Mechanism of triclosan toxicity: Mitochondrial dysfunction including complex II inhibition, superoxide release and uncoupling of oxidative phosphorylation.

PubMed

Teplova, Vera V; Belosludtsev, Konstantin N; Kruglov, Alexey G

2017-06-05

Triclosan (5-chloro-2'-(2,4-dichlorophenoxy)phenol), a widely used antibacterial agent, exerts adverse effects on the organism of mammals. Recent research reviled that triclosan at low micromolar concentrations causes mitochondrial dysfunction in many cell types, but the mechanisms of its effect are not fully understood. Here we show that exposure to triclosan disrupted membrane potential, prevented the calcium uptake-driven high-amplitude mitochondrial swelling, stimulated the respiration in the presence of complex I substrates, and suppressed the ADP-stimulated respiration in the presence of complex II substrate, succinate. Triclosan directly inhibited complex II activity. Similar to the complex II inhibitor thenoyltrifluoroacetone, triclosan induced the oxidation of the cytochromes b566 and b562 and caused the release of mitochondrial superoxide. Opposite to thenoyltrifluoroacetone, triclosan increased superoxide release synergistically with myxothiazol but not with antimycin A, indicating different topology of superoxide-producing sites. We concluded that triclosan is unique by its capability of acting as both a protonophore and an unusual complex II inhibitor, which interferes with the mitochondrial respiration by blocking the electron transfer between ubiquinone at the Q d -binding site and heme b. Our data can provide an insight into the mechanisms of the carcinogenic effect of triclosan in the liver and other tissues. Copyright © 2017 Elsevier B.V. All rights reserved.

A cluster of carboxylic groups in PsbO protein is involved in proton transfer from the water oxidizing complex of Photosystem II.

PubMed

Shutova, Tatiana; Klimov, Vyacheslav V; Andersson, Bertil; Samuelsson, Göran

2007-06-01

The hypothesis presented here for proton transfer away from the water oxidation complex of Photosystem II (PSII) is supported by biochemical experiments on the isolated PsbO protein in solution, theoretical analyses of better understood proton transfer systems like bacteriorhodopsin and cytochrome oxidase, and the recently published 3D structure of PS II (Pdb entry 1S5L). We propose that a cluster of conserved glutamic and aspartic acid residues in the PsbO protein acts as a buffering network providing efficient acceptors of protons derived from substrate water molecules. The charge delocalization of the cluster ensures readiness to promptly accept the protons liberated from substrate water. Therefore protons generated at the catalytic centre of PSII need not be released into the thylakoid lumen as generally thought. The cluster is the beginning of a localized, fast proton transfer conduit on the lumenal side of the thylakoid membrane. Proton-dependent conformational changes of PsbO may play a role in the regulation of both supply of substrate water to the water oxidizing complex and the resultant proton transfer.

Mitochondrial Targeted Coenzyme Q, Superoxide, and Fuel Selectivity in Endothelial Cells

PubMed Central

Fink, Brian D.; O'Malley, Yunxia; Dake, Brian L.; Ross, Nicolette C.; Prisinzano, Thomas E.; Sivitz, William I.

2009-01-01

Background Previously, we reported that the “antioxidant” compound “mitoQ” (mitochondrial-targeted ubiquinol/ubiquinone) actually increased superoxide production by bovine aortic endothelial (BAE) cell mitochondria incubated with complex I but not complex II substrates. Methods and Results To further define the site of action of the targeted coenzyme Q compound, we extended these studies to include different substrate and inhibitor conditions. In addition, we assessed the effects of mitoquinone on mitochondrial respiration, measured respiration and mitochondrial membrane potential in intact cells, and tested the intriguing hypothesis that mitoquinone might impart fuel selectivity in intact BAE cells. In mitochondria respiring on differing concentrations of complex I substrates, mitoquinone and rotenone had interactive effects on ROS consistent with redox cycling at multiple sites within complex I. Mitoquinone increased respiration in isolated mitochondria respiring on complex I but not complex II substrates. Mitoquinone also increased oxygen consumption by intact BAE cells. Moreover, when added to intact cells at 50 to 1000 nM, mitoquinone increased glucose oxidation and reduced fat oxidation, at doses that did not alter membrane potential or induce cell toxicity. Although high dose mitoquinone reduced mitochondrial membrane potential, the positively charged mitochondrial-targeted cation, decyltriphenylphosphonium (mitoquinone without the coenzyme Q moiety), decreased membrane potential more than mitoquinone, but did not alter fuel selectivity. Therefore, non-specific effects of the positive charge were not responsible and the quinone moiety is required for altered nutrient selectivity. Conclusions In summary, the interactive effects of mitoquinone and rotenone are consistent with redox cycling at more than one site within complex I. In addition, mitoquinone has substrate dependent effects on mitochondrial respiration, increases repiration by intact cells, and alters fuel selectivity favoring glucose over fatty acid oxidation at the intact cell level. PMID:19158951

Mitochondrial targeted coenzyme Q, superoxide, and fuel selectivity in endothelial cells.

PubMed

Fink, Brian D; O'Malley, Yunxia; Dake, Brian L; Ross, Nicolette C; Prisinzano, Thomas E; Sivitz, William I

2009-01-01

Previously, we reported that the "antioxidant" compound "mitoQ" (mitochondrial-targeted ubiquinol/ubiquinone) actually increased superoxide production by bovine aortic endothelial (BAE) cell mitochondria incubated with complex I but not complex II substrates. To further define the site of action of the targeted coenzyme Q compound, we extended these studies to include different substrate and inhibitor conditions. In addition, we assessed the effects of mitoquinone on mitochondrial respiration, measured respiration and mitochondrial membrane potential in intact cells, and tested the intriguing hypothesis that mitoquinone might impart fuel selectivity in intact BAE cells. In mitochondria respiring on differing concentrations of complex I substrates, mitoquinone and rotenone had interactive effects on ROS consistent with redox cycling at multiple sites within complex I. Mitoquinone increased respiration in isolated mitochondria respiring on complex I but not complex II substrates. Mitoquinone also increased oxygen consumption by intact BAE cells. Moreover, when added to intact cells at 50 to 1000 nM, mitoquinone increased glucose oxidation and reduced fat oxidation, at doses that did not alter membrane potential or induce cell toxicity. Although high dose mitoquinone reduced mitochondrial membrane potential, the positively charged mitochondrial-targeted cation, decyltriphenylphosphonium (mitoquinone without the coenzyme Q moiety), decreased membrane potential more than mitoquinone, but did not alter fuel selectivity. Therefore, non-specific effects of the positive charge were not responsible and the quinone moiety is required for altered nutrient selectivity. In summary, the interactive effects of mitoquinone and rotenone are consistent with redox cycling at more than one site within complex I. In addition, mitoquinone has substrate dependent effects on mitochondrial respiration, increases repiration by intact cells, and alters fuel selectivity favoring glucose over fatty acid oxidation at the intact cell level.

Production of a metal-binding exopolysaccharide by Paenibacillus jamilae using two-phase olive-mill waste as fermentation substrate.

PubMed

Morillo, Jose Antonio; Aguilera, Margarita; Ramos-Cormenzana, Alberto; Monteoliva-Sánchez, Mercedes

2006-09-01

The present study investigated the use of two-phase olive mill waste (TPOMW) as substrate for the production of exopolysaccharide (EPS) by the endospore-forming bacilli Paenibacillus jamilae. This microorganism was able to grow and produce EPS in aqueous extracts of TPOMW as a unique source of carbon. The effects of substrate concentration and the addition of inorganic nutrients were investigated. Maximal polymer yield in 100-ml batch-culture experiments (2 g l(-1)) was obtained in cultures prepared with an aqueous extract of 20% TPOMW (w/v). An inhibitory effect was observed on growth and EPS production when TPOMW concentration was increased. Nutrient supplementation (nitrate, phosphate, and other inorganic nutrients) did not increase yield. Finally, an adsorption experiment of Pb (II), Cd (II), Cu (II), Zn (II), Co (II), and Ni (II) by EPS is reported. Lead was preferentially complexed by the polymer, with a maximal uptake of 230 mg/g EPS.

Substrate stiffness regulates cadherin-dependent collective migration through myosin-II contractility

PubMed Central

Ng, Mei Rosa; Besser, Achim

2012-01-01

The mechanical microenvironment is known to influence single-cell migration; however, the extent to which mechanical cues affect collective migration of adherent cells is not well understood. We measured the effects of varying substrate compliance on individual cell migratory properties in an epithelial wound-healing assay. Increasing substrate stiffness increased collective cell migration speed, persistence, and directionality as well as the coordination of cell movements. Dynamic analysis revealed that wounding initiated a wave of motion coordination from the wound edge into the sheet. This was accompanied by a front-to-back gradient of myosin-II activation and establishment of cell polarity. The propagation was faster and farther reaching on stiff substrates, indicating that substrate stiffness affects the transmission of directional cues. Manipulation of myosin-II activity and cadherin–catenin complexes revealed that this transmission is mediated by coupling of contractile forces between neighboring cells. Thus, our findings suggest that the mechanical environment integrates in a feedback with cell contractility and cell–cell adhesion to regulate collective migration. PMID:23091067

Visualizing the Reaction Cycle in an Iron(II)- and 2-(Oxo)-glutarate-Dependent Hydroxylase.

