Improvement of stability of nitrile hydratase via protein fragment swapping

Nitrile hydratase (NHase), which catalyzes the hydration of nitriles to amides, is the key enzyme for the production of amides in industries. However, the poor stability of this enzyme under the reaction conditions is a drawback of its industrial application. In this study, we aimed to improve the stability of NHase (PpNHase) from Pseudomonas putida NRRL-18668 using a homologous protein fragment swapping strategy. One thermophilic NHase fragment from Comamonas testosteroni 5-MGAM-4D and two fragments from Pseudonocardia thermophila JCM3095 were selected to swap the corresponding fragments of PpNHase. Seven chimeric NHases were designed using STAR (site targeted amino recombination) software and molecular dynamics to determine the crossover sites for fragment recombination. All constructed chimeric NHases showed 1.4- to 3.5-fold enhancement in thermostability and six of them become more tolerant to high-concentration product. Notably, one of these NHases, 3AB, exhibited a 1.4 ± 0.05-fold increase in activity compared to the wild-type PpNHase. Circular dichroism spectrum analysis and homology modeling revealed that the 3AB slightly differed in secondary structure from wild-type PpNHase. The 3AB constructed in this study is useful for further industrial application, and the method for designing the chimeric protein using homologous protein fragment swapping without a decrease in activity may be a strategy to improve the stability of other enzymes.     

Biochemical characterization of a 27 kDa 1,3-β-d-glucanase from Trichoderma asperellum induced by cell wall of Rhizoctonia solani

Trichoderma asperellum produces two extracellular 1,3-β-d-glucanase upon induction with cell walls from Rhizoctonia solani. A minor 1,3-β-d-glucanase was purified to homogeneity by ion exchange chromatography on Q-Sepharose and gel filtration on Sephacryl S-100. A typical procedure provided 13.8-fold purification with 70% yield. SDS-PAGE of the purified enzyme showed a single protein band of molecular weight 27 kDa. The enzyme exhibited optimum catalytic activity at pH 3.6 and 45 °C. It was thermostable at 40 °C, and retained 75% activity after 60 min at 45 °C. The K_m and V_max values for 1,3-β-d-glucanase, using laminarin as substrate, were 0.323 mg ml⁻¹ and 0.315 U min⁻¹, respectively. The enzyme was strongly inhibited by Hg²⁺ and SDS. The enzyme was only active toward glucans containing β-1,3-linkages. Peptide sequences showed similarity with two endo-1,3(4)-β-d-glucanases from Aspergillus fumigatus Af293when compared against GenBank non-redundant database.     

Transition metal complexes of a tridentate ligand bearing two pendant pyridine bases: The X-ray crystal structure of pentacoordinate copper(II) complex

The synthesis of a tridentate ligand, N,N′-bis(2-pyridinyl)-2,6-pyridinedicarboxamide [H₂L] is described together with its manganese(II), cobalt(II), nickel(II), copper(II), zinc(II) and cadmium(II) complexes which were characterized based on elemental analysis, conductivity measurements, spectral, magnetic and thermal studies. The IR spectral studies of all the complexes exhibit a similar feature about the ligating nature of the ligand to the metal ions and revealed that the ligand has coordinated through the nitrogens of the deprotonated amides and the central pyridine. The two pendant pyridine nitrogens in all the complexes are protonated and involved in hydrogen bonding with the oxygens of amide groups. This observation is confirmed by the single-crystal X-ray crystallographic studies of copper(II) complex. The geometry around the copper atom can be viewed as a distorted trigonal bipyramid with τ = 0.74 [structural parameter, τ = (β − α)/60; where α and β are the two basal angles in a five coordinate complex]. The electrochemical study of the copper(II) complex shows single quasi-reversible redox peak [Cu(II) ↔ Cu(I)]. The EPR spectrum of copper(II) complex exhibits rhombic pattern [g₁ = 2.0276, g₂ = 2.0926 and g₃ = 2.18].     

