Clifford J. Unkefer

The role of the buried aspartate of Escherichia coli thioredoxin in the activation of the mixed disulfide intermediate.

The structurally homologous protein disulfide isomerases and thioredoxins exhibit a 105 variation of redox equilibria. It is demonstrated that the kinetic distinction among these protein family members lies primarily in the rate of breakdown of the mixed disulfide intermediate. The conserved buried acid group serves as a proton transfer catalyst for the buried active site cysteine in the formation and breakdown of the mixed disulfide. The reduction rate of Escherichia coli thioredoxin by dithiothreitol is directly proportional to the fraction of Asp-26 in the protonated form over the pH range of 6–9. The kinetic role of Asp-26 is further probed via differential solvent kinetic isotope effect measurements versus a D26N variant. The differential solvent isotope effect of 0.6 is consistent with a direct proton donation to the thiolate leaving group (Cys-35) via an enforced general acid catalysis by trapping mechanism. Such a donation necessitates a structural rearrangement as these two buried side chains are separated by 6 Å in both the oxidized and reduced forms of the protein.

Intestinal absorption and tissue distribution of [14C]pyrroloquinoline quinone in mice

Abstract Pyrroloquinoline quinone (PQQ) functions as a cofactor for prokaryotic oxido-reductases, such as methanol dehydrogenase and membrane-bound glucose dehydrogenase. In animals fed chemically defined diets, PQQ improves reproductive outcome and neonatal growth. Consequently, the present study was undertaken to determine the extent to which PQQ is absorbed by the intestine, its tissue distribution, and route of excretion. About 28 μg of PQQ (0.42 μCi/μmol), labeled with 14C derived from l-tyrosine, was administered orally to Swiss-Webster mice (18–20 g) to estimate absorption. PQQ was readily absorbed (62%, range 19–89%) in the lower intestine, and was excreted by the kidneys (81% of the absorbed dose) within 24 hr. The only tissues that retained significant amounts of [14C]PQQ at 24 hr were skin and kidney. For kidney, it was assumed that retention of [14C]PQQ represented primarily PQQ destined for excretion. For skin, the concentration of [14C]PQQ increased from 0.3% of the absorbed dose at 6 hr to 1.3% at 24 hr. Furthermore, most of the [14C]PQQ in blood (>95%) was associated with the blood cell fraction, rather than plasma.

The assignment of carbonyl resonances in 13C-N.M.R. spectra of peracetylated mono- and oligo-saccharides containing d-glucose and d-mannose: An alternative method for structural determination of complex carbohydrates

In the present study, proton homonuclear (COSY) and 13C-1H heteronuclear shift-correlation, n.m.r. spectroscopies have been used to assign the carbonyl carbon resonances of peracetylated D-gluco- and D-mannopyranose monosaccharides and oligosaccharides containing residues of parent D-glucopyranose monomers. Chemical shifts of these assigned resonances, particularly those arising from acetyl groups near to aglycon substitution sites, were found to be sensitive to the position and configuration of glycosidic linkages present. In addition, evidence is presented that indicates that the shifts of these carbonyl carbon resonances depend on long-range interactions with other peracetylated pyranose monomers resulting from folding of the oligosaccharide chain. These results suggest that carbonyl carbon resonances of peracetylated carbohydrates may be useful probes of oligosaccharide structure.

Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds

MOTIVATION Our knowledge of the metabolites in cells and their reactions is far from complete as revealed by metabolomic measurements that detect many more small molecules than are documented in metabolic databases. Here, we develop an approach for predicting the reactivity of small-molecule metabolites in enzyme-catalyzed reactions that combines expert knowledge, computational chemistry and machine learning. RESULTS We classified 4843 reactions documented in the KEGG database, from all six Enzyme Commission classes (EC 1-6), into 80 reaction classes, each of which is marked by a characteristic functional group transformation. Reaction centers and surrounding local structures in substrates and products of these reactions were represented using SMARTS. We found that each of the SMARTS-defined chemical substructures is widely distributed among metabolites, but only a fraction of the functional groups in these substructures are reactive. Using atomic properties of atoms in a putative reaction center and molecular properties as features, we trained support vector machine (SVM) classifiers to discriminate between functional groups that are reactive and non-reactive. Classifier accuracy was assessed by cross-validation analysis. A typical sensitivity [TP/(TP+FN)] or specificity [TN/(TN+FP)] is ≈0.8. Our results suggest that metabolic reactivity of small-molecule compounds can be predicted with reasonable accuracy based on the presence of a potentially reactive functional group and the chemical features of its local environment. AVAILABILITY The classifiers presented here can be used to predict reactions via a web site (http://cellsignaling.lanl.gov/Reactivity/). The web site is freely available.

Reconstruction of Metabolic Networks from High-Throughput Metabolite Profiling Data : In Silico Analysis of Red Blood Cell Metabolism

Abstract:  We investigate the ability of algorithms developed for reverse engineering of transcriptional regulatory networks to reconstruct metabolic networks from high‐throughput metabolite profiling data. For benchmarking purposes, we generate synthetic metabolic profiles based on a well‐established model for red blood cell metabolism. A variety of data sets are generated, accounting for different properties of real metabolic networks, such as experimental noise, metabolite correlations, and temporal dynamics. These data sets are made available online. We use ARACNE, a mainstream algorithm for reverse engineering of transcriptional regulatory networks from gene expression data, to predict metabolic interactions from these data sets. We find that the performance of ARACNE on metabolic data is comparable to that on gene expression data.

Studies on the biosynthesis of paraherquamide. Construction of the amino acid framework

Abstract It has been previously established in this laboratory that the β-methyl-β-hydroxyproline moiety of the potent anthelmintic agent paraherquamide A, is biosynthetically derived from l -isoleucine. The downstream events from l -Ile to paraherquamide A have now been investigated. The synthesis of [1- 13 C]-labeled l -β-methylproline is described by means of a Hoffman–Loeffler–Freytag reaction sequence from [1- 13 C]- l -Ile. This amino acid is shown to be a direct biosynthetic precursor to paraherquamide A by feeding and incorporation experiments in growing cultures of Penicillium fellutanum . Three tryptophan-containing dipeptides of l -β-methylproline have been constructed: [ 13 C 2 ]-2-(1,1-dimethyl-2-propenyl)- l -tryptophanyl-3( S )-methyl- l -proline; [ 13 C 2 ]-3( S )-methyl- l -prolyl-2-(1,1-dimethyl-2-propenyl)- l -tryptophan and [ 13 C 2 ]- cyclo -2-(1,1-dimethyl-2-propenyl)- l -tryptophan-3( S )-methyl- l -proline. [α- 15 N, 1- 13 C]-2-(1,1-Dimethyl-2-propenyl)- l -tryptophan was also prepared but none of these substances were found to serve as biosynthetic precursors to paraherquamide A.

Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites

MOTIVATION Our knowledge of metabolism is far from complete, and the gaps in our knowledge are being revealed by metabolomic detection of small-molecules not previously known to exist in cells. An important challenge is to determine the reactions in which these compounds participate, which can lead to the identification of gene products responsible for novel metabolic pathways. To address this challenge, we investigate how machine learning can be used to predict potential substrates and products of oxidoreductase-catalyzed reactions. RESULTS We examined 1956 oxidation/reduction reactions in the KEGG database. The vast majority of these reactions (1626) can be divided into 12 subclasses, each of which is marked by a particular type of functional group transformation. For a given transformation, the local structures of reaction centers in substrates and products can be characterized by patterns. These patterns are not unique to reactants but are widely distributed among KEGG metabolites. To distinguish reactants from non-reactants, we trained classifiers (linear-kernel Support Vector Machines) using negative and positive examples. The input to a classifier is a set of atomic features that can be determined from the 2D chemical structure of a compound. Depending on the subclass of reaction, the accuracy of prediction for positives (negatives) is 64 to 93% (44 to 92%) when asking if a compound is a substrate and 71 to 98% (50 to 92%) when asking if a compound is a product. Sensitivity analysis reveals that this performance is robust to variations of the training data. Our results suggest that metabolic connectivity can be predicted with reasonable accuracy from the presence or absence of local structural motifs in compounds and their readily calculated atomic features. AVAILABILITY Classifiers reported here can be used freely for noncommercial purposes via a Java program available upon request.

Biosynthesis of the 3,4-Dihydroxybenzoate Moieties of Petrobactin by Bacillus anthracis

The biosynthesis of the 3,4-dihydroxybenzoate moieties of the siderophore petrobactin, produced by B. anthracis str. Sterne, was probed by isotopic feeding experiments in iron-deficient media with a mixture of unlabeled and D-[(13)C6]glucose at a ratio of 5:1 (w/w). After isolation of the labeled siderophore, analysis of the isotopomers was conducted via one-dimensional (1)H and (13)C NMR spectroscopy, as well as (13)C-(13)C DQFCOSY spectroscopy. Isotopic enrichment and (13)C-(13)C coupling constants in the aromatic ring of the isolated siderophore suggested the predominant route for the construction of the carbon backbone of 3,4-DHB (1) involved phosphoenol pyruvate and erythrose-4-phosphate as ultimate precursors. This observation is consistent with that expected if the shikimate pathway is involved in the biosynthesis of these moieties. Enrichment attributable to phosphoenol pyruvate precursors was observed at C1 and C6 of the aromatic ring, as well as into the carboxylate group, while scrambling of the label into C2 was not. This pattern suggests 1 was biosynthesized from early intermediates of the shikimate pathway and not through later shikimate intermediates or aromatic amino acid precursors.

Excretion and metabolism of 1-nitropyrene in rats after oral or intraperitoneal administration☆

Many nitro-substituted polycyclic aromatic hydrocarbons (NPAHs) have been identified as environmental pollutants and have been found to be mutagens and carcinogens in bacteria and mammalian systems. They require metabolism to express their biological activity. The metabolism and excretion of 1-nitropyrene (NP), a prevalent NPAH, by Fischer-344 rats after intraperitoneal (ip) or oral administration was studied. Radiolabeled NP was administered to rats (10 mg NP/kg body wt), and urine and feces were collected for 7 days. After ip administration of [14C]NP, 60% of the radioactivity was found in the urine and 20% in the feces. Likewise, 55 and 35% of the orally administered 14C was found in urine and feces, respectively. Both urine and feces were analyzed by high-pressure liquid chromatography for metabolites. The majority of the radioactivity in both urine and feces was associated with very polar metabolites, none accounting for more than 10% of the dose. Small amounts (less than 1% of the dose) of aminopyrene (AP), acetylaminopyrene, and NP were detected. A urinary metabolite (3-8% of the dose) was found that converted to acetylaminopyrene phenol (two isomers) when urine was heated overnight at 37 degrees C at pH 4.5. More of this metabolite (2.2 times) as well as AP (1.8 times), was excreted after oral than after ip administration of NP. The NP metabolites found in this study demonstrate that reduction of the nitro group is a significant route of NP metabolism in rats. Since nitroreduction appears to be necessary in the activation of NPAHs to bacterial mutagens, this indicates that similar metabolic pathways are present in rats (catalyzed by mammalian and/or gut bacterial enzymes) and that activation of NPAHs to carcinogens or toxins by nitroreduction is possible.

Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation.

A 1.1 Å resolution, room-temperature X-ray structure and a 2.1 Å resolution neutron structure of a chitin-degrading lytic polysaccharide monooxygenase domain from the bacterium Jonesia denitrificans (JdLPMO10A) show a putative dioxygen species equatorially bound to the active site copper. Both structures show an elongated density for the dioxygen, most consistent with a Cu(II)-bound peroxide. The coordination environment is consistent with Cu(II). In the neutron and X-ray structures, difference maps reveal the N-terminal amino group, involved in copper coordination, is present as a mixed ND2 and ND-, suggesting a role for the copper ion in shifting the pKa of the amino terminus.