Intracellular Trapping of CycloSal-Pronucleotides by Enzymatic Cleavage

A new synthesis for cycloSal-pronucleotides bearing enzymatically cleavable triggers is presented. This trigger is introduced to trap the pronucleotide inside cells. The general concept and hydrolysis data in different media are discussed.     

Effect of the substrate and catalyst chirality on the diastereoselective epoxidation of limonene using Jacobsen‐type catalysts

Chiral and achiral Jacobsen's catalysts in their homogeneous form or immobilized on Al‐MCM‐41 exhibit similar catalytic activity during diastereoselective epoxidation of limonene when in situ generated dimethyldioxirane is used as oxidizing agent. Experimental observations suggest that not only the catalyst chiral center but also the substrate chiral center participates in the preferential formation of most diastereomers. Remarkable turnover numbers (TON), up to 288, was achieved over the heterogeneous catalysts in comparison to their homogeneous counterparts (TON up to 46). Catalyst leaching rather than catalyst oxidative degradation was identified as the main source of catalyst deactivation during reutilization tests. Chirality, 2010. © 2009 Wiley‐Liss, Inc.     

Enantioselective and diastereoselective separation of synthetic pyrethroid insecticides on a novel chiral stationary phase by high-performance liquid chromatography

A novel chiral packing material for high-performance liquid chromatography (HPLC) was prepared by connecting (R)-1-phenyl-2-(4-methylphenyl) ethylamine (PTE) amide derivative of (S)-isoleucine to aminopropyl silica gel through 2-amino-3,5-dinitro-1-carboxamido-benzene unit. This chiral stationary phase was applied to the enantioselective and diastereoselective separation of five pyrethroid insecticides by HPLC under normal phase condition. To achieve satisfactory baseline separation an optimization of the variables of mobile phase composition was required. The two enantiomers of fenpropathrin and four stereoisomers of fenvalerate were baseline separated using hexane-1,2-dichloroethane-2-propanol as mobile phase. The results show that the enantioselectivity of CSP is better than Pirkle type 1-A column for these compounds. Only partial separations for the cypermethrin and cyfluthrin stereoisomers were observed. Seven peaks and eight peaks were observed for cypermethrin and cyfluthrin, respectively. The elution orders were assigned by using different stereoisomer-enriched products.     

A practical and green approach toward synthesis of 2,4,5-trisubstituted imidazoles without adding catalyst

A simple, efficient, and inexpensive procedure has been developed for the synthesis of 2,4,5-triaryl imidazoles by a three-component, one-pot condensation of benzyl, aldehydes, and ammonium acetate in refluxing ethanol without adding catalyst. The "catalyzed-by-itself" approach shows a new direction in green synthesis of the title products.     

Enantioselective and diastereoselective Michael addition of ketone/aldehyde to trans-nitroolefins catalyzed by a novel chiral pyrrolidine-thiourea

The direct Michael addition reaction of cyclohexanone/aliphatic aldehydes with nitroolefins, catalyzed by a novel chiral pyrrolidine-thiourea catalyst 1a, is described. The desired 1,4-adducts were obtained in moderate yields with enantioselectivities up to 99% ee and dr up to 99:1 of the syn product.     

The chemistry of the collagen cross-links. A convenient synthesis of the reduction products of several collagen cross-links and cross-link precursors

New synthetic routes to the reduction products of several collagen cross-links and cross-link precursors are described. By the use of these routes hydroxynorleucine, 5,6-dihydroxynorleucine, hydroxylysinonorleucine and hydroxylysinohydroxynorleucine can be synthesized via one common synthetic intermediate. The synthetic routes provide a convenient source of these unusual amino acids, as well as confirming the structure of hydroxylysinohydroxynorleucine and the other lysine-derived residues found in borohydride-reduced collagens.     

Conformational solution studies of the anti-microbial temporin A retro-analogues by using NMR spectroscopy.

Temporin A (TA) is a small, basic and highly hydrophobic peptide, isolated from the skin of the European red frog, Rana temporaria. The TA (FLPLIGRVLSGIL-NH2) displays a broad spectrum of anti-microbial activity against Gram-positive bacteria and fungi Candida albicans. In this study we investigate the solution structure of two TA retro-analogues, (6-1)(7-13)-TA (GILPLFRVLSGIL-NH2) and retro-TA (LIGSLVRGILPLF-NH2) by using nuclear magnetic resonance (NMR). The 3D solution structure of the analogues was established by using inter-proton distances and vicinal coupling constants in the Simulated Annealing (SA) calculations (XPLOR program). The NMR conformational studies show the existence of the helical structure in the middle part of the (6-1)(7-13)-TA peptide and an unordered structure of the retro-TA analogue under the D3-TFE/H2O (3:7, v/v) conditions. Our investigations have shown that the hydrophobic cluster at N-terminus with the Pro amino acid residue in position 3 or 4, the helical structure and the amphipathic character of the peptide are responsible for the anti-microbial activity of the TA analogues.     

Meglumine as a green,efficient and reusable catalyst for synthesis and molecular docking studies of bis(indolyl)methanes as antioxidant agents

An efficient and convenient Meglumine catalyzed procedure for the synthesis of bis(indolyl) methanes at ambient temperature under aqueous conditions in high yields. The catalytic reaction proceeds very smoothly. Clean reaction, ease of product isolation/purification, easily available reactants, metal free and environmentally friendly reaction conditions are the notable advantages of the present methodology. All the entitled compounds were characterized by IR, ¹H, ¹³C NMR, mass spectra and evaluated for their antioxidant (DPPH, H₂O₂ and NO scavenging methods). They exhibited potent in vitro antioxidant activity dose-dependently. The binding interactions and molecular docking studies for entitled compounds were studied against 3MNG protein. 4d exhibited marked binding affinity with excellent docking score of −7.6 K.cal/mol and emerged as a lead compound.     

Picomole-level mapping of protein disulfides by mass spectrometry following partial reduction and alkylation

We have deduced the disulfide bond linkage patterns, at very low protein levels (<0.5 nmol), in two cysteine-rich polypeptide domains using a new strategy involving partial reduction/alkylation of the protein, followed by peptide mapping and tanden mass spectrometry (MS/MS) sequencing on a nanoflow liquid chromatography-MS/MS system. The substrates for our work were the cysteine-rich ectodomain of human Fn14, a member of the tumor necrosis factor receptor family, and the IgV domain of murine TIM-1 (T-cell, Ig domain, and mucin domain-1). We have successfully determined the disulfide linkages for Fn14 and independently confirmed those of the IgV domain of TIM-1, whose crystal structure was published recently. The procedures that we describe here can be used to determine the disulfide structures for proteins with complex characteristics. They will also provide a means to obtain important information for structure-function studies and to ensure correct protein folding and batch-to-batch consistency in commercially produced recombinant proteins.     

Ferric chelate reduction by suspension culture cells and roots of soybean: A kinetic comparison

The abilities of suspension cultures and intact roots of soybean (Glycine max L. cv. Hawkeye) to reduce ferric chelate were compared. Ferric chelate was supplied as ferric hydroxyethylethylenediaminetriacetic acid (FeHEDTA) and reduction was measured spectrophotometrically using bathophenan-throlinedisulfonic acid (BPDS) as the ferrous scavenger. Ferric chelate reduction by cell suspension cultures showed typical saturation kinetics; however, no difference was observed between cells that had been continuously grown with Fe (+Fe) and those that had been grown for four days without added Fe (–Fe). Values for K_m and V_max, determined from a Lineweaver-Burk plot, were 57 M and nmoles mg^-1 dry weight for the +Fe cells and 50 M and 22 nmoles mg^-1 dry weight for the -Fe cells, respectively. Ferric chelate reduction by Fe-deficient roots also exhibited saturation kinetics, while roots grown with adequate Fe did not reduce ferric chelate. The K_m and V_max values for Fe-deficient roots were 45 M and 20 nmoles mg^-1 dry weight, respectively, and did not differ from values obtained for cells in culture. This study offers strong evidence that the mechanism responsible for the reduction of ferric chelate is the same for cultured cells and roots and that the process is controlled at the cellular level. We propose that suspension cultures can be used as an alternative to intact roots in the study of ferric chelate reduction.     

Enhanced diastereoselective synthesis of t‐Butyl 6‐cyano‐(3R,5R)‐dihydroxyhexanoate by using aldo‐keto reductase and glucose dehydrogenase co‐producing engineered Escherichia coli

t‐Butyl 6‐cyano‐(3R,5R)‐dihydroxyhexanoate ((3R,5R)‐ 2 ) is a key chiral diol precursor of atorvastatin calcium (Lipitor®). We have constructed a Kluyveromyces lactis aldo‐keto reductase mutant KlAKR‐Y295W/W296L (KlAKRm) by rational design in previous research, which displayed high activity and excellent diastereoselectivity (de_p > 99.5%) toward t‐butyl 6‐cyano‐(5R)‐hydroxy‐3‐oxohexanoate ((5R)‐ 1 ). To realize in situ cofactor regeneration, a robust KlAKRm and Exiguobacterium sibiricum glucose dehydrogenase (EsGDH) co‐producer E. coli BL 21(DE3) pETDuet‐esgdh (MCS1)/pET‐28b (+)‐klakrm was constructed in this work. Under the optimized conditions, AKR and GDH activities of E. coli BL 21(DE3) pETDuet‐esgdh (MCS1)/pET‐28b (+)‐klakrm peaked at 249.9 U/g DCW (dry cellular weight) and 29100 U/g DCW, respectively. It completely converted (5R)‐ 1 at substrate loading size of up to 60.0 g/L (5R)‐ 1 in the absence of exogenous NADH, which was one‐fifth higher than that of the separately prepared KlAKRm and EsGDH under the same conditions. In this manner, a biocatalytic process for (3R,5R)‐ 2 with productivity of 243.2 kg/m³ d was developed. Compared with the combination of separate expressed KlAKRm with EsGDH, co‐expression of KlAKRm and EsGDH has the advantages of alleviating cell cultivation burden and elevating substrate load. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1235–1242, 2017     

Organic matter mineralization in an organic-rich sediment: Experimental stimulation of sulfate reduction by fish food pellets

Abstract The combined effects of organic matter additions and temperature on short chain fatty acid (SCFA) turnover, sulfate reduction and nutrient accumulation were examined in an organic-rich fish farm sediment. Fish food pellets, which contribute significantly to the organic matter loss from fish farms, were added to surface sediment at three loadings (2.8; 14.0; 28.0 mg ww g⁻¹ ww sediment; equivalent to organic matter loadings measured during fish farming) and incubated for 30 days in anaerobic bags at 5°C and 15°C. SCFA accumulated to high levels (acetate up to 85 mM, propionate up to 17 mM, butyrate up to 25 mM) in sediments amended with food pellets, and sulfate reduction was stimulated up to 30 times relative to unamended sediments. Sulfate reducers appeared saturated with substrates (SCFA) even in the lowest additions. A low C/N ratio (0.4–1.8) of the major mineralization products (TCO₂ and NH₄⁺) indicated preferential nitrogen mineralization in amended sediment compared with the total particulate pool (C/N = 8.8–11.9) and added food pellets (C/N = 8.4).     

A chitin-oligomer binding peptide obtained by screening of a phage display random peptide library and its affinity modulation corresponding to oxidation–reduction state

Screening of a phage display random 9-mer peptide library, in which cysteine residues were at the both terminals of the 7-mer random region, was performed to obtain an oligopeptide that recognizes a chitin-oligomer. Affinity of the obtained peptide (Cys-Ser-Arg-Thr-Thr-Arg-Thr-Arg-Cys) to chitotriose was modulated by its oxidation–reduction state. Only the oxidized form exhibited specific binding to the target molecule, chitotriose. This is the first report of reversible affinity modulation of a synthetic oligopeptide which can recognize a neutral saccharide.     

Detection of specific chromosome reduction in rice somatic hybrids with the A, B, and C genomes by multi-color genomic in situ hybridization

 A multi-color genomic in situ hybridization (McGISH) method has been developed. Three different rice genomes, A, B and C, involved in rice somatic hybrids were distinguished using three different fluorescent signals. All the rice chromosomes from the different genomes could be identified by different fluorescent colors, and the distribution of each genome in the nucleus was clearly visualized under a fluorescence microscope. The relationship between chromosomal constitution and morphological variations observed in the somatic hybrids, and the utility of McGISH, are discussed based on the results currently obtained. Received: 21 November 1997 / Accepted: 9 December 1997     

Optimization of the mediated electrocatalytic reduction of NAD+ by cyclic voltammetry and construction of electrochemically driven enzyme bioreactor

The optimal concentrations of diaphorase, methyl viologen (MV²⁺) and NAD⁺ in the mediated electrocatalytic reduction of NAD⁺ were decided by applying cyclic voltammetry. The steady-state catalytic current was achieved under the conditions of 1.5 U diaphorase ml^–1, 0.2 mM MV²⁺, and 4.8 mM NAD⁺ at the scan rate of 2 mV s^–1, suggesting that the rate of the electrocatalytic reaction is the highest under the former conditions. However, NAD⁺ was effective at 0.3 mM as it was at 4.8 mM when the electrocatalysis is coupled with an enzymatic synthesis requiring NADH. In effect, the electrochemical procedure under the conditions of 1.5 U diaphorase ml^–1, 0.2 mM MV²⁺, and 0.3 mM NAD⁺ worked satisfactorily to drive an enzymatic reduction of pyruvate to d-lactate in the presence of d-lactate dehydrogenase.     

Flow cytometry for real-time measurement of guanine nucleotide binding and exchange by Ras-like GTPases

Ras-like small GTPases cycle between GTP-bound active and GDP-bound inactive conformational states to regulate diverse cellular processes. Despite their importance, detailed kinetic or comparative studies of family members are rarely undertaken due to the lack of real-time assays measuring nucleotide binding or exchange. Here we report a bead-based flow cytometric assay that quantitatively measures the nucleotide binding properties of glutathione-S-transferase (GST) chimeras for prototypical Ras family members Rab7 and Rho. Measurements are possible in the presence or absence of Mg²⁺, with magnesium cations principally increasing affinity and slowing nucleotide dissociation rates 8- to 10-fold. GST-Rab7 exhibited a 3-fold higher affinity for guanosine diphosphate (GDP) relative to guanosine triphosphate (GTP) that is consistent with a 3-fold slower dissociation rate of GDP. Strikingly, GST-Rab7 had a marked preference for GTP with ribose ring-conjugated BODIPY FL. The more commonly used γ-NH-conjugated BODIPY FL GTP analogue failed to bind to GST-Rab7. In contrast, both BODIPY analogues bound equally well to GST-RhoA and GST-RhoC. Comparisons of the GST-Rab7 and GST-RhoA GTP binding pockets provide a structural basis for the observed binding differences. In sum, the flow cytometric assay can be used to measure nucleotide binding properties of GTPases in real time and to quantitatively assess differences between GTPases.     

Enzyme identification and development of a whole-cell biotransformation for asymmetric reduction of o-chloroacetophenone

Chiral 1‐(o‐chlorophenyl)‐ethanols are key intermediates in the synthesis of chemotherapeutic substances. Enantioselective reduction of o‐chloroacetophenone is a preferred method of production but well investigated chemo‐ and biocatalysts for this transformation are currently lacking. Based on the discovery that Candida tenuis xylose reductase converts o‐chloroacetophenone with useful specificity (k_cat/K_m = 340 M⁻¹ s⁻¹) and perfect S‐stereoselectivity, we developed whole‐cell catalysts from Escherichia coli and Saccharomyces cerevisiae co‐expressing recombinant reductase and a suitable system for recycling of NADH. E. coli surpassed S. cerevisiae sixfold concerning catalytic productivity (3 mmol/g dry cells/h) and total turnover number (1.5 mmol substrate/g dry cells). o‐Chloroacetophenone was unexpectedly “toxic,” and catalyst half‐life times of only 20 min (E. coli) and 30 min (S. cerevisiae) in the presence of 100 mM substrate restricted the time of batch processing to maximally ∼5 h. Systematic reaction optimization was used to enhance the product yield (≤60%) of E. coli catalyzed conversion of 100 mM o‐chloroacetophenone which was clearly limited by catalyst instability. Supplementation of external NAD⁺ (0.5 mM) to cells permeabilized with polymyxin B sulfate (0.14 mM) resulted in complete conversion providing 98 mM S‐1‐(o‐chlorophenyl)‐ethanol. The strategies considered for optimization of reduction rate should be generally useful, however, especially under process conditions that promote fast loss of catalyst activity. Biotechnol. Bioeng. 2011; 108:797–803. © 2010 Wiley Periodicals, Inc.     

A comparison of inhibition of French-bean and soybean nitrogen fixation by nitrate, 1% oxygen or direct assimilate deprivation

Inhibition by NO⁻₃ of acetylene reduction in bean ( Phaseolus vulgaris L. cv. Contender) and soybean ( Glycine max L. cv. Amsoy 71) was measured in parallel with nodule carbohydrate and nitrate metabolism. In bean the onset of inhibition of C₂H₂ reduction (6 h) coincided with decreased import of assimilates and a lowering of carbohydrate pools (sucrose, glucose and starch). Nitrate reductase (EC 1.6.6.1) activity was induced in all plant organs after 3 h but no nitrite was detected in the nodules. In soybean, nodule carbohydrate concentrations and import of assimilates into the nodules increased markedly between 6 to 24 h after supply of nitrate when the nitrogenase (EC 1.7.99.2) was progressively inhibited. High nitrate reductase activity was observed in the nodules and nitrites accumulated because of insufficient nitrite reductase activity. The nitrate-induced inhibition of nitrogenase was compared with the inhibition observed with low oxygen around the roots (1% O²) or with direct assimilate deprivation (girdling or decapitation). Soybean and bean appeared equally sensitive to these treatments as regards to acetylene reduction. The results are discussed in relation to the current hypotheses explaining nitrate-induced inhibition of dinitrogen fixation: assimilate deprivation or nitrite poisoning. Present data are in favour of the first for bean and of the second for soybean.     

A rapid and sensitive ion chromatographic technique for the determination of sulfate and sulfate reduction rates in freshwater lake sediments

Abstract Newly developed low capacity columns were used in suppressed ion chromatography for rapid and highly reproducible determination of SO₄²⁻ in porewater samples from freshwater sediments without preconcentration of samples. With a 50 μl injection the detection limit for SO₄²⁻ was ca. 50 pmol (= 1 μ M) with a precision of 1–3% at the 10–200 μM level and <1% at concentrations above 200 μM. SO₄²⁻ could be measured in 4–5 min with the routinely used eluent (3.0 mM NaHCO₃/0.8 mM Na₂CO₃). When the strength of the eluent was increased to 3.0 mM NaHCO₃/2.0 mM Na₂CO₃, sulfate analysis was possible in less than 3 min, provided that samples were nitrate-free. Under these conditions S₂O₃²⁻ could also be sensitively determined in about 6 min. Examples of application of the method are given for measurements of sulfate reduction rates in freshwater sediment samples from Lake Constance.