Coordination changes and auto-hydroxylation of FIH-1: uncoupled O2-activation in a human hypoxia sensor

Hypoxia sensing is the generic term for pO₂-sensing in humans and other higher organisms. These cellular responses to pO₂ are largely controlled by enzymes that belong to the Fe(II) α-ketoglutarate (αKG) dependent dioxygenase superfamily, including the human enzyme called the factor inhibiting HIF (FIH-1), which couples O₂-activation to the hydroxylation of the hypoxia inducible factor α (HIFα). Uncoupled O₂-activation by human FIH-1 was studied by exposing the resting form of FIH-1 (αKG + Fe)FIH-1, to air in the absence of HIFα. Uncoupling lead to two distinct enzyme oxidations, one a purple chromophore (λ_max = 583 nm) arising from enzyme auto-hydroxylation of Trp²⁹⁶, forming an Fe(III)-O-Trp²⁹⁶ chromophore [Y.-H. Chen, L.M. Comeaux, S.J. Eyles, M.J. Knapp, Chem. Commun. (2008), doi:10.1039/B809099H]; the other a yellow chromophore due to Fe(III) in the active site, which under some conditions also contained variable levels of an oxygenated surface residue (oxo)Met²⁷⁵. The kinetics of purple FIH-1 formation were independent of Fe(II) and αKG concentrations, however, product yield was saturable with increasing [αKG] and required excess Fe(II). Yellow FIH-1 was formed from (succinate + Fe)FIH-1, or by glycerol addition to (αKG + Fe)FIH-1, suggesting that glycerol could intercept the active oxidant from the FIH-1 active site and prevent hydroxylation. Both purple and yellow FIH-1 contained high-spin, rhombic Fe(III) centers, as shown by low temperature EPR. XAS indicated distorted octahedral Fe(III) geometries, with subtle differences in inner-shell ligands for yellow and purple FIH-1. EPR of Co(II)-substituted FIH-1 (αKG + Co)FIH-1, indicated a mixture of 5-coordinate and 6-coordinate enzyme forms, suggesting that resting FIH-1 can readily undergo uncoupled O₂-activation by loss of an H₂O ligand from the metal center.     

Triterpenoid saponins from a cytotoxic root extract of Sideroxylonfoetidissimum subsp. gaumeri

Evaluation of the cytotoxicity of an ethanolic root extract of Sideroxylonfoetidissimum subsp. gaumeri (Sapotaceae) revealed activity against the murine macrophage-like cell line RAW 264.7. Systematic bioassay-guided fractionation of this extract gave an active saponin-containing fraction from which four saponins were isolated. Use of 1D (¹H, ¹³C, DEPT135) and 2D (COSY, TOCSY, HSQC, and HMBC) NMR, mass spectrometry and sugar analysis gave their structures as 3-O-(β-d-glucopyranosyl-(1 → 6)-β-d-glucopyranosyl)-28-O-(α-l-rhamnopyranosyl-(1 → 3)[β-d-xylopyranosyl-(1 → 4)]-β-d-xylopyranosyl-(1 → 4)-α-l-rhamnopyranosyl-(1 → 2)-α-l-arabinopyranosyl)-16α-hydroxyprotobassic acid, 3-O-β-d-glucopyranosyl-28-O-(α-l-rhamnopyranosyl-(1 → 3)[β-d-xylopyranosyl-(1 → 4)]-β-d-xylopyranosyl-(1 → 4)-α-l-rhamnopyranosyl-(1 → 2)-α-l-arabinopyranosyl)-16α-hydroxyprotobassic acid, 3-O-(β-d-glucopyranosyl-(1 → 6)-β-d-glucopyranosyl)-28-O-(α-l-rhamnopyranosyl-(1 → 3)-β-d-xylopyranosyl-(1 → 4)[β-d-apiofuranosyl-(1 → 3)]-α-l-rhamnopyranosyl-(1 → 2)-α-l-arabinopyranosyl)-16α-hydroxyprotobassic acid, and the known compound, 3-O-β-d-glucopyranosyl-28-O-(α-l-rhamnopyranosyl-(1 → 3)[β-d-xylopyranosyl-(1 → 4)]-β-d-xylopyranosyl-(1 → 4)-α-l-rhamnopyranosyl-(1 → 2)-α-l-arabinopyranosyl)-protobassic acid. Two further saponins were obtained from the same fraction, but as a 5:4 mixture comprising 3-O-(β-d-glucopyranosyl)-28-O-(α-l-rhamnopyranosyl-(1 → 3)-β-d-xylopyranosyl-(1 → 4)[β-d-apiofuranosyl-(1 → 3)]-α-l-rhamnopyranosyl-(1 → 2)-α-l-arabinopyranosyl)-16α-hydroxyprotobassic acid and 3-O-(β-d-apiofuranosyl-(1 → 3)-β-d-glucopyranosyl)-28-O-(α-l-rhamnopyranosyl-(1 → 3)[β-d-xylopyranosyl-(1 → 4)]-β-d-xylopyranosyl-(1 → 4)-α-l-rhamnopyranosyl-(1 → 2)-α-l-arabinopyranosyl)-16α-hydroxyprotobassic acid, respectively. This showed greater cytotoxicity (IC₅₀ = 11.9 ± 1.5 μg/ml) towards RAW 264.7 cells than the original extract (IC₅₀ = 39.5 ± 4.1 μg/ml), and the saponin-containing fraction derived from it (IC₅₀ = 33.7 ± 6.2 μg/ml).     

Enzyme kinetics of ginsenosidase type IV hydrolyzing 6-O-multi-glycosides of protopanaxatriol type ginsenosides

In this work, the kinetics of ginsenosidase type IV hydrolyzing the 6-O-multi-glycosides of protopanaxatriol type ginsenosides (PPT) from Aspergillus sp.39g strain were investigated. The enzyme molecular weight was about 56 kDa. The enzyme hydrolyzes the 6-O-α-l-(1 → 2)-rhamnoside of ginsenoside Re and 6-O-β-d-(1 → 2)-xyloside of R1 into Rg1, and subsequently hydrolyzes 6-O-β-d-glucoside of Rg1 into F1. The enzyme hydrolyzes 6-O-α-l-(1 → 2)-rhamnoside of Rg2 and 6-O-β-d-(1 → 2)-glucoside of Rf into Rh1, and subsequently hydrolyzes 6-O-β-d-glucoside of Rh1 into its aglycone. The enzyme K_m and V_max for Re were 22.2 mM, and 7.94 mM/h; the K_m and V_max for R1 were 7.06 mM and 1.61 mM/h; the enzyme transformation velocity (V₀) at 5 mM substrate was 1.46 mM/h for Re, and 0.67 mM/h for R1. Therefore, the enzyme hydrolysis on the Re rhamnoside was faster than that on R1 xyloside. The enzyme V₀ on Rg1 was 0.05 mM/h that indicated the enzyme hardly hydrolyzed the 6-O-β-d-glucoside of Rg1. The enzyme kinetic parameters of Rg2 and Rf were 5.74 and 9.43 mM for K_m; 2.70 and 2.84 mM/h for V_max; 1.26 and 0.98 mM/h for V₀ at 5 mM substrate, respectively. Thus the enzyme hydrolysis on Rg2 rhamnoside was faster than that on the glucoside of Rf.     

A novel NADP-dependent dehydrogenase activity for 7α/β- and 11β-hydroxysteroids in human liver nuclei: A third 11β-hydroxysteroid dehydrogenase

Human tissue from uninvolved liver of cancer patients was fractionated using differential centrifugation and characterized for 11βHSD enzyme activity against corticosterone, dehydrocorticosterone, 7α- and 7β-hydroxy-dehydroepiandrosterone, and 7-oxo-dehydroepiandrosterone. An enzyme activity was observed in nuclear protein fractions that utilized either NADP⁺ or NAD⁺, but not NADPH and NADH, as pyridine nucleotide cofactor with K_m values of 12 ± 2 and 390 ± 2 μM, compared to the K_m for microsomal 11βHSD1 of 43 ± 8 and 264 ± 24 μM, respectively. The K_m for corticosterone in the NADP⁺-dependent nuclear oxidation reaction was 102 ± 16 nM, compared to 4.3 ± 0.8 μM for 11βHSD1. The K_cat values for nuclear activity with NADP⁺ was 1687 nmol/min/mg/μmol, compared to 755 nmol/min/mg/μmol for microsomal 11βHSD1 activity. Inhibitors of 11βHSD1 decreased both nuclear and microsomal enzyme activities, suggesting that the nuclear activity may be due to an enzyme similar to 11βHSD Type 1 and 2.     

Steroidal saponins from the leaves of Beaucarnea recurvata

Thirteen steroidal saponins were isolated from the leaves of Beaucarnea recurvata Lem. Their structures were established using one- and two-dimensional NMR spectroscopy and mass spectrometry. Six of them were identified as: 26-O-β-d-glucopyranosyl (25S)-furosta-5,20(22)-diene 1β,3β,26-triol 1-O-α-l-rhamnopyranosyl-(1 → 2) β-d-fucopyranoside, 26-O-β-d-glucopyranosyl (25S)-furosta-5,20(22)-diene 1β,3β,26-triol 1-O-α-l-rhamnopyranosyl-(1 → 2)-4-O-acetyl-β-d-fucopyranoside, 26-O-β-d-glucopyranosyl (25R)-furosta-5,20(22)-diene-23-one-1β,3β,26-triol 1-O-α-l-rhamnopyranosyl-(1 → 2) β-d-fucopyranoside, 26-O-β-d-glucopyranosyl (25S)-furosta-5-ene-1β,3β,22α,26-tetrol 1-O-α-l-rhamnopyranosyl-(1 → 4)-6-O-acetyl-β-d-glucopyranoside, 26-O-β-d-glucopyranosyl (25S)-furosta-5-ene-1β,3β,22α,26-tetrol 1-O-α-l-rhamnopyranosyl-(1 → 2) β-d-fucopyranoside, and 24-O-β-d-glucopyranosyl (25R)-spirost-5-ene-1β,3β,24-triol 1-O-α-l-rhamnopyranosyl-(1 → 2)-4-O-acetyl-β-d-fucopyranoside. The chemotaxonomic classification of B. recurvata in the family Ruscaceae was discussed.     

Triterpenoidal saponins of Pulsatilla koreana roots

Sixteen (1-16) triterpenoidal saponins were isolated from the roots of Pulsatilla koreana, of which four were determined as the previously unknown 23-hydroxy-3β-[(O-α-L-arabinopyranosyl)oxy]lup-20(29)-en-28-oic acid 28-O-β-D-glucopyranosyl ester (1), 23-hydroxy-3β-[(O-α-L-rhamnopyranosyl-(1 → 2)-α-L-arabinopyranosyl)oxy]lup-20(29)-en-28-oic acid 28-O-β-D-glucopyranosyl ester (2), 3β-[(O-α-L-rhamnopyranosyl-(1 → 2)-α-L-arabinopyranosyl)oxy]lup-20(29)-en-28-oic acid 28-O-β-D-glucopyranosyl-(1 → 6)-β-D-glucopyranosyl ester (3), and 3β-[(O-α-L-rhamnopyranosyl-(1 → 2)-O-[β-D-glucopyranosyl-(1 → 4)]-α-L-arabinopyranosyl)oxy]lup-20(29)-en-28-oic acid 28-O-α-L-rhamnopyranosyl-(1 → 4)-O-β-D-glucopyranosyl-(1 → 6)-β-D-glucopyranosyl ester (4), respectively, based on spectroscopic analysis. The inhibition of the lipopolysaccharide-induced nitric oxide production of sixteen isolated compounds was evaluated in RAW 264.7 cells at concentrations ranging from 1 μM to 100 μM.     

Acylated flavonol tetraglycosides from Delphinium gracile

An ethanol extract of the aerial parts of Delphinium gracile DC. yielded five flavonol glycosides quercetin-3-O-{[β-d-xylopyranosyl (1 → 3)-4-O-(E-p-caffeoyl)-α-l-rhamnopyranosyl (1 → 6)][β-d-glucopyranosyl (1 → 2)]}-β-d-glucopyranoside (1), quercetin-3-O-{[β-d-xylopyranosyl (1 → 3)-4-O-(E-p-coumaroyl)-α-l-rhamnopyranosyl (1 → 6)][β-d-glucopyranosyl (1 → 2)]}-β-d-glucopyranoside (2), quercetin-3-O-{[β-d-xylopyranosyl (1 → 3)-4-O-(Z-p-coumaroyl)-α-l-rhamnopyranosyl (1 → 6)][β-d-glucopyranosyl (1 → 2)]}-β-d-glucopyranoside (3), kaempferol-3-O-{[β-d-glucopyranosyl (1 → 3)-4-O-(E-p-coumaroyl)-α-l-rhamnopyranosyl (1 → 6)][β-d-glucopyranoside-7-O-(4-O-acetyl)-α-l-rhamnopyranoside (4) kaempferol-3-O-{[β-d-glucopyranosyl (1 → 3)-4-O-(E-p-coumaroyl)-α-l-rhamnopyranosyl (1 → 6)][β-d-glucopyranoside-7-O-(4-O-acetyl)-α-l-rhamnopyranoside (5) in addition to 4-(β-d-glucopyranosyloxy)-6-methyl-2H-pyran-2-one (6) and rutin. Structures were elucidated by spectroscopic methods.     

Metabolism of galactosyl-oligosaccharides in Stellaria media - Discovery of stellariose synthase, a novel type of galactosyltransferase

The raffinose family oligosaccharides (RFOs), including raffinose (Gal-α(1 → 6)-Glc-α(1 → 2)β-Fru), stachyose (Gal-α(1 → 6)-Gal-α(1 → 6)-Glc-α(1 → 2)β-Fru) and higher degree of polymerization RFOs are the most widespread galactosyl-oligosaccharides (GOS) in the plant kingdom. Stellaria media is a typical representative of the Caryophyllaceae, a plant family lacking stachyose and the typical galactosyl extensions of stachyose. During cold treatment raffinose, lychnose (Gal-α(1 → 6)-Glc-α(1 → 2)β-Fru-α(1 → 1)-Gal) and stellariose (Gal-α(1 → 6)-[Gal-α(1 → 4)]-Glc-α(1 → 2)β-Fru-α(1 → 1)-Gal) were found to accumulate in S. media stems. Next to these prominent oligosaccharides, two extra GOS were discovered.Biochemical analyses (enzymatic incubations and mild acid hydrolysis) and mass spectrometry identified the first, most abundant oligosaccharide as Glc-α(1 → 2)β-Fru-α(1 → 1)-Gal, a breakdown product of lychnose. The structure of this trisaccharide was confirmed by full NMR characterization. The second, less abundant compound (termed mediose) was identified as Gal-α(1 → 6)-[Gal-α(1 → 4)]Glc-α(1 → 2)β-Fru after biochemical analyses. By partial enzyme purification the presence of discrete lychnose synthase (raffinose:raffinose 1^Fru galactosyltransferase) and stellariose synthase (raffinose:lychnose 4^Glc galactosyltransferase) activities were shown.A model is presented explaining the structural diversity of GOS in S. media. In the absence of stachyose, raffinose is further elongated by lychnose synthase and stellariose synthase to produce lychnose, mediose and stellariose. Most likely, these compounds are also subject to partial trimming by endogenous α-galactosidases.     

Bioactive saponins from Microsechium helleri and Sicyos bulbosus

Eleven oleanane-type saponins (1-11) have been isolated from Microsechium helleri and Sicyos bulbosus roots and were evaluated for their antifeedant, nematicidal and phytotoxic activities. Saponins {3-O-β-d-glucopyranosyl (1 → 3)-β-d-glucopyranosyl-2β,3β,16α,23-tetrahydroxyolean-12-en-28-oic acid 28-O-α-l-rhamnopyranosyl-(1 → 3)-β-d-xylopyranosyl-(1 → 4)-[β-d-xylopyranosyl-(1 → 3)]-α-l-rhamnopyranosyl-(1 → 2)-α-l-arabinopyranoside} (1), and {3-O-β-d-glucopyranosyl-2β,3β,16α,23-tetrahydroxyolean-12-en-28-oic acid 28-O-α-l-rhamnopyranosyl-(1 → 3)-β-d-xylopyranosyl-(1 → 4)-[β-d-xylopyranosyl-(1 → 3)]-α-l-rhamnopyranosyl-(1 → 2)-α-l-arabinopyranoside} (2) were also isolated from M. helleri roots together with the two known compounds 3 and 4. Seven known structurally related saponins (5-11) were isolated from S. bulbosus roots. The structures of these compounds were established as bayogenin and polygalacic glycosides using one- and two-dimensional NMR spectroscopy and mass spectrometry. Compounds 7, 10, bayogenin (12) and polygalacic acid (13) showed significant (p < 0.05) postingestive effects on Spodoptera littoralis larvae, compounds 5-11 and 12 showed variable nematicidal effects on Meloydogyne javanica and all tested saponins had variable phytotoxic effects on several plant species (Lycopersicum esculentum, Lolium perenne and Lactuca sativa). These are promising results in the search for natural pesticides from the Cucurbitaceae family.     

The effect of halogen atom on the molecular quadratic nonlinearity of half sandwich complexes in the presence of an acceptor

Half sandwich complexes of the type [CpM(CO)_nX] {X = Cl, Br, I; If, M = Fe, Ru; n = 2 and if M = Mo; n = 3} and [CpNiPPh₃X] {X = Cl, Br, I} have been synthesized and their second order molecular nonlinearity (β) measured at 1064 nm in CHCl₃ by the hyper-Rayleigh scattering technique. Iron complexes consistently display larger β values than ruthenium complexes while nickel complexes have marginally larger β values than iron complexes. In the presence of an acceptor ligand such as CO or PPh₃, the role of the halogen atom is that of a π donor. The better overlap of Cl orbitals with Fe and Ni metal centres make Cl a better π donor than Br or I in the respective complexes. Consequently, M-π interaction is stronger in Fe/Ni-Cl complexes. The value of β decreases as one goes down the halogen group. For the complexes of 4d metal ions where the metal-ligand distance is larger, the influence of π orbital overlap appears to be less important, resulting in moderate changes in β as a function of halogen substitution.     

Cycloartane glycosides from Astragalus campylosema Boiss. ssp. campylosema

Four cycloartane glycosides, 3-O-[α-l-arabinopyranosyl-(1 → 2)-β-d-xylopyranosyl]-3β,6α,16β,23α,25-pentahydroxy-20(R),24(S)-epoxycycloartane (1), 3-O-[α-l-arabinopyranosyl-(1 → 2)-β-d-xylopyranosyl]-16-O-hydroxyacetoxy-23-O-acetoxy-3β,6α,25-trihydroxy-20(R),24(S)-epoxycycloartane (2), 3-O-[α-l-arabinopyranosyl-(1 → 2)-β-d-xylopyranosyl]-3β,6α,23α,25-tetrahydroxy-20(R),24(R)-16β,24;20,24-diepoxycycloartane (3), 3-O-[α-l-arabinopyranosyl-(1 → 2)-β-d-xylopyranosyl]-25-O-β-d-glucopyranosyl-3β,6α,16β,25-tetrahydroxy-20(R),24(S)-epoxycycloartane (4), along with three known cycloartane glycosides were isolated from the MeOH extract of the roots of Astragalus campylosema ssp. campylosema. Their structures were established by the extensive use of 1D- and 2D-NMR experiments along with ESIMS and HRMS analysis. The occurrence of the hydroxyl function at position 23 (1-2) and of the ketalic function at C-24 (3) are very unusual findings in the cycloartane class.     

Acylated triterpene saponins from the roots of Securidaca longepedunculata

Four triterpene saponins, 3-O-β-d-glucopyranosylpresenegenin 28-O-β-d-apiofuranosyl-(1 → 3)-β-d-xylopyranosyl-(1 → 4)-[β-d-apiofuranosyl-(1 → 3)]-α-l-rhamnopyranosyl-(1 → 2)-{4-O-[(E)-3,4,5-trimethoxycinnamoyl]}-β-d-fucopyranosyl ester, 3-O-β-d-glucopyranosylpresenegenin 28-O-β-d-apiofuranosyl-(1 → 3)-β-d-xylopyranosyl-(1 → 4)-[β-d-apiofuranosyl-(1 → 3)]-α-l-rhamnopyranosyl-(1 → 2)-[(6-O-acetyl)-β-d-glucopyranosyl-(1 → 3)]-{4-O-[(E)-3,4,5-trimethoxycinnamoyl]}-β-d-fucopyranosyl ester, 3-O-β-d-glucopyranosylpresenegenin 28-O-β-d-apiofuranosyl-(1 → 3)-β-d-xylopyranosyl-(1 → 4)-[β-d-apiofuranosyl-(1 → 3)]-α-l-rhamnopyranosyl-(1 → 2)-[β-d-galactopyranosyl-(1 → 3)]-{4-O-[(E)-3,4,5-trimethoxycinnamoyl]}-β-d-fucopyranosyl ester, and 3-O-β-d-glucopyranosylpresenegenin 28-O-β-d-apiofuranosyl-(1 → 3)-[α-l-arabinopyranosyl-(1 → 4)]-β-d-xylopyranosyl-(1 → 4)-[β-d-apiofuranosyl-(1 → 3)]-α-l-rhamnopyranosyl-(1 → 2)-{4-O-[(E)-3,4,5-trimethoxycinnamoyl]}-β-d-fucopyranosyl ester, were isolated from the roots of Securidaca longepedunculata, together with three known compounds. Their structures were established mainly by 2D NMR techniques and mass spectrometry.     

Cloning,characterization, hypoxia and heat shock response of hypoxia inducible factor-1 (HIF-1) from the small abalone Haliotis diversicolor

In this study, hypoxia inducible factor-1α (HIF-1α) and hypoxia inducible factor-1β (HIF-1β) from small abalone Haliotis diversicolor were cloned. The cDNA of H. diversicolor HIF-1α (HdHIF-1α) is 2833 bp encoding a protein of 711aa and H. diversicolor HIF-1β (HdHIF-1β) is 1919 bp encoding a protein of 590aa. Similar to other species' HIF-1, HdHIF-1 has one basic helix–loop–helix (bHLH) domain and two Per-Arnt-Sim (PAS) domains, and HdHIF-1α has a oxygen-dependent degradation domain (ODDD) with two proline hydroxylation motifs and a C-terminal transactivation domain (C-TAD) with an asparagine hydroxylation motif. Under normoxic conditions, HdHIF-1α and HdHIF-1β mRNAs were constitutively present in all examined tissues. Under hypoxia (2.0 mg/L DO at 25 °C) stress, HdHIF-1α expression was up-regulated in gills at 4 h, 24 h and 96 h, and in hemocytes at 24 h and 96 h, while HdHIF-1β remained relatively constant. Under thermal stress (31 °C), HdHIF-1α expression was significantly increased in gills at 4 h, and hemocytes at 0 h and 4 h, while HdHIF-1β expression still remained relatively constant. These results suggested that HIF-1α may play an important role in adaption to poor environment in H. diversicolor.     

Theoretical calculations of the catalytic triad in short-chain alcohol dehydrogenases/reductases

Three highly conserved active site residues (Ser, Tyr, and Lys) of the family of short-chain alcohol dehydrogenases/reductases (SDRs) were demonstrated to be essential for catalytic activity and have been denoted the catalytic triad of SDRs. In this study computational methods were adopted to study the ionization properties of these amino acids in SDRs from Drosophila melanogaster and Drosophila lebanonensis. Three enzyme models, with different ionization scenarios of the catalytic triad that might be possible when inhibitors bind to the enzyme cofactor complex, were constructed. The binding of the two alcohol competitive inhibitors were studied using automatic docking by the Internal Coordinate Mechanics program, molecular dynamic (MD) simulations with the AMBER program package, calculation of the free energy of ligand binding by the linear interaction energy method, and the hydropathic interactions force field. The calculations indicated that deprotonated Tyr acts as a strong base in the binary enzyme-NAD⁺ complex. Molecular dynamic simulations for 5 ns confirmed that deprotonated Tyr is essential for anchoring and orientating the inhibitors at the active site, which might be a general trend for the family of SDRs. The findings here have implications for the development of therapeutically important SDR inhibitors.     

Positively Cooperative Binding of Zinc Ions to Bacillus cereus 569/H/9 β-Lactamase II Suggests that the Binuclear Enzyme Is the Only Relevant Form for Catalysis

Metallo-β-lactamases catalyze the hydrolysis of most β-lactam antibiotics and hence represent a major clinical concern. While enzymes belonging to subclass B1 have been shown to display maximum activity as dizinc species, the actual metal-to-protein stoichiometry and the affinity for zinc are not clear. We have further investigated the process of metal binding to the β-lactamase II from Bacillus cereus 569/H/9 (known as BcII). Zinc binding was monitored using complementary biophysical techniques, including circular dichroism in the far-UV, enzymatic activity measurements, competition with a chromophoric chelator, mass spectrometry, and nuclear magnetic resonance. Most noticeably, mass spectrometry and nuclear magnetic resonance experiments, together with catalytic activity measurements, demonstrate that two zinc ions bind cooperatively to the enzyme active site (with K₁/K₂ ≥ 5) and, hence, that catalysis is associated with the dizinc enzyme species only. Furthermore, competitive experiments with the chromophoric chelator Mag-Fura-2 indicates K₂ < 80 nM. This contrasts with cadmium binding, which is clearly a noncooperative process with the mono form being the only species significantly populated in the presence of 1 molar equivalent of Cd(II). Interestingly, optical measurements reveal that although the apo and dizinc species exhibit undistinguishable tertiary structural organizations, the metal-depleted enzyme shows a significant decrease in its α-helical content, presumably associated with enhanced flexibility.     

Inhibition of martentoxin on neuronal BK channel subtype (alpha+beta4): implications for a novel interaction model

Martentoxin as a 37-residue peptide was capable of blocking large-conductance Ca²⁺-activated K⁺ (BK) channels in adrenal medulla chromaffin cells. This study investigated the pharmacological discrimination of martentoxin on BK channel subtypes. The results showed that the iberiotoxin-insensitive neuronal BK channels (α+β4) could be potently blocked by martentoxin (IC₅₀ = ∼80 nM). In contrast, the iberiotoxin-sensitive BK channel consisting of only α-subunit was less sensitive to martentoxin. Distinctively, martentoxin inhibited neuronal BK channels (α+β4) with a novel interaction mode. Two possible interaction sites of neuronal BK channels (α+β4) might be responsible for the binding with martentoxin: one for trapping and the other located at the pore region for blocking. In addition, the inhibition of martentoxin on neuronal BK channels (α+β4) depended on cytoplasmic Ca²⁺ concentration. On the other hand, in vivo experiments from EEG recordings suggested that neuronal BK channels (α+β4) were the primary target of martentoxin. Therefore, this research not only sheds light on a unique ligand for neuronal BK channels (α+β4), but also highlights a novel model approach for the interaction between K⁺ channels and specific-ligands.     

Exploring the catalytic potential of the 3-His mononuclear nonheme Fe(II) center: discovery and characterization of an unprecedented maltol cleavage activity

Mononuclear nonheme iron enzymes (MNHEs) catalyze a range of very diverse reactions in O₂ metabolism, but they share a common principle active-site organization. To investigate a putative catalytic promiscuity of these enzymatic metal centers, we studied the reactivity of the 3-His ligated metal center of diketone cleaving enzyme (Dke1) toward non-native substrates, with a focus on alternative O₂ dependent reactions. From a screening approach, which aims at eliminating steric factors by including minimal substrate-substructures, three alternative, ‘non-β-dicarbonyl-cleavage’ reactions are identified, among them an unprecedented oxygenation of maltol. Maltol cleavage is characterized by steady state and fast kinetic measurements and shows an O₂ concentration dependent rate determining step k_cat/K_M(O₂) of 0.3 mM^− 1 s^− 1 and a strict coupling of O₂ reduction and substrate oxidation. Furthermore, the catalytic potential of the 3-His metal center for O₂ dependent catechol ring-cleavage and phenylpyruvate oxidation (PP) is demonstrated.