Design and synthesis of 6-(6-D-ribitylamino-2,4-dihydroxypyrimidin-5-yl)-1-hexyl phosphonic acid, a potent inhibitor of lumazine synthase.

A novel inhibitor of lumazine synthase, the penultimate enzyme in the biosynthesis of riboflavin, has been synthesized. The inhibitor was designed by computer graphics molecular modeling using a hypothetical structure of the enzyme-inhibitor complex. The new compound is relatively potent when compared with the known inhibitors, and displays a KI of 109 microM.

Bacillus subtilis↗
PubMed1999

Effects of hypothermia and lamotrigine on trace-conditioned learning after global cerebral ischemia in rabbits.

Acquisition of the trace-conditioned eye blink response (CR) is mediated by a variety of brain structures, including the cerebellum, the hippocampus, and brain stem nuclei. We examined the effects of a neuronal sodium channel antagonist (lamotrigine) on the ability of rabbits to acquire an eye blink CR after 6.5 min of cerebral ischemia. New Zealand white rabbits (n = 31) were randomly assigned to sham (S), normothermic ischemia (N), hypothermic (30 degrees C) ischemia-(H), or lamotrigine (50 mg/kg) treated (L) groups. In the N, H, and L groups, 6.5 min of global cerebral ischemia was produced using an inflatable neck tourniquet. Trace conditioning was started on the 7th postischemic day. The conditioned stimulus consisted of a tone (85 dB, 6 kHz) presented for 100 ms. The unconditioned stimulus was an air puff (150 ms duration) directed at the cornea. The interval between the end of the conditioned stimulus and the start of the unconditioned stimulus (the trace interval, TI) was 300 ms in duration. A trace-conditioned response was defined as an eye blink that was initiated during the TI. Eighty trials were delivered daily for 15 days. Neurologic deficits were greatest in the N group, and these animals had fewer CRs (149 +/- 157) than animals in the S (509 +/- 214) or H (461 +/- 149) groups (P < 0.05 by analysis of variance). Animals in the L group had a total number of CRs (380 +/- 253) that was intermediate between the S and N groups. Histologic evidence of neural injury was greatest in the N group. This study demonstrates that a brief episode of cerebral ischemia results in the impairment of this test of neurobehavioral function. Both hypothermia and lamotrigine were able to attenuate the impairment of eye blink trace-conditioned responses produced by cerebral ischemia.

Animals↗
PubMed1999

Crystal structure of 7,8-dihydroneopterin triphosphate epimerase.

BACKGROUND: Dihydroneopterin triphosphate (H2NTP) is the central substrate in the biosynthesis of folate and tetrahydrobiopterin. Folate serves as a cofactor in amino acid and purine biosynthesis and tetrahydrobiopterin is used as a cofactor in amino acid hydroxylation and nitric oxide synthesis. In bacteria, H2NTP enters the folate biosynthetic pathway after nonenzymatic dephosphorylation; in vertebrates, H2NTP is used to synthesize tetrahydrobiopterin. The dihydroneopterin triphosphate epimerase of Escherichia coli catalyzes the inversion of carbon 2' of H2NTP. RESULTS: The crystal structure of the homo-octameric protein has been solved by a combination of multiple isomorphous replacement, Patterson search techniques and cyclic averaging and has been refined to a crystallographic R factor of 18.8% at 2.9 A resolution. The enzyme is a torus-shaped, D4 symmetric homo-octamer with approximate dimensions of 65 x 65 A. Four epimerase monomers form an unusual 16-stranded antiparallel beta barrel by tight association between the N- and C-terminal beta strands of two adjacent subunits. Two tetramers associate in a head-to-head fashion to form the active enzyme complex. CONCLUSIONS: The folding topology, quaternary structure and amino acid sequence of epimerase is similar to that of the dihydroneopterin aldolase involved in the biosynthesis of the vitamin folic acid. The monomer fold of epimerase is also topologically similar to that of GTP cyclohydrolase I (GTP CH-1), 6-pyrovoyl tetrahydropterin synthase (PTPS) and uroate oxidase (UO). Despite a lack of significant sequence homology these proteins share a common subunit fold and oligomerize to form central beta barrel structures employing different cyclic symmetry elements, D4, D5, D3 and D2, respectively. Moreover, these enzymes have a topologically equivalent acceptor site for the 2-amino-4-oxo pyrimidine (2-oxo-4-oxo pyrimidine in uroate oxidase) moiety of their respective substrates.

Amino Acid Sequence↗
PubMed1999

Application of amino acid type-specific 1H- and 14N-labeling in a 2H-, 15N-labeled background to a 47 kDa homodimer: potential for NMR structure determination of large proteins.

NMR investigations of larger macromolecules (> 20 kDa) are severely hindered by rapid 1H and 13C transverse relaxation. Replacement of non-exchangeable protons with deuterium removes many efficient 1H-1H and 1H-13C relaxation pathways. The main disadvantage of deuteration is that many of the protons which would normally be the source of NOE-based distance restraints are removed. We report the development of a novel labeling strategy which is based on specific protonation and 14N-labeling of the residues phenylalanine, tyrosine, threonine, isoleucine and valine in a fully deuterated, 15N-labeled background. This allows the application of heteronuclear half-filters, 15N-editing and 1H-TOCSY experiments to select for particular magnetization transfer pathways. Results from investigations of a 47 kDa dimeric protein labeled in this way demonstrated that the method provides useful information for the structure determination of large proteins.

Amino Acid Sequence↗
PubMed1999

NMR studies on the 46-kDa dimeric protein, 3,4-dihydroxy-2-butanone 4-phosphate synthase, using 2H, 13C, and 15N-labelling.

3,4-Dihydroxy-2-butanone 4-phosphate synthase catalyses the release of C-4 from the substrate, ribulose phosphate, via a complex series of rearrangement reactions. The cognate ribB gene of Escherichia coli was hyperexpressed in a recombinant E. coli strain. The protein was shown to be a 46-kDa homodimer by hydrodynamic analysis. A variety of protein samples labelled with different grades of 13C, 15N and 2H, i.e. one with 100% 2H and 15N, one with 75% 2H, 99% 13C, 15N, and one with 100% 2H, 99% 13C,15N were prepared. Despite the large molecular size, 2- and 3-dimensional NMR spectra of reasonable quality were obtained. Attempts at the assignment of individual 13C, 15N and 1H signals show, in principle, the feasibility of structure determination. The number of NMR signals shows unequivocally that the homodimeric protein obeys strict C2 symmetry.

Base Sequence↗
PubMed1999

Biosynthesis of bitter acids in hops. A (13)C-NMR and (2)H-NMR study on the building blocks of humulone.

The biosynthesis of humulone, an antibacterial bitter acid from hops, was studied by isotope-incorporation experiments using (13)C-labelled glucose or (2)H(2)O. (13)C enrichments, (2)H enrichments and (13)C(13)C coupling patterns identify isovaleryl-CoA, malonyl-CoA and dimethylallyl pyrophosphate as precursors for humulone. Dimethylallyl pyrophosphate, which serves as a building block for the bitter acid, is generated via the deoxyxylulose pathway of terpenoid biosynthesis. The data confirm that a symmetrical intermediate is involved in humulone formation.

Acyl Coenzyme A↗
PubMed1998

(-)-2C-methyl-D-erythrono-1,4-lactone is formed after application of the terpenoid precursor 1-deoxy-D-xylulose.

Application of [1,2-14C]1-deoxy-D-xylulose, the committed precursor of terpenoids, thiamine and pyridoxol, to a variety of plant species resulted in the labelling of an unknown metabolite. The isolation and purification of this metabolite from Ipomoea purpurea plants fed with 1-deoxy-D-xylulose (DX), followed by NMR analysis, resulted in the identification of its structure as (-)-2C-methyl-D-erythrono-1,4-lactone (MDEL). MDEL has been previously isolated as a stress metabolite of certain plants. A hypothetical biosynthetic scheme is given.

Lactones↗
PubMed1998

Biosynthesis of pteridines. NMR studies on the reaction mechanisms of GTP cyclohydrolase I, pyruvoyltetrahydropterin synthase, and sepiapterin reductase.

GTP cyclohydrolase I catalyzes a ring expansion affording dihydroneopterin triphosphate from GTP. [1',2',3',4',5'-13C5, 2'-2H1]GTP was prepared enzymatically from [U-13C6]glucose for use as enzyme substrate. Multinuclear NMR experiments showed that the reaction catalyzed by GTP cyclohydrolase I involves the release of a proton from C-2' of GTP that is exchanged with the bulk solvent. Subsequently, a proton is reintroduced stereospecifically from the bulk solvent. This is in line with an Amadori rearrangement mechanism. The proton introduced from solvent occupies the pro-7R position in the enzyme product. The data also confirm that the reaction catalyzed by pyruvoyltetrahydropterin synthase results in the incorporation of solvent protons into positions C-6 and C-3' of the enzyme product. On the other hand, the reaction catalyzed by sepiapterin reductase does not involve any detectable incorporation of solvent protons into tetrahydrobiopterin.

Alcohol Oxidoreductases↗
PubMed1998

Cyclohexa-1,5-diene-1-carbonyl-CoA hydratase [corrected], an enzyme involved in anaerobic metabolism of benzoyl-CoA in the denitrifying bacterium Thauera aromatica.

Many aromatic compounds can be metabolized by bacteria under anoxic conditions via benzoyl-CoA as the common intermediate. The central pathway of benzoyl-CoA metabolism is initiated by an ATP-driven reduction of the aromatic ring producing cyclohexa-1,5-diene-1-carbonyl-CoA. The 1,5-dienoyl-CoA intermediate is thought to be transformed to 6-hydroxycyclohex-1-ene-1-carbonyl-CoA by a specific dienoyl-CoA hydratase catalyzing the formal addition of water to one of the double bonds. This dienoyl-CoA hydratase was detected in the denitrifying bacterium Thauera aromatica after anaerobic growth with benzoate. Substrate and product were confirmed and a convenient spectrophotometric assay was developed. The equilibrium concentrations of substrate and product were almost equal. Enzyme activity was induced after anoxic growth with benzoate, in contrast to acetate. The enzyme of 28 kDa was purified from T. aromatica and was found to be highly specific for the cyclic 1,5-dienoyl-CoA. A second 29-kDa enoyl-CoA hydratase acted on crotonyl-CoA; this highly active enoyl-CoA hydratase also acted slowly on cyclohex-1-ene-1-carbonyl-CoA. The regulation of expression of dienoyl-CoA hydratase activity, the kinetic constants, the substrate specificity, and the specific activity of the enzyme in cell extract provide evidence that dienoyl-CoA hydratase is the second enzyme of the central benzoyl-CoA pathway of anaerobic aromatic metabolism in T. aromatica. Extracts of Rhodopseudomonas palustris contained high activity of cyclohex-1-ene-1-carbonyl-CoA hydratase, but no 1,5-dienoyl-CoA hydratase activity. It appears that a variant of the benzoyl-CoA pathway is operating in R. palustris in which hydration of the 1,5-dienoyl-CoA does not take place. Rather, cyclohex-1-ene-1-carbonyl-CoA is hydrated to 2-hydroxycyclohexane-1-carbonyl-CoA [corrected].

Acyl Coenzyme A↗
PubMed1998

Biosynthesis of the diterpene verrucosan-2beta-ol in the phototrophic eubacterium Chloroflexus aurantiacus. A retrobiosynthetic NMR study.

The biosynthesis of verrucosan-2beta-ol in the green phototrophic eubacterium Chloroflexus aurantiacus was investigated by in vivo incorporation of singly or doubly 13C-labeled acetate. The 13C labeling of the isolated diterpene was analyzed by one- and two-dimensional NMR spectroscopy. The 13C-labeling patterns of verrucosan-2beta-ol were compared with the labeling patterns of intermediary metabolites (acetyl-CoA, pyruvate, and glyceraldehyde 3-phosphate) which were deduced from amino acids and nucleosides by retrobiosynthetic analysis. The results show that verrucosan-2beta-ol is synthesized via mevalonate and not via the deoxyxylulose pathway, which was discovered recently in some eubacteria, algae, and plants. A scheme for the formation of the unusual tetracyclic ring system is offered. The cyclization process is initiated by the solvolysis of pyrophosphate from geranyllinaloyl pyrophosphate and the mechanism involves a Wagner-Meerwein rearrangement, a 1,5-hydride shift, and a cyclopropylcarbinyl to cyclopropylcarbinyl rearrangement.

Acetyl Coenzyme A↗
PubMed1998

Solution structure of the antitermination protein NusB of Escherichia coli: a novel all-helical fold for an RNA-binding protein.

The NusB protein of Escherichia coli is involved in the regulation of rRNA biosynthesis by transcriptional antitermination. In cooperation with several other proteins, it binds to a dodecamer motif designated rrn boxA on the nascent rRNA. The antitermination proteins of E.coli are recruited in the replication cycle of bacteriophage lambda, where they play an important role in switching from the lysogenic to the lytic cycle. Multidimensional heteronuclear NMR experiments were performed with recombinant NusB protein labelled with 13C, 15N and 2H. The three-dimensional structure of the protein was solved from 1926 NMR-derived distances and 80 torsion angle restraints. The protein folds into an alpha/alpha-helical topology consisting of six helices; the arginine-rich N-terminus appears to be disordered. Complexation of the protein with an RNA dodecamer equivalent to the rrn boxA site results in chemical shift changes of numerous amide signals. The overall packing of the protein appears to be conserved, but the flexible N-terminus adopts a more rigid structure upon RNA binding, indicating that the N-terminus functions as an arginine-rich RNA-binding motif (ARM).

Amino Acid Sequence↗
PubMed1998

Biosynthesis of pteridines in Escherichia coli. Structural and mechanistic similarity of dihydroneopterin-triphosphate epimerase and dihydroneopterin aldolase.

An open reading frame located at 69.0 kilobases on the Escherichia coli chromosome was shown to code for dihydroneopterin aldolase, catalyzing the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate. The gene was subsequently designated folB. The FolB protein shows 30% identity to the paralogous dihydroneopterin-triphosphate epimerase, which is specified by the folX gene located at 2427 kilobases on the E. coli chromosome. The folX and folB gene products were both expressed to high yield in recombinant E. coli strains, and the recombinant proteins were purified to homogeneity. Both enzymes form homo-octamers. Aldolase can use L-threo-dihydroneopterin and D-erythro-dihydroneopterin as substrates for the formation of 6-hydroxymethyldihydropterin, but it can also catalyze the epimerization of carbon 2' of dihydroneopterin and dihydromonapterin at appreciable velocity. Epimerase catalyzes the epimerization of carbon 2' in the triphosphates of dihydroneopterin and dihydromonapterin. However, the enzyme can also catalyze the cleavage of the position 6 side chain of several pteridine derivatives at a slow rate. Steady-state kinetic parameters are reported for the various enzyme-catalyzed reactions. We propose that the polarization of the 2'-hydroxy group of the substrate could serve as the initial reaction step for the aldolase as well as for the epimerase activity. A deletion mutant obtained by targeting the folX gene of E. coli has normal growth properties on complete medium as well as on minimal medium. Thus, the physiological role of the E. coli epimerase remains unknown. The open reading frame ygiG of Hemophilus influenzae specifies a protein with the catalytic properties of an aldolase. However, the genome of H. influenzae does not specify a dihydroneopterin-triphosphate epimerase.

Aldehyde-Lyases↗
PubMed1998

Rearrangement reactions in the biosynthesis of molybdopterin--an NMR study with multiply 13C/15N labelled precursors.

The genes moaABC of Escherichia coli were ligated into the expression vector pNCO113. The resulting plasmid was transformed into a moeA mutant of E. coli. From cultures of the recombinant strain, a pteridine designated compound Z could be isolated at 5 mg/liter. Compound Z is a product of precursor Z, a biosynthetic precursor of molybdopterin. Cultures of the recombinant E. coli strain were supplied with [U-(13)C6]glucose, [U-(13)C5]ribulose 5-phosphate, or [7-(15)N,8-(13)C]guanine. The culture medium also contained a large excess of unlabeled glucose. Compound Z as well as nucleosides obtained by hydrolysis of RNA were isolated from the bacterial cultures, and their heavy isotope distribution was investigated by one-dimensional and two-dimensional NMR spectroscopy. The labelling patterns of compound Z show that the carbon atoms of a pentose or pentulose are diverted to the ring atoms C6 and C7 and to the side chain atoms C2', C3' and C4' of compound Z. Carbon atom C1' of compound Z is derived from carbon atom C8 of a guanine derivative. The remodeling of the carbon skeleton of the pentose and purine moieties proceed via intramolecular rearrangement reactions.

Carbon Isotopes↗
PubMed1998

31P-NMR spectroscopy of human and Paracoccus denitrificans electron transfer flavoproteins, and 13C- and 15N-NMR spectroscopy of human electron transfer flavoprotein in the oxidised and reduced states.

Human and Paracoccus denitrificans wild-type electron transfer flavoproteins have been investigated by 31P-NMR in the oxidised and reduced states. The 31P chemical shifts of the diphosphate moiety of the protein-bound FAD were similar in the proteins and were independent of the redox state. The chemical shifts were remarkably similar to those of ferredoxin-NADP+ reductase and, to a lesser degree, with those of NADPH-cytochrome P-450 reductase. The wild-type human electron transfer apoprotein was reconstituted with [2,4a-13C2]FAD, [4,10a-13C2]FAD, or [U-15N4]FAD. The reconstituted proteins were studied by 13C- and 15N-NMR techniques in the oxidised and reduced states. The chemical shifts were compared with those of free flavin in aqueous solution or in chloroform, and those of flavoproteins published in the literature. In the oxidised state, strong hydrogen bonds exist between residues of the apoprotein and C(2)O and N(5) of FAD. The N(1) atom is also hydrogen bonded and, as shown by X-ray data, involves the C'(4)-OH group of FAD. The sp2 hybridisation of N(10) is small compared to other flavoproteins. In the reduced state, there are strong hydrogen bonds involving C(2)O and N(5) of FAD. The N(1) atom is ionised as observed also in other flavoproteins when investigated by NMR. The intramolecular hydrogen bond between the C'(4)-OH group and the N(1) atom of FAD is maintained in the reduced state, suggesting an involvement in the stabilisation of a certain configuration of the diphosphate group of protein-bound FAD in both redox states. The N(10) atom in the reduced protein is highly sp3 hybridised in comparison to those of other flavoproteins.

Apoproteins↗
PubMed1998

Evidence for local 32 symmetry in homotrimeric riboflavin synthase of Escherichia coli.

Riboflavin synthase is a trimer of identical 23-kDa subunits. The primary structure is characterized by considerable similarity of the C-terminal and N-terminal parts. Recombinant riboflavin synthase of Escherichia coli and Bacillus subtilis was crystallized by the vapor diffusion method. Crystals of E. coli riboflavin synthase belong to the orthorhombic system, space group P2(1)2(1)2(1), with unit cell dimensions a = 53.2 A, b = 117.6 A, c = 150.9 A, alpha = beta = gamma = 90 degrees. They diffract to better than 3.3 A resolution and have presumably one trimer in the asymmetric unit. The self rotation function indicates local 32 symmetry. Twofold local symmetry is an unexpected result in a trimeric protein. In conjunction with primary structure arguments and mechanistic considerations, we propose that the protein is a pseudohexamer where each of the peptide subunits fold into two topologically similar domains.

Bacillus subtilis↗
PubMed1998

Acute normovolaemic haemodilution does not aggravate gastric mucosal acidosis during cardiac surgery.

OBJECTIVE: Acute normovolaemic haemodilution with subsequent autologous blood transfusion after surgery is widely used to reduce homologous blood requirements during cardiac surgery. The hypothesis tested was whether a low intraoperative haematocrit (Hct) resulting from haemodilution decreases gastric mucosal pH (pHi). DESIGN: Prospective clinical investigation. SETTING: University Hospital of Vienna, Austria. PATIENTS: 16 consecutive patients scheduled for elective cardiac surgery. INTERVENTIONS: The patients were randomly assigned to one of two groups: In 10 patients (group 1), 500 ml of blood was withdrawn and stored after anaesthesia induction. An equal amount of 6% hydroxyethyl starch was simultaneously infused. After discontinuation of cardiopulmonary bypass (CPB), the autologous blood unit was transfused. Six patients (group 2), who were not subjected to haemodilution and autologous blood transfusion served as controls. In all patients, a gastric tonometry probe was inserted. MEASUREMENTS AND RESULTS: Measurements of pHi and Hct were performed before and after acute normovolaemic haemodilution, during pulsatile hypothermic (30-32 degrees C) CPB, after rewarming, and 30 min after autologous blood transfusion in group 1, and at corresponding time intervals in group 2. Repeated measures analysis of variance and the Mann-Whitney U test were used for statistical analysis. Data are presented as means +/- standard error of the mean. Haemodilution in group 1 caused a significant and persistent decrease in Hct (after haemodilution in group 1 34 +/- 1 vs 40 +/- 1% in group 2). In both groups, pHi decreased during rewarming and after termination of CPB. However, in group 1, pHi was better preserved than in group 2 (rewarming: 7.44 +/- 0.02 vs 7.34 +/- 0.04; after CPB: 7.38 +/- 0.03 vs 7.28 +/- 0.02; p < 0.05). CONCLUSIONS: Acute normovolaemic haemodilution does not aggravate gastric mucosal acidosis during cardiac surgery.

Acidosis↗
PubMed1998

Synthesis of 2,6-dioxo-(1H,3H)-9-N-ribitylpurine and 2,6-dioxo-(1H,3H)-8-aza-9-N-ribitylpurine as inhibitors of lumazine synthase and riboflavin synthase.

2,6-Dioxo-(1H,3H)-9-N-ribitylpurine (6) and 2,6-dioxo-(1H,3H)-8-aza-9-N-ribitylpurine (7) have been synthesized and evaluated as inhibitors of lumazine synthase and riboflavin synthase. Reaction of 5-amino-6-ribitylaminouracil hydrochloride (8) with diethoxymethyl acetate (9) afforded the purine 6, while diazotization of 8 afforded the 8-aza purine 7. Compounds 6 and 7 were evaluated against lumazine synthase of Bacillus subtilis and riboflavin synthase of Escherichia coli. Both 6 and 7 were better inhibitors of lumazine synthase than riboflavin synthase. The 8-azapurine 7 had a lower KI (0.33 and 0.39 mM) than the purine 6 (0.47 and 0.54 mM) when evaluated with lumazine synthase and riboflavin synthase, respectively.

Bacillus subtilis↗