PubMed

Mitchell, Andrew J; Dunham, Noah P; Martinie, Ryan J; Bergman, Jonathan A; Pollock, Christopher J; Hu, Kai; Allen, Benjamin D; Chang, Wei-Chen; Silakov, Alexey; Bollinger, J Martin; Krebs, Carsten; Boal, Amie K

2017-10-04

Iron(II)- and 2-(oxo)-glutarate-dependent oxygenases catalyze diverse oxidative transformations that are often initiated by abstraction of hydrogen from carbon by iron(IV)-oxo (ferryl) complexes. Control of the relative orientation of the substrate C-H and ferryl Fe-O bonds, primarily by direction of the oxo group into one of two cis-related coordination sites (termed inline and offline), may be generally important for control of the reaction outcome. Neither the ferryl complexes nor their fleeting precursors have been crystallographically characterized, hindering direct experimental validation of the offline hypothesis and elucidation of the means by which the protein might dictate an alternative oxo position. Comparison of high-resolution X-ray crystal structures of the substrate complex, an Fe(II)-peroxysuccinate ferryl precursor, and a vanadium(IV)-oxo mimic of the ferryl intermediate in the l-arginine 3-hydroxylase, VioC, reveals coordinated motions of active site residues that appear to control the intermediate geometries to determine reaction outcome.

Surface Structures Formed by a Copper(II) Complex of Alkyl-Derivatized Indigo

PubMed Central

Honda, Akinori; Noda, Keisuke; Tamaki, Yoshinori; Miyamura, Kazuo

2016-01-01

Assembled structures of dyes have great influence on their coloring function. For example, metal ions added in the dyeing process are known to prevent fading of color. Thus, we have investigated the influence of an addition of copper(II) ion on the surface structure of alkyl-derivatized indigo. Scanning tunneling microscope (STM) analysis revealed that the copper(II) complexes of indigo formed orderly lamellar structures on a HOPG substrate. These lamellar structures of the complexes are found to be more stable than those of alkyl-derivatized indigos alone. Furthermore, 2D chirality was observed. PMID:28773957

Structural and Biochemical Characterization of the Type II Fructose-1,6-bisphosphatase GlpX from Escherichia coli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, G.; Singer, A.; Lunin, V. V.

2009-02-06

Gluconeogenesis is an important metabolic pathway, which produces glucose from noncarbohydrate precursors such as organic acids, fatty acids, amino acids, or glycerol. Fructose-1,6-bisphosphatase, a key enzyme of gluconeogenesis, is found in all organisms, and five different classes of these enzymes have been identified. Here we demonstrate that Escherichia coli has two class II fructose-1,6-bisphosphatases, GlpX and YggF, which show different catalytic properties. We present the first crystal structure of a class II fructose-1,6-bisphosphatase (GlpX) determined in a free state and in the complex with a substrate (fructose 1,6-bisphosphate) or inhibitor (phosphate). The crystal structure of the ligand-free GlpX revealed amore » compact, globular shape with two {alpha}/{beta}-sandwich domains. The core fold of GlpX is structurally similar to that of Li{sup +}-sensitive phosphatases implying that they have a common evolutionary origin and catalytic mechanism. The structure of the GlpX complex with fructose 1,6-bisphosphate revealed that the active site is located between two domains and accommodates several conserved residues coordinating two metal ions and the substrate. The third metal ion is bound to phosphate 6 of the substrate. Inorganic phosphate strongly inhibited activity of both GlpX and YggF, and the crystal structure of the GlpX complex with phosphate demonstrated that the inhibitor molecule binds to the active site. Alanine replacement mutagenesis of GlpX identified 12 conserved residues important for activity and suggested that Thr{sup 90} is the primary catalytic residue. Our data provide insight into the molecular mechanisms of the substrate specificity and catalysis of GlpX and other class II fructose-1,6-bisphosphatases.« less

Copper(II) and zinc(II) dinuclear enzymes model compounds: The nature of the metal ion in the biological function

NASA Astrophysics Data System (ADS)

Ferraresso, L. G.; de Arruda, E. G. R.; de Moraes, T. P. L.; Fazzi, R. B.; Da Costa Ferreira, A. M.; Abbehausen, C.

2017-12-01

First series transition metals are used abundantly by nature to perform catalytic transformations of several substrates. Furthermore, the cooperative activity of two proximal metal ions is common and represents a highly efficient catalytic system in living organisms. In this work three dinuclear μ-phenolate bridged metal complexes were prepared with copper(II) and zinc(II), resulting in a ZnZn, CuCu and CuZn with the ligand 2-ethylaminodimethylamino phenol (saldman) as model compounds of superoxide dismutase (CuCu and CuZn) and metallo-β-lactamases (ZnZn). Metals are coordinated in a μ-phenolate bridged symmetric system. Cu(II) presents a more distorted structure, while zinc is very symmetric. For this reason, [CuCu(saldman)] shows higher water solubility and also higher lability of the bridge. The antioxidant and hydrolytic beta-lactamase-like activity of the complexes were evaluated. The lability of the bridge seems to be important for the antioxidant activity and is suggested to because of [CuCu(saldman)] presents a lower antioxidant capacity than [CuZn(saldman)], which showed to present a more stable bridge in solution. The hydrolytic activity of the bimetallic complexes was assayed using nitrocefin as substrate and showed [ZnZn(saldman)] as a better catalyst than the Cu(II) analog. The series demonstrates the importance of the nature of the metal center for the biological function and how the reactivity of the model complex can be modulated by coordination chemistry.

Recent advances in heterobimetallic palladium(II)/copper(II) catalyzed domino difunctionalization of carbon-carbon multiple bonds.

PubMed

Beccalli, Egle M; Broggini, Gianluigi; Gazzola, Silvia; Mazza, Alberto

2014-09-21

The double functionalization of carbon-carbon multiple bonds in one-pot processes has emerged in recent years as a fruitful tool for the rapid synthesis of complex molecular scaffolds. This review covers the advances in domino reactions promoted by the couple palladium(ii)/copper(ii), which was proven to be an excellent catalytic system for the functionalization of substrates.

Structural dynamics of the MecA-ClpC complex: a type II AAA+ protein unfolding machine.

PubMed

Liu, Jing; Mei, Ziqing; Li, Ningning; Qi, Yutao; Xu, Yanji; Shi, Yigong; Wang, Feng; Lei, Jianlin; Gao, Ning

2013-06-14

The MecA-ClpC complex is a bacterial type II AAA(+) molecular machine responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for degradation. The six subunits of the MecA-ClpC complex form a closed barrel-like structure, featured with three stacked rings and a hollow passage, where substrates are threaded and translocated through successive pores. Although the general concepts of how polypeptides are unfolded and translocated by internal pore loops of AAA(+) proteins have long been conceived, the detailed mechanistic model remains elusive. With cryoelectron microscopy, we captured four different structures of the MecA-ClpC complexes. These complexes differ in the nucleotide binding states of the two AAA(+) rings and therefore might presumably reflect distinctive, representative snapshots from a dynamic unfolding cycle of this hexameric complex. Structural analysis reveals that nucleotide binding and hydrolysis modulate the hexameric complex in a number of ways, including the opening of the N-terminal ring, the axial and radial positions of pore loops, the compactness of the C-terminal ring, as well as the relative rotation between the two nucleotide-binding domain rings. More importantly, our structural and biochemical data indicate there is an active allosteric communication between the two AAA(+) rings and suggest that concerted actions of the two AAA(+) rings are required for the efficiency of the substrate unfolding and translocation. These findings provide important mechanistic insights into the dynamic cycle of the MecA-ClpC unfoldase and especially lay a foundation toward the complete understanding of the structural dynamics of the general type II AAA(+) hexamers.

Structural analysis of group II chitinase (ChtII) catalysis completes the puzzle of chitin hydrolysis in insects.

PubMed

Chen, Wei; Qu, Mingbo; Zhou, Yong; Yang, Qing

2018-02-23

Chitin is a linear homopolymer of N -acetyl-β-d-glucosamines and a major structural component of insect cuticles. Chitin hydrolysis involves glycoside hydrolase family 18 (GH18) chitinases. In insects, chitin hydrolysis is essential for periodic shedding of the old cuticle ecdysis and proceeds via a pathway different from that in the well studied bacterial chitinolytic system. Group II chitinase (ChtII) is a widespread chitinolytic enzyme in insects and contains the greatest number of catalytic domains and chitin-binding domains among chitinases. In Lepidopterans, ChtII and two other chitinases, ChtI and Chi-h, are essential for chitin hydrolysis. Although ChtI and Chi-h have been well studied, the role of ChtII remains elusive. Here, we investigated the structure and enzymology of Of ChtII, a ChtII derived from the insect pest Ostrinia furnacalis We present the crystal structures of two catalytically active domains of Of ChtII, Of ChtII-C1 and Of ChtII-C2, both in unliganded form and complexed with chitooligosaccharide substrates. We found that Of ChtII-C1 and Of ChtII-C2 both possess long, deep substrate-binding clefts with endochitinase activities. Of ChtII exhibited structural characteristics within the substrate-binding cleft similar to those in Of Chi-h and Of ChtI. However, Of ChtII lacked structural elements favoring substrate binding beyond the active sites, including an extra wall structure present in Of Chi-h. Nevertheless, the numerous domains in Of ChtII may compensate for this difference; a truncation containing one catalytic domain and three chitin-binding modules ( Of ChtII-B4C1) displayed activity toward insoluble polymeric substrates that was higher than those of Of Chi-h and Of ChtI. Our observations provide the last piece of the puzzle of chitin hydrolysis in insects. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Methylene blue improves mitochondrial respiration and decreases oxidative stress in a substrate-dependent manner in diabetic rat hearts.

PubMed

Duicu, Oana M; Privistirescu, Andreea; Wolf, Adrian; Petruş, Alexandra; Dănilă, Maria D; Raţiu, Corina D; Muntean, Danina M; Sturza, Adrian

2017-11-01

Diabetic cardiomyopathy has been systematically associated with compromised mitochondrial energetics and increased generation of reactive oxygen species (ROS) that underlie its progression to heart failure. Methylene blue is a redox drug with reported protective effects mainly on brain mitochondria. The purpose of the present study was to characterize the effects of acute administration of methylene blue on mitochondrial respiration, H 2 O 2 production, and calcium sensitivity in rat heart mitochondria isolated from healthy and 2 months (streptozotocin-induced) diabetic rats. Mitochondrial respiratory function was assessed by high-resolution respirometry. H 2 O 2 production and calcium retention capacity were measured spectrofluorimetrically. The addition of methylene blue (0.1 μmol·L -1 ) elicited an increase in oxygen consumption of mitochondria energized with complex I and II substrates in both normal and diseased mitochondria. Interestingly, methylene blue elicited a significant increase in H 2 O 2 release in the presence of complex I substrates (glutamate and malate), but had an opposite effect in mitochondria energized with complex II substrate (succinate). No changes in the calcium retention capacity of healthy or diabetic mitochondria were found in the presence of methylene blue. In conclusion, in cardiac mitochondria isolated from diabetic and nondiabetic rat hearts, methylene blue improved respiratory function and elicited a dichotomic, substrate-dependent effect on ROS production.

Copper-Hydroperoxo Mediated N-Debenzylation Chemistry Mimicking Aspects of Copper Monoxygenases

PubMed Central

Maiti, Debabrata; Narducci Sarjeant, Amy A.; Karlin, Kenneth D.

2008-01-01

Substantial oxidative N-debenzylation reaction along with PhCH=O formation occurs from a hydroperoxo copper(II) complex which has a dibenzylamino substrate (-N(CH2Ph)2 appended as a substituent on one pyridyl group of its tripodal tetradentate TMPA {≡ TPA ≡ tris(2-pyridylmethyl)amine)} ligand framework. During the course of the (LN(CH2Ph)2)CuII(−OOH) reactivity, formation of a substrate and −OOH (an oxygen atom) derived alkoxo CuII(−OR) complex occurs. The observation that the same CuII(−OR) species occurs from CuI/PhIO chemistry suggests the possibility that a copper-oxo (cupryl) reactive intermediate forms during alkoxo species formation, and new ESI-MS data obtained provides some further support for this high-valent intermediate. Net H-atom abstraction chemistry is proposed, based on kinetic isotope effect studies provided here and that previously published for a closely related CuII(−OOH) species incorporating dimethylamine (-N(CH3)2) as the internal substrate (J. Am. Chem. Soc. 2007, 129, 6720-6721); the CuI/PhIO reactivity, with similar isotope effect results, provides further support. The reactivity of these chemical systems closely resembles proposed oxidative N-dealkylation mechanisms effected by the copper-monooxygenases dopamine β-monooxygenase (DβM) or peptidylglycine-α-hydroxylating monooxygenase (PHM). PMID:18783212

Polymer Light-Emitting Diode (PLED) Process Development

DTIC Science & Technology

2003-12-01

conclusions and recommendations for Phase II of the Flexible Display Program. 15. SUBJECT TERMS LIGHT EMITTING DIODES LIQUID CRYSTAL DISPLAY SYSTEMS...space for Phase I and II confined by backplane complexity and substrate form...12 Figure 6. Semi automated I-V curve measurement setup consisting of Keithley power supply, computer and

Phosphoester hydrolysis: the incoming substrate turns the bridging hydroxido nucleophile into a terminal one.

PubMed

Gouré, Eric; Carboni, Michaël; Troussier, Angélique; Lebrun, Colette; Pécaut, Jacques; Jacquot, Jean-François; Dubourdeaux, Patrick; Clémancey, Martin; Blondin, Geneviève; Latour, Jean-Marc

2015-05-26

Identifying the active nucleophile in hydrolysis reactions catalyzed by binuclear hydrolases is a recurrent problem and a matter of intense debate. We report on the phosphate ester hydrolysis by a Fe(III)Fe(II) complex of a binucleating ligand. This complex presents activities in the range of those observed for similar biomimetic compounds in the literature. The specific electronic properties of the Fe(III)Fe(II) complex allowed us to use (1)H NMR and Mössbauer spectroscopies to investigate the nature of the various species present in the solution in the pH range of 5-10. Both techniques showed that the hydrolysis activity is associated to a μ-hydroxido Fe(III)Fe(II) species. Further (1)H NMR experiments show that binding of anions or the substrate changes this bonding mode suggesting that a terminal hydroxide is the likely nucleophile in these hydrolysis reactions. This view is further supported by the structure determination of the hydrolysis product. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectroscopic, and thermal studies of some new binuclear transition metal(II) complexes with hydrazone ligands containing acetoacetanilide and isoxazole.

PubMed

Chen, Zhimin; Wu, Yiqun; Gu, Donghong; Gan, Fuxi

2007-11-01

A new chelating ligand, 2-(2-(5-tert-butylisoxazol-3-yl)hydrazono)-N-(2,4-dimethylphenyl)-3-oxobutanamide (HL), and its four binuclear transition metal complexes, M(2)(L)(2) (micro-OCH(3))(2) [M=Ni(II), Co(II), Cu(II), Zn(II)], were synthesized using the procedure of diazotization, coupling and metallization. Their structures were postulated based on elemental analysis, (1)H NMR, MALDI-MS, FT-IR spectra and UV-vis electronic absorption spectra. Smooth films of these complexes on K9 glass substrates were prepared using the spin-coating method and their absorption properties were evaluated. The thermal properties of the metal(II) complexes were investigated by thermogravimetry (TG) and differential scanning calorimetry (DSC). Different thermodynamic and kinetic parameters namely activation energy (E*), enthalpy of activation (DeltaH*), entropy of activation (DeltaS*) and free energy change of activation (DeltaG*) are calculated using Coats-Redfern (CR) equation.

"Off-On"switching electrochemiluminescence biosensor for mercury(II) detection based on molecular recognition technology.

PubMed

Cheng, Lin; Wei, BingGuo; He, Ling Ling; Mao, Ling; Zhang, Jie; Ceng, JinXiang; Kong, DeRong; Chen, ChaDan; Cui, HanFeng; Hong, Nian; Fan, Hao

2017-02-01

A novel "off-On" electrogenerated chemiluminescence (ECL) biosensor has been developed for the detection of mercury(II) based on molecular recognition technology. The ECL mercury(II) biosensor comprises two main parts: an ECL substrate and an ECL intensity switch. The ECL substrate was made by modifying the complex of Ruthenium(II) tris-(bipyridine)(Ru(bpy) 3 2+ )/Cyclodextrins-Au nanoparticles(CD-AuNps)/Nafion on the surface of glass carbon electrode (GCE), and the ECL intensity switch is the single hairpin DNA probe designed according to the "molecular recognition" strategy which was functionalized with ferrocene tag at one end and attached to Cyclodextrins (CD) on modified GCE through supramolecular noncovalent interaction. We demonstrated that, in the absence of Hg(II) ion, the probe keeps single hairpin structure and resulted in a quenching of ECL of Ru(bpy) 3 2+ . Whereas, in the presence of Hg(II) ion, the probe prefers to form the T-Hg(II)-T complex and lead to an obvious recovery of ECL of Ru(bpy) 3 2+ , which provided a sensing platform for the detection of Hg(II) ion. Using this sensing platform, a simple, rapid and selective "off-On" ECL biosensor for the detection of mercury(II) with a detection limit of 0.1 nM has been developed. Copyright © 2016. Published by Elsevier Inc.

The role of chloride in the mechanism of O(2) activation at the mononuclear nonheme Fe(II) center of the halogenase HctB.

PubMed

Pratter, Sarah M; Light, Kenneth M; Solomon, Edward I; Straganz, Grit D

2014-07-02

Mononuclear nonheme Fe(II) (MNH) and α-ketoglutarate (α-KG) dependent halogenases activate O2 to perform oxidative halogenations of activated and nonactivated carbon centers. While the mechanism of halide incorporation into a substrate has been investigated, the mechanism by which halogenases prevent oxidations in the absence of chloride is still obscure. Here, we characterize the impact of chloride on the metal center coordination and reactivity of the fatty acyl-halogenase HctB. Stopped-flow kinetic studies show that the oxidative transformation of the Fe(II)-α-KG-enzyme complex is >200-fold accelerated by saturating concentrations of chloride in both the absence and presence of a covalently bound substrate. By contrast, the presence of substrate, which generally brings about O2 activation at enzymatic MNH centers, only has an ∼10-fold effect in the absence of chloride. Circular dichroism (CD) and magnetic CD (MCD) studies demonstrate that chloride binding triggers changes in the metal center ligation: chloride binding induces the proper binding of the substrate as shown by variable-temperature, variable-field (VTVH) MCD studies of non-α-KG-containing forms and the conversion from six-coordinate (6C) to 5C/6C mixtures when α-KG is bound. In the presence of substrate, a site with square pyramidal five-coordinate (5C) geometry is observed, which is required for O2 activation at enzymatic MNH centers. In the absence of substrate an unusual trigonal bipyramidal site is formed, which accounts for the observed slow, uncoupled reactivity. Molecular dynamics simulations suggest that the binding of chloride to the metal center of HctB leads to a conformational change in the enzyme that makes the active site more accessible to the substrate and thus facilitates the formation of the catalytically competent enzyme-substrate complex. Results are discussed in relation to other MNH dependent halogenases.

Mitochondrial generation of superoxide and hydrogen peroxide as the source of mitochondrial redox signaling.

PubMed

Brand, Martin D

2016-11-01

This review examines the generation of reactive oxygen species by mammalian mitochondria, and the status of different sites of production in redox signaling and pathology. Eleven distinct mitochondrial sites associated with substrate oxidation and oxidative phosphorylation leak electrons to oxygen to produce superoxide or hydrogen peroxide: oxoacid dehydrogenase complexes that feed electrons to NAD + ; respiratory complexes I and III, and dehydrogenases, including complex II, that use ubiquinone as acceptor. The topologies, capacities, and substrate dependences of each site have recently clarified. Complex III and mitochondrial glycerol 3-phosphate dehydrogenase generate superoxide to the external side of the mitochondrial inner membrane as well as the matrix, the other sites generate superoxide and/or hydrogen peroxide exclusively in the matrix. These different site-specific topologies are important for redox signaling. The net rate of superoxide or hydrogen peroxide generation depends on the substrates present and the antioxidant systems active in the matrix and cytosol. The rate at each site can now be measured in complex substrate mixtures. In skeletal muscle mitochondria in media mimicking muscle cytosol at rest, four sites dominate, two in complex I and one each in complexes II and III. Specific suppressors of two sites have been identified, the outer ubiquinone-binding site in complex III (site III Qo ) and the site in complex I active during reverse electron transport (site I Q ). These suppressors prevent superoxide/hydrogen peroxide production from a specific site without affecting oxidative phosphorylation, making them excellent tools to investigate the status of the sites in redox signaling, and to suppress the sites to prevent pathologies. They allow the cellular roles of mitochondrial superoxide/hydrogen peroxide production to be investigated without catastrophic confounding bioenergetic effects. They show that sites III Qo and I Q are active in cells and have important roles in redox signaling (e.g. hypoxic signaling and ER-stress) and in causing oxidative damage in a variety of biological contexts. Copyright © 2016 Elsevier Inc. All rights reserved.

Biomimetic Modeling of Copper Complexes: A Study of Enantioselective Catalytic Oxidation on D-(+)-Catechin and L-( − )-Epicatechin with Copper Complexes

PubMed Central

Mutti, Francesco G.; Pievo, Roberta; Sgobba, Maila; Gullotti, Michele; Santagostini, Laura

2008-01-01

The biomimetic catalytic oxidations of the dinuclear and trinuclear copper(II) complexes versus two catechols, namely, D-(+)-catechin and L-( − )-epicatechin to give the corresponding quinones are reported. The unstable quinones were trapped by the nucleophilic reagent, 3-methyl-2-benzothiazolinone hydrazone (MBTH), and have been calculated the molar absorptivities of the different quinones. The catalytic efficiency is moderate, as inferred by kinetic constants, but the complexes exhibit significant enantio-differentiating ability towards the catechols, albeit for the dinuclear complexes, this enantio-differentiating ability is lower. In all cases, the preferred enantiomeric substrate is D-(+)-catechin to respect the other catechol, because of the spatial disposition of this substrate. PMID:18825268

Structure and function of archaeal prefoldin, a co-chaperone of group II chaperonin.

PubMed

Ohtaki, Akashi; Noguchi, Keiichi; Yohda, Masafumi

2010-01-01

Molecular chaperones are key cellular components involved in the maintenance of protein homeostasis and other unrelated functions. Prefoldin is a chaperone that acts as a co-factor of group II chaperonins in eukaryotes and archaea. It assists proper folding of protein by capturing nonnative proteins and delivering it to the group II chaperonin. Eukaryotic prefoldin is a multiple subunit complex composed of six different polypeptide chains. Archaeal prefoldin, on the other hand, is a heterohexameric complex composed of two alpha and four beta subunits, and forms a double beta barrel assembly with six long coiled coils protruding from it like a jellyfish with six tentacles. Based on the structural information of the archaeal prefoldin, substrate recognition and prefoldin-chaperonin binding mechanisms have been investigated. In this paper, we review a series of studies on the molecular mechanisms of archaeal PFD function. Particular emphasis will be placed on the molecular structures revealed by X-ray crystallography and molecular dynamics induced by binding to nonnative protein substrates.

Substrate specificities and intracellular distributions of three N-glycan processing enzymes functioning at a key branch point in the insect N-glycosylation pathway.

PubMed

Geisler, Christoph; Jarvis, Donald L

2012-03-02

Man(α1-6)[GlcNAc(β1-2)Man(α1-3)]ManGlcNAc(2) is a key branch point intermediate in the insect N-glycosylation pathway because it can be either trimmed by a processing β-N-acetylglucosaminidase (FDL) to produce paucimannosidic N-glycans or elongated by N-acetylglucosaminyltransferase II (GNT-II) to produce complex N-glycans. N-acetylglucosaminyltransferase I (GNT-I) contributes to branch point intermediate production and can potentially reverse the FDL trimming reaction. However, there has been no concerted effort to evaluate the relationships among these three enzymes in any single insect system. Hence, we extended our previous studies on Spodoptera frugiperda (Sf) FDL to include GNT-I and -II. Sf-GNT-I and -II cDNAs were isolated, the predicted protein sequences were analyzed, and both gene products were expressed and their acceptor substrate specificities and intracellular localizations were determined. Sf-GNT-I transferred N-acetylglucosamine to Man(5)GlcNAc(2), Man(3)GlcNAc(2), and GlcNAc(β1-2)Man(α1-6)[Man(α1-3)]ManGlcNAc(2), demonstrating its role in branch point intermediate production and its ability to reverse FDL trimming. Sf-GNT-II only transferred N-acetylglucosamine to Man(α1-6)[GlcNAc(β1-2)Man(α1-3)]ManGlcNAc(2), demonstrating that it initiates complex N-glycan production, but cannot use Man(3)GlcNAc(2) to produce hybrid or complex structures. Fluorescently tagged Sf-GNT-I and -II co-localized with an endogenous Sf Golgi marker and Sf-FDL co-localized with Sf-GNT-I and -II, indicating that all three enzymes are Golgi resident proteins. Unexpectedly, fluorescently tagged Drosophila melanogaster FDL also co-localized with Sf-GNT-I and an endogenous Drosophila Golgi marker, indicating that it is a Golgi resident enzyme in insect cells. Thus, the substrate specificities and physical juxtapositioning of GNT-I, GNT-II, and FDL support the idea that these enzymes function at the N-glycan processing branch point and are major factors determining the net outcome of the insect cell N-glycosylation pathway.

Synthesis, characterization and properties of some divalent metal(II) complexes: Their electrochemical, catalytic, thermal and antimicrobial activity studies

NASA Astrophysics Data System (ADS)

Tümer, Mehmet; Ekinci, Duygu; Tümer, Ferhan; Bulut, Akif

2007-07-01

In this study, we synthesized the amine compound 2-(2-aminoethyliminomethyl)phenol (H 3A) as the starting material, and then we prepared the polydentate Schiff base ligands from the reactions of the amine compound (H 3A) with phtaldialdehyde (H 2L), 4-methyl-2,6-di-formlyphenol (H 3L 1) and 4- t-butyl-2,6-di-formylphenol (H 3L 2) in the ethanol solution. Moreover, the complexes Cd(II), Cu(II), Co(II), Ni(II), Zn(II) and Sn(II) of the ligands H 2L, H 3L 1 and H 3L 2 have been prepared. All compounds have been characterized by the analytical and spectroscopic methods. In addition, the magnetic susceptibility and molar conductance measurements have been made. The catalytic properties of the mono- and binuclear Co(II) and Cu(II) complexes have been studied on the 3,5-di- tert-butylcatechol (3,5-DTBC) and ascorbic acid (aa) as a substrate. The oxidative C-C coupling properties of the Co(II) and Cu(II) complexes have been investigated on the sterically hindered 2,6-di- tert-butylphenol (dtbp). The antimicrobial activity properties of the ligands and their mono- and binuclear complexes have been studied against the bacteria and fungi. The results have been compared to the antibacterial and fungi drugs. The TGA curves show that the decomposition takes place in three steps for all complexes. Electrochemical properties of the complexes Cu(II) and Ni(II) have been investigated for the first time in acetonitrile by cyclic voltammetry.

Zn(II)-Coordinated Quantum Dot-FRET Nanosensors for the Detection of Protein Kinase Activity

PubMed Central

Lim, Butaek; Park, Ji-In; Lee, Kyung Jin; Lee, Jin-Won; Kim, Tae-Wuk; Kim, Young-Pil

2015-01-01

We report a simple detection of protein kinase activity using Zn(II)-mediated fluorescent resonance energy transfer (FRET) between quantum dots (QDs) and dye-tethered peptides. With neither complex chemical ligands nor surface modification of QDs, Zn(II) was the only metal ion that enabled the phosphorylated peptides to be strongly attached on the carboxyl groups of the QD surface via metal coordination, thus leading to a significant FRET efficiency. As a result, protein kinase activity in intermixed solution was efficiently detected by QD-FRET via Zn(II) coordination, especially when the peptide substrate was combined with affinity-based purification. We also found that mono- and di-phosphorylation in the peptide substrate could be discriminated by the Zn(II)-mediated QD-FRET. Our approach is expected to find applications for studying physiological function and signal transduction with respect to protein kinase activity. PMID:26213934

Zn(II)-Coordinated Quantum Dot-FRET Nanosensors for the Detection of Protein Kinase Activity.

PubMed

Lim, Butaek; Park, Ji-In; Lee, Kyung Jin; Lee, Jin-Won; Kim, Tae-Wuk; Kim, Young-Pil

2015-07-23

We report a simple detection of protein kinase activity using Zn(II)-mediated fluorescent resonance energy transfer (FRET) between quantum dots (QDs) and dye-tethered peptides. With neither complex chemical ligands nor surface modification of QDs, Zn(II) was the only metal ion that enabled the phosphorylated peptides to be strongly attached on the carboxyl groups of the QD surface via metal coordination, thus leading to a significant FRET efficiency. As a result, protein kinase activity in intermixed solution was efficiently detected by QD-FRET via Zn(II) coordination, especially when the peptide substrate was combined with affinity-based purification. We also found that mono- and di-phosphorylation in the peptide substrate could be discriminated by the Zn(II)-mediated QD-FRET. Our approach is expected to find applications for studying physiological function and signal transduction with respect to protein kinase activity.

Accumulation of Succinate in Cardiac Ischemia Primarily Occurs via Canonical Krebs Cycle Activity.

PubMed

Zhang, Jimmy; Wang, Yves T; Miller, James H; Day, Mary M; Munger, Joshua C; Brookes, Paul S

2018-05-29

Succinate accumulates during ischemia, and its oxidation at reperfusion drives injury. The mechanism of ischemic succinate accumulation is controversial and is proposed to involve reversal of mitochondrial complex II. Herein, using stable-isotope-resolved metabolomics, we demonstrate that complex II reversal is possible in hypoxic mitochondria but is not the primary succinate source in hypoxic cardiomyocytes or ischemic hearts. Rather, in these intact systems succinate primarily originates from canonical Krebs cycle activity, partly supported by aminotransferase anaplerosis and glycolysis from glycogen. Augmentation of canonical Krebs cycle activity with dimethyl-α-ketoglutarate both increases ischemic succinate accumulation and drives substrate-level phosphorylation by succinyl-CoA synthetase, improving ischemic energetics. Although two-thirds of ischemic succinate accumulation is extracellular, the remaining one-third is metabolized during early reperfusion, wherein acute complex II inhibition is protective. These results highlight a bifunctional role for succinate: its complex-II-independent accumulation being beneficial in ischemia and its complex-II-dependent oxidation being detrimental at reperfusion. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Multimetallic Systems for the Photocatalytic Production of Fuels from Abundant Sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunbar, Kim R.; Turro, Claudia

The reported findings herein are a result of a collaboration between the groups of Claudia Turro at The Ohio State University (DE-SC0010542) and Kim R. Dunbar at Texas A&M University (DE-SC0010721). The Turro and Dunbar groups jointly discovered that cationic d 7–d 7 Rh 2(II,II) complexes bridged by electron-donating formamidinate (form) ligands possess redox-active excited states that are relatively long-lived and can engage in charge transfer reactions. As part of the present grant we designed new complexes that exhibit strong absorption from the UV to ~800 nm. The Rh 2(II,II) complexes under investigation are poised to undergo catalytic reduction ofmore » substrates because they are robust to changes in metal oxidation state, the two metals and the two diimine ligands, together with the non-innocent bridges, can be used to store redox equivalents, making these complexes capable of coupling one-electron events with multi-electron transformations. We discovered the electrocatalytic reduction of H + and CO 2 by complexes that are able to electrocatalytically reduce H + to H 2 with high turnover frequencies (TOFs) and overpotentials, η, of ~0.5 V,8 as well as to reduce CO 2 to HCOOH. We now have experimental evidence that both the production of H 2 from H + and HCOOH. The molecular catalysts are stable after the acid and/or CO 2 is consumed since electrocatalysis is restored at the same rate upon the addition of substrate to the cell.8,9 Moreover, we showed that the catalysis is not a result of a decomposition product deposited on the electrode, since placing an electrode from an active electrocatalytic solution into one that does not contain catalyst completely shuts down the reactivity. We are currently exploring the reactivity of these complexes in hydride transfer reactions with other substrates and in the presence of CO 2 and reducing agents, as well as attempting to grow single crystals for x-ray diffraction.« less

Structural, Spectroscopic, and Electrochemical Properties of Nonheme Fe(II)-Hydroquinonate Complexes: Synthetic Models of Hydroquinone Dioxygenases

PubMed Central

Baum, Amanda E.; Park, Heaweon; Wang, Denan; Lindeman, Sergey V.; Fiedler, Adam T.

2012-01-01

Using the tris(3,5-diphenylpyrazol-1-yl)borate (Ph2Tp) supporting ligand, a series of mono- and dinuclear ferrous complexes containing hydroquinonate (HQate) ligands have been prepared and structurally characterized with X-ray crystallography. The monoiron(II) complexes serve as faithful mimics of the substrate-bound form of hydroquinone dioxygenases (HQDOs) – a family of nonheme Fe enzymes that catalyze the oxidative cleavage of 1,4-dihydroxybenzene units. Reflecting the variety of HQDO substrates, the synthetic complexes feature both mono- and bidentate HQate ligands. The bidentate HQates cleanly provide five-coordinate, high-spin Fe(II) complexes with the general formula [Fe(Ph2Tp)(HLX)] (1X), where HLX is a HQate(1-) ligand substituted at the 2-position with a benzimidazolyl (1A), acetyl (1B and 1C), or methoxy (1D) group. In contrast, the monodentate ligand 2,6-dimethylhydroquinone (H2LF) exhibited a greater tendency to bridge between two Fe(II) centers, resulting in formation of [Fe2(Ph2Tp)2(μ-LF)(MeCN)] [2F(MeCN)]. However, addition of one equivalent of “free” pyrazole (Ph2pz) ligand provided the mononuclear complex, [Fe(Ph2Tp)(HLF)(Ph2pz)] [1F(Ph2pz)], which is stabilized by an intramolecular hydrogen bond between the HLF and Ph2pz donors. Complex 1F(Ph2pz) represents the first crystallographically-characterized example of a monoiron complex bound to an untethered HQate ligand. The geometric and electronic structures of the Fe/HQate complexes were further probed with spectroscopic (UV-vis absorption, 1H NMR) and electrochemical methods. Cyclic voltammograms of complexes in the 1X series revealed an Fe-based oxidation between 0 and −300 mV (vs. Fc+/0), in addition to irreversible oxidation(s) of the HQate ligand at higher potentials. The one-electron oxidized species (1Xox) were examined with UV-vis absorption and electron paramagnetic resonance (EPR) spectroscopies. PMID:22930005

Engineering the magnetic coupling and anisotropy at the molecule–magnetic surface interface in molecular spintronic devices

PubMed Central

Campbell, Victoria E.; Tonelli, Monica; Cimatti, Irene; Moussy, Jean-Baptiste; Tortech, Ludovic; Dappe, Yannick J.; Rivière, Eric; Guillot, Régis; Delprat, Sophie; Mattana, Richard; Seneor, Pierre; Ohresser, Philippe; Choueikani, Fadi; Otero, Edwige; Koprowiak, Florian; Chilkuri, Vijay Gopal; Suaud, Nicolas; Guihéry, Nathalie; Galtayries, Anouk; Miserque, Frederic; Arrio, Marie-Anne; Sainctavit, Philippe; Mallah, Talal

2016-01-01

A challenge in molecular spintronics is to control the magnetic coupling between magnetic molecules and magnetic electrodes to build efficient devices. Here we show that the nature of the magnetic ion of anchored metal complexes highly impacts the exchange coupling of the molecules with magnetic substrates. Surface anchoring alters the magnetic anisotropy of the cobalt(II)-containing complex (Co(Pyipa)2), and results in blocking of its magnetization due to the presence of a magnetic hysteresis loop. In contrast, no hysteresis loop is observed in the isostructural nickel(II)-containing complex (Ni(Pyipa)2). Through XMCD experiments and theoretical calculations we find that Co(Pyipa)2 is strongly ferromagnetically coupled to the surface, while Ni(Pyipa)2 is either not coupled or weakly antiferromagnetically coupled to the substrate. These results highlight the importance of the synergistic effect that the electronic structure of a metal ion and the organic ligands has on the exchange interaction and anisotropy occurring at the molecule–electrode interface. PMID:27929089

Protein-DNA interactions define the mechanistic aspects of circle formation and insertion reactions in IS2 transposition.

PubMed

Lewis, Leslie A; Astatke, Mekbib; Umekubo, Peter T; Alvi, Shaheen; Saby, Robert; Afrose, Jehan; Oliveira, Pedro H; Monteiro, Gabriel A; Prazeres, Duarte Mf

2012-01-26

Transposition in IS3, IS30, IS21 and IS256 insertion sequence (IS) families utilizes an unconventional two-step pathway. A figure-of-eight intermediate in Step I, from asymmetric single-strand cleavage and joining reactions, is converted into a double-stranded minicircle whose junction (the abutted left and right ends) is the substrate for symmetrical transesterification attacks on target DNA in Step II, suggesting intrinsically different synaptic complexes (SC) for each step. Transposases of these ISs bind poorly to cognate DNA and comparative biophysical analyses of SC I and SC II have proven elusive. We have prepared a native, soluble, active, GFP-tagged fusion derivative of the IS2 transposase that creates fully formed complexes with single-end and minicircle junction (MCJ) substrates and used these successfully in hydroxyl radical footprinting experiments. In IS2, Step I reactions are physically and chemically asymmetric; the left imperfect, inverted repeat (IRL), the exclusive recipient end, lacks donor function. In SC I, different protection patterns of the cleavage domains (CDs) of the right imperfect inverted repeat (IRR; extensive in cis) and IRL (selective in trans) at the single active cognate IRR catalytic center (CC) are related to their donor and recipient functions. In SC II, extensive binding of the IRL CD in trans and of the abutted IRR CD in cis at this CC represents the first phase of the complex. An MCJ substrate precleaved at the 3' end of IRR revealed a temporary transition state with the IRL CD disengaged from the protein. We propose that in SC II, sequential 3' cleavages at the bound abutted CDs trigger a conformational change, allowing the IRL CD to complex to its cognate CC, producing the second phase. Corroborating data from enhanced residues and curvature propensity plots suggest that CD to CD interactions in SC I and SC II require IRL to assume a bent structure, to facilitate binding in trans. Different transpososomes are assembled in each step of the IS2 transposition pathway. Recipient versus donor end functions of the IRL CD in SC I and SC II and the conformational change in SC II that produces the phase needed for symmetrical IRL and IRR donor attacks on target DNA highlight the differences.

Protein-DNA interactions define the mechanistic aspects of circle formation and insertion reactions in IS2 transposition

PubMed Central

2012-01-01

Background Transposition in IS3, IS30, IS21 and IS256 insertion sequence (IS) families utilizes an unconventional two-step pathway. A figure-of-eight intermediate in Step I, from asymmetric single-strand cleavage and joining reactions, is converted into a double-stranded minicircle whose junction (the abutted left and right ends) is the substrate for symmetrical transesterification attacks on target DNA in Step II, suggesting intrinsically different synaptic complexes (SC) for each step. Transposases of these ISs bind poorly to cognate DNA and comparative biophysical analyses of SC I and SC II have proven elusive. We have prepared a native, soluble, active, GFP-tagged fusion derivative of the IS2 transposase that creates fully formed complexes with single-end and minicircle junction (MCJ) substrates and used these successfully in hydroxyl radical footprinting experiments. Results In IS2, Step I reactions are physically and chemically asymmetric; the left imperfect, inverted repeat (IRL), the exclusive recipient end, lacks donor function. In SC I, different protection patterns of the cleavage domains (CDs) of the right imperfect inverted repeat (IRR; extensive in cis) and IRL (selective in trans) at the single active cognate IRR catalytic center (CC) are related to their donor and recipient functions. In SC II, extensive binding of the IRL CD in trans and of the abutted IRR CD in cis at this CC represents the first phase of the complex. An MCJ substrate precleaved at the 3' end of IRR revealed a temporary transition state with the IRL CD disengaged from the protein. We propose that in SC II, sequential 3' cleavages at the bound abutted CDs trigger a conformational change, allowing the IRL CD to complex to its cognate CC, producing the second phase. Corroborating data from enhanced residues and curvature propensity plots suggest that CD to CD interactions in SC I and SC II require IRL to assume a bent structure, to facilitate binding in trans. Conclusions Different transpososomes are assembled in each step of the IS2 transposition pathway. Recipient versus donor end functions of the IRL CD in SC I and SC II and the conformational change in SC II that produces the phase needed for symmetrical IRL and IRR donor attacks on target DNA highlight the differences. PMID:22277150

Structure of the Ni(II) complex of Escherichia coli peptide deformylase and suggestions on deformylase activities depending on different metal(II) centres.

PubMed

Yen, Ngo Thi Hai; Bogdanović, Xenia; Palm, Gottfried J; Kühl, Olaf; Hinrichs, Winfried

2010-02-01

Crystal structures of polypeptide deformylase (PDF) of Escherichia coli with nickel(II) replacing the native iron(II) have been solved with chloride and formate as metal ligands. The chloro complex is a model for the correct protonation state of the hydrolytic hydroxo ligand and the protonated status of the Glu133 side chain as part of the hydrolytic mechanism. The ambiguity that recently some PDFs have been identified with Zn(2+) ion as the active-site centre whereas others are only active with Fe(2+) (or Co(2+), Ni(2+) is discussed with respect to Lewis acid criteria of the metal ion and substrate activation by the CD loop.

Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase from Burkholderia ambifaria AMMD

PubMed Central

Qin, Hui-Min; Miyakawa, Takuya; Jia, Min Ze; Nakamura, Akira; Ohtsuka, Jun; Xue, You-Lin; Kawashima, Takashi; Kasahara, Takuya; Hibi, Makoto; Ogawa, Jun; Tanokura, Masaru

2013-01-01

A novel dioxygenase from Burkholderia ambifaria AMMD (SadA) stereoselectively catalyzes the C3-hydroxylation of N-substituted branched-chain or aromatic L-amino acids, especially N-succinyl-L-leucine, coupled with the conversion of α-ketoglutarate to succinate and CO2. To elucidate the structural basis of the substrate specificity and stereoselective hydroxylation, we determined the crystal structures of the SadA.Zn(II) and SadA.Zn(II).α-KG complexes at 1.77 Å and 1.98 Å resolutions, respectively. SadA adopted a double-stranded β-helix fold at the core of the structure. In addition, an HXD/EXnH motif in the active site coordinated a Zn(II) as a substitute for Fe(II). The α-KG molecule also coordinated Zn(II) in a bidentate manner via its 1-carboxylate and 2-oxo groups. Based on the SadA.Zn(II).α-KG structure and mutation analyses, we constructed substrate-binding models with N-succinyl-L-leucine and N-succinyl-L-phenylalanine, which provided new insight into the substrate specificity. The results will be useful for the rational design of SadA variants aimed at the recognition of various N-succinyl L-amino acids. PMID:23724013

Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition

PubMed Central

Kumar, Prashant; Reithofer, Viktoria; Reisinger, Manuel; Wallner, Silvia; Pavkov-Keller, Tea; Macheroux, Peter; Gruber, Karl

2016-01-01

Human dipeptidyl-peptidase III (hDPP III) is a zinc-dependent hydrolase cleaving dipeptides off the N-termini of various bioactive peptides. Thus, the enzyme is likely involved in a number of physiological processes such as nociception and is also implicated in several forms of cancer. We present high-resolution crystal structures of hDPP III in complex with opioid peptides (Met-and Leu-enkephalin, endomorphin-2) as well as with angiotensin-II and the peptide inhibitor IVYPW. These structures confirm the previously reported large conformational change of the enzyme upon ligand binding and show that the structure of the closed conformation is independent of the nature of the bound peptide. The overall peptide-binding mode is also conserved ensuring the correct positioning of the scissile peptide bond with respect to the catalytic zinc ion. The structure of the angiotensin-II complex shows, how longer peptides are accommodated in the binding cleft of hDPP III. Differences in the binding modes allow a distinction between real substrates and inhibitory peptides or “slow” substrates. The latter displace a zinc bound water molecule necessitating the energetically much less favoured anhydride mechanism as opposed to the favoured promoted-water mechanism. The structural data also form the necessary framework for the design of specific hDPP III inhibitors. PMID:27025154

Remodeling pathway control of mitochondrial respiratory capacity by temperature in mouse heart: electron flow through the Q-junction in permeabilized fibers.

PubMed

Lemieux, Hélène; Blier, Pierre U; Gnaiger, Erich

2017-06-06

Fuel substrate supply and oxidative phosphorylation are key determinants of muscle performance. Numerous studies of mammalian mitochondria are carried out (i) with substrate supply that limits electron flow, and (ii) far below physiological temperature. To analyze potentially implicated biases, we studied mitochondrial respiratory control in permeabilized mouse myocardial fibers using high-resolution respirometry. The capacity of oxidative phosphorylation at 37 °C was nearly two-fold higher when fueled by physiological substrate combinations reconstituting tricarboxylic acid cycle function, compared with electron flow measured separately through NADH to Complex I or succinate to Complex II. The relative contribution of the NADH pathway to physiological respiratory capacity increased with a decrease in temperature from 37 to 25 °C. The apparent excess capacity of cytochrome c oxidase above physiological pathway capacity increased sharply under hypothermia due to limitation by NADH-linked dehydrogenases. This mechanism of mitochondrial respiratory control in the hypothermic mammalian heart is comparable to the pattern in ectotherm species, pointing towards NADH-linked mt-matrix dehydrogenases and the phosphorylation system rather than electron transfer complexes as the primary drivers of thermal sensitivity at low temperature. Delineating the link between stress and remodeling of oxidative phosphorylation is important for understanding metabolic perturbations in disease evolution and cardiac protection.

Physical Fitness and Mitochondrial Respiratory Capacity in Horse Skeletal Muscle

PubMed Central

Lemieux, Hélène; Mouithys-Mickalad, Ange; Serteyn, Didier

2012-01-01

Background Within the animal kingdom, horses are among the most powerful aerobic athletic mammals. Determination of muscle respiratory capacity and control improves our knowledge of mitochondrial physiology in horses and high aerobic performance in general. Methodology/Principal Findings We applied high-resolution respirometry and multiple substrate-uncoupler-inhibitor titration protocols to study mitochondrial physiology in small (1.0–2.5 mg) permeabilized muscle fibres sampled from triceps brachii of healthy horses. Oxidative phosphorylation (OXPHOS) capacity (pmol O2•s−1•mg−1 wet weight) with combined Complex I and II (CI+II) substrate supply (malate+glutamate+succinate) increased from 77±18 in overweight horses to 103±18, 122±15, and 129±12 in untrained, trained and competitive horses (N = 3, 8, 16, and 5, respectively). Similar to human muscle mitochondria, equine OXPHOS capacity was limited by the phosphorylation system to 0.85±0.10 (N = 32) of electron transfer capacity, independent of fitness level. In 15 trained horses, OXPHOS capacity increased from 119±12 to 134±37 when pyruvate was included in the CI+II substrate cocktail. Relative to this maximum OXPHOS capacity, Complex I (CI)-linked OXPHOS capacities were only 50% with glutamate+malate, 64% with pyruvate+malate, and 68% with pyruvate+malate+glutamate, and ∼78% with CII-linked succinate+rotenone. OXPHOS capacity with glutamate+malate increased with fitness relative to CI+II-supported ETS capacity from a flux control ratio of 0.38 to 0.40, 0.41 and 0.46 in overweight to competitive horses, whereas the CII/CI+II substrate control ratio remained constant at 0.70. Therefore, the apparent deficit of the CI- over CII-linked pathway capacity was reduced with physical fitness. Conclusions/Significance The scope of mitochondrial density-dependent OXPHOS capacity and the density-independent (qualitative) increase of CI-linked respiratory capacity with increased fitness open up new perspectives of integrative and comparative mitochondrial respiratory physiology. PMID:22529950

Antioxidant, electrochemical, thermal, antimicrobial and alkane oxidation properties of tridentate Schiff base ligands and their metal complexes

NASA Astrophysics Data System (ADS)

Ceyhan, Gökhan; Çelik, Cumali; Uruş, Serhan; Demirtaş, İbrahim; Elmastaş, Mahfuz; Tümer, Mehmet

2011-10-01

In this study, two Schiff base ligands (HL 1 and HL 2) and their Cu(II), Co(II), Ni(II), Pd(II) and Ru(III) metal complexes were synthesized and characterized by the analytical and spectroscopic methods. Alkane oxidation activities of the metal complexes were studied on cyclohexane as substrate. The ligands and their metal complexes were evaluated for their antimicrobial activity against Corynebacterium xerosis, Bacillus brevis, Bacillus megaterium, Bacillus cereus, Mycobacterium smegmatis, Staphylococcus aureus, Micrococcus luteus and Enterococcus faecalis (as Gram-positive bacteria) and Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Yersinia enterocolitica, Klebsiella fragilis, Saccharomyces cerevisiae, and Candida albicans (as Gram-negative bacteria). The antioxidant properties of the Schiff base ligands were evaluated in a series of in vitro tests: 1,1-diphenyl-2-picrylhydrazyl (DPPH rad ) free radical scavenging and reducing power activity of superoxide anion radical generated non-enzymatic systems. Electrochemical and thermal properties of the compounds were investigated.

Manganese ions enhance mitochondrial H2O2 emission from Krebs cycle oxidoreductases by inducing permeability transition.

PubMed

Bonke, Erik; Siebels, Ilka; Zwicker, Klaus; Dröse, Stefan

2016-10-01

Manganese-induced toxicity has been linked to mitochondrial dysfunction and an increased generation of reactive oxygen species (ROS). We could recently show in mechanistic studies that Mn 2+ ions induce hydrogen peroxide (H 2 O 2 ) production from the ubiquinone binding site of mitochondrial complex II (II Q ) and generally enhance H 2 O 2 formation by accelerating the rate of superoxide dismutation. The present study with intact mitochondria reveals that manganese additionally enhances H 2 O 2 emission by inducing mitochondrial permeability transition (mPT). In mitochondria fed by NADH-generating substrates, the combination of Mn 2+ and different respiratory chain inhibitors led to a dynamically increasing H 2 O 2 emission which was sensitive to the mPT inhibitor cyclosporine A (CsA) as well as Ru-360, an inhibitor of the mitochondrial calcium uniporter (MCU). Under these conditions, flavin-containing enzymes of the mitochondrial matrix, e.g. the mitochondrial 2-oxoglutaratedehydrogenase (OGDH), were major sources of ROS. With succinate as substrate, Mn 2+ stimulated ROS production mainly at complex II, whereby the applied succinate concentration had a marked effect on the tendency for mPT. Also Ca 2+ increased the rate of H 2 O 2 emission by mPT, while no direct effect on ROS-production of complex II was observed. The present study reveals a complex scenario through which manganese affects mitochondrial H 2 O 2 emission: stimulating its production from distinct sites (e.g. site II Q ), accelerating superoxide dismutation and enhancing the emission via mPT which also leads to the loss of soluble components of the mitochondrial antioxidant systems and favors the ROS production from flavin-containing oxidoreductases of the Krebs cycle. Copyright © 2016 Elsevier Inc. All rights reserved.

Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Dell, William B.; Agarwal, Pratul K.; Meilleur, Flora

Lytic polysaccharide monooxygenases have attracted vast attention owing to their abilities to disrupt glycosidic bonds via oxidation instead of hydrolysis and to enhance enzymatic digestion of recalcitrant substrates including chitin and cellulose. Here, we determined the high-resolution X-ray crystal structures of an enzyme from Neurospora crassa in the resting state and of a copper(II) dioxo intermediate complex formed in the absence of substrate. X-ray crystal structures also revealed “pre-bound” molecular oxygen adjacent to the active site. An examination of protonation states enabled by neutron crystallography and density functional theory calculations identified a role for a conserved histidine in promoting oxygenmore » activation. Our results provide a new structural description of oxygen activation by substrate free lytic polysaccharide monooxygenases and provide insights that can be extended to reactivity in the enzyme–substrate complex.« less

Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase

DOE PAGES

O'Dell, William B.; Agarwal, Pratul K.; Meilleur, Flora

2016-12-22

Lytic polysaccharide monooxygenases have attracted vast attention owing to their abilities to disrupt glycosidic bonds via oxidation instead of hydrolysis and to enhance enzymatic digestion of recalcitrant substrates including chitin and cellulose. Here, we determined the high-resolution X-ray crystal structures of an enzyme from Neurospora crassa in the resting state and of a copper(II) dioxo intermediate complex formed in the absence of substrate. X-ray crystal structures also revealed “pre-bound” molecular oxygen adjacent to the active site. An examination of protonation states enabled by neutron crystallography and density functional theory calculations identified a role for a conserved histidine in promoting oxygenmore » activation. Our results provide a new structural description of oxygen activation by substrate free lytic polysaccharide monooxygenases and provide insights that can be extended to reactivity in the enzyme–substrate complex.« less

Structural Investigations of the Nickel-Induced Inhibition of Truncated Constructs of the JMJD2 Family of Histone Demethylases Using X-ray Absorption Spectroscopy

PubMed Central

Giri, Nitai Charan; Passantino, Lisa; Sun, Hong; Zoroddu, Maria Antonietta; Costa, Max; Maroney, Michael J.

2013-01-01

Occupational and/or environmental exposure to nickel has been implicated in various types of cancer, and in vitro exposure to nickel compounds results in accumulation of Ni(II) ions in cells. One of the major targets of Ni(II) ions inside the cell is Fe(II)- and αKG-dependent dioxygenases. Using JMJD2A and JMJD2C as examples, we show that JMJD2 family of histone demethylases, which are products of putative oncogenes as well as Fe(II)- and αKG-dependent dioxygenases, are highly sensitive to inhibition by Ni(II) ions. In this work, X-ray absorption spectroscopy (XAS) has been used to investigate the Fe(II) active site of truncated JMJD2A and JMJD2C (1 – 350 aa) in the presence and absence of αKG and/or substrate to obtain mechanistic details of the early steps in catalysis that precede O2 binding in histone demethylation by the JMJD2 family of histone demethylases. Zinc K-edge XAS has been performed on the resting JMJD2A (with iron in the active site) to confirm the presence of the expected structural zinc site. XAS of the Ni(II)-substituted enzymes has also been performed to investigate the inhibition of these enzymes by Ni(II) ions. Our XAS results indicate that the five-coordinate Fe(II) center in the resting enzyme is retained in the binary and ternary complexes. In contrast, the Ni(II) center is six-coordinate in the resting enzyme, binary and ternary complexes. XAS results indicate that both Fe(II) and Ni(II) bind αKG in the binary and ternary complexes. The electron density build-up that is observed at the Fe(II) center in the presence of αKG and substrate is not observed at the Ni(II) center. Thus, both electronic and steric factors are responsible for Ni-induced inhibition of the JMJD2 family of histone demethylases. Ni-induced inhibition of these enzymes may explain the alteration of the epigenetic mechanism of gene expression that is responsible for Ni-induced carcinogenesis. PMID:23692052

Anionic Palladium(0) and Palladium(II) Ate Complexes.

PubMed

Kolter, Marlene; Böck, Katharina; Karaghiosoff, Konstantin; Koszinowski, Konrad

2017-10-16

Palladium ate complexes are frequently invoked as important intermediates in Heck and cross-coupling reactions, but so far have largely eluded characterization at the molecular level. Here, we use electrospray-ionization mass spectrometry, electrical conductivity measurements, and NMR spectroscopy to show that the electron-poor catalyst [L 3 Pd] (L=tris[3,5-bis(trifluoromethyl)phenyl]phosphine) readily reacts with Br - ions to afford the anionic, zero-valent ate complex [L 3 PdBr] - . In contrast, more-electron-rich Pd catalysts display lower tendencies toward the formation of ate complexes. Combining [L 3 Pd] with LiI and an aryl iodide substrate (ArI) results in the observation of the Pd II ate complex [L 2 Pd(Ar)I 2 ] - . © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Combined experimental and theoretical approach to understand the reactivity of a mononuclear Cu(II)-hydroperoxo complex in oxygenation reactions.

PubMed

Kamachi, Takashi; Lee, Yong-Min; Nishimi, Tomonori; Cho, Jaeheung; Yoshizawa, Kazunari; Nam, Wonwoo

2008-12-18

A copper(II) complex bearing a pentadentate ligand, [Cu(II)(N4Py)(CF(3)SO(3))(2)] (1) (N4Py = N,N-bis(2-pyridylmethyl)bis(2-pyridyl)methylamine), was synthesized and characterized with various spectroscopic techniques and X-ray crystallography. A mononuclear Cu(II)-hydroperoxo complex, [Cu(II)(N4Py)(OOH)](+) (2), was then generated in the reaction of 1 and H(2)O(2) in the presence of base, and the reactivity of the intermediate was investigated in the oxidation of various substrates at -40 degrees C. In the reactivity studies, 2 showed a low oxidizing power such that 2 reacted only with triethylphosphine but not with other substrates such as thioanisole, benzyl alcohol, 1,4-cyclohexadiene, cyclohexene, and cyclohexane. In theoretical work, we have conducted density functional theory (DFT) calculations on the epoxidation of ethylene by 2 and a [Cu(III)(N4Py)(O)](+) intermediate (3) at the B3LYP level. The activation barrier is calculated to be 39.7 and 26.3 kcal/mol for distal and proximal oxygen attacks by 2, respectively. This result indicates that the direct ethylene epoxidation by 2 is not a plausible pathway, as we have observed in the experimental work. In contrast, the ethylene epoxidation by 3 is a downhill and low-barrier process. We also found that 2 cannot be a precursor to 3, since the homolytic cleavage of the O-O bond of 2 is very endothermic (i.e., 42 kcal/mol). On the basis of the experimental and theoretical results, we conclude that a mononuclear Cu(II)-hydroperoxo species bearing a pentadentate N5 ligand is a sluggish oxidant in oxygenation reactions.

P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates

PubMed Central

Sansó, Miriam; Levin, Rebecca S.; Lipp, Jesse J.; Wang, Vivien Ya-Fan; Greifenberg, Ann Katrin; Quezada, Elizabeth M.; Ali, Akbar; Ghosh, Animesh; Larochelle, Stéphane; Rana, Tariq M.; Geyer, Matthias; Tong, Liang; Shokat, Kevan M.; Fisher, Robert P.

2016-01-01

The transcription cycle of RNA polymerase II (Pol II) is regulated at discrete transition points by cyclin-dependent kinases (CDKs). Positive transcription elongation factor b (P-TEFb), a complex of Cdk9 and cyclin T1, promotes release of paused Pol II into elongation, but the precise mechanisms and targets of Cdk9 action remain largely unknown. Here, by a chemical genetic strategy, we identified ∼100 putative substrates of human P-TEFb, which were enriched for proteins implicated in transcription and RNA catabolism. Among the RNA processing factors phosphorylated by Cdk9 was the 5′-to-3′ “torpedo” exoribonuclease Xrn2, required in transcription termination by Pol II, which we validated as a bona fide P-TEFb substrate in vivo and in vitro. Phosphorylation by Cdk9 or phosphomimetic substitution of its target residue, Thr439, enhanced enzymatic activity of Xrn2 on synthetic substrates in vitro. Conversely, inhibition or depletion of Cdk9 or mutation of Xrn2-Thr439 to a nonphosphorylatable Ala residue caused phenotypes consistent with inefficient termination in human cells: impaired Xrn2 chromatin localization and increased readthrough transcription of endogenous genes. Therefore, in addition to its role in elongation, P-TEFb regulates termination by promoting chromatin recruitment and activation of a cotranscriptional RNA processing enzyme, Xrn2. PMID:26728557

Copper(II) complexes as catalyst for the aerobic oxidation of o-phenylenediamine to 2,3-diaminophenazine

NASA Astrophysics Data System (ADS)

Khattar, Raghvi; Yadav, Anjana; Mathur, Pavan

2015-05-01

Two new mononuclear copper(II) complexes [Cu (L) (NO3)2] (1) and [Cu (L) Br2] (2) where (L = bis(1-(pyridin-2-ylmethyl)-benzimidazol-2-ylmethyl)ether) are synthesized and characterized by single-crystal X-ray diffraction analysis, elemental analysis, UV-Visible, IR spectroscopy, EPR and cyclic voltammetry. The complexes exhibit different coordination structures; the E1/2 value of the complex (1) is found to be relatively more cathodic than that of complex (2). X-band EPR spectra at low temperature in DMF supports a tetragonally distorted complex (1) while complex (2) shows three different g values suggesting a rhombic geometry. These complexes were utilized as a catalyst for the aerobic oxidation of o-phenylenediamine to 2,3-diaminophenazine assisted by molecular oxygen. The initial rate of reaction is dependent on the concentration of Cu(II) complex as well as substrate, and was found to be higher for the nitrate bound complex, while presence of acetate anion acts as a mild inhibitor of the reaction, as it is likely to pick up protons generated during the course of reaction. The inhibition suggests that the generated protons are further required in another important catalytic step.

Radical pathway in catecholase activity with zinc-based model complexes of compartmental ligands.

PubMed

Guha, Averi; Chattopadhyay, Tanmay; Paul, Nanda Dulal; Mukherjee, Madhuparna; Goswami, Somen; Mondal, Tapan Kumar; Zangrando, Ennio; Das, Debasis

2012-08-20

Four dinuclear and three mononuclear Zn(II) complexes of phenol-based compartmental ligands (HL(1)-HL(7)) have been synthesized with the aim to investigate the viability of a radical pathway in catecholase activity. The complexes have been characterized by routine physicochemical studies as well as X-ray single-crystal structure analysis: [Zn(2)(H(2)L(1))(OH)(H(2)O)(NO(3))](NO(3))(3) (1), [Zn(2)L(2)Cl(3)] (2), [Zn(2)L(3)Cl(3)] (3), [Zn(2)(L(4))(2)(CH(3)COO)(2)] (4), [Zn(HL(5))Cl(2)] (5), [Zn(HL(6))Cl(2)] (6), and [Zn(HL(7))Cl(2)] (7) [L(1)-L(3) and L(5)-L(7) = 2,6-bis(R-iminomethyl)-4-methylphenolato, where R= N-ethylpiperazine for L(1), R = 2-(N-ethyl)pyridine for L(2), R = N-ethylpyrrolidine for L(3), R = N-methylbenzene for L(5), R = 2-(N-methyl)thiophene for L(6), R = 2-(N-ethyl)thiophene for L(7), and L(4) = 2-formyl-4-methyl-6-N-methylbenzene-iminomethyl-phenolato]. Catecholase-like activity of the complexes has been investigated in methanol medium by UV-vis spectrophotometric study using 3,5-di-tert-butylcatechol as model substrate. All complexes are highly active in catalyzing the aerobic oxidation of 3,5-di-tert-butylcatechol (3,5-DTBC) to 3,5-di-tert-butylbenzoquinone (3,5-DTBQ). Conversion of 3,5-DTBC to 3,5-DTBQ catalyzed by mononuclear complexes (5-7) is observed to proceed via formation of two enzyme-substrate adducts, ES1 and ES2, detected spectroscopically, a finding reported for the first time in any Zn(II) complex catalyzed oxidation of catechol. On the other hand, no such enzyme-substrate adduct has been identified, and 3,5-DTBC to 3,5-DTBQ conversion is observed to be catalyzed by the dinuclear complexes (1-4) very smoothly. EPR experiment suggests generation of radicals in the presence of 3,5-DTBC, and that finding has been strengthened by cyclic voltammetric study. Thus, it may be proposed that the radical pathway is probably responsible for conversion of 3,5-DTBC to 3,5-DTBQ promoted by complexes of redox-innocent Zn(II) ion. The ligand-centered radical generation has further been verified by density functional theory calculation.

Unraveling orbital hybridization of triplet emitters at the metal-organic interface.

PubMed

Ewen, Pascal R; Sanning, Jan; Doltsinis, Nikos L; Mauro, Matteo; Strassert, Cristian A; Wegner, Daniel

2013-12-27

We have investigated the structural and electronic properties of phosphorescent planar platinum(II) complexes at the interface of Au(111) with submolecular resolution using combined scanning tunneling microscopy and spectroscopy as well as density functional theory. Our analysis shows that molecule-substrate coupling and lateral intermolecular interactions are weak. While the ligand orbitals remain essentially unchanged upon contact with the substrate, we found modified electronic behavior at the Pt atom due to local hybridization and charge transfer to the substrate. Thus, this novel class of phosphorescent molecules exhibits well-defined and tunable interaction with its local environment.

EXAFS study of mercury(II) sorption to Fe- and Al-(hydr)oxides - II. Effects of chloride and sulfate

USGS Publications Warehouse

Kim, C.S.; Rytuba, J.J.; Brown, Gordon E.

2004-01-01

Common complexing ligands such as chloride and sulfate can significantly impact the sorption of Hg(II) to particle surfaces in aqueous environmental systems. To examine the effects of these ligands on Hg(II) sorption to mineral sorbents, macroscopic Hg(II) uptake measurements were conducted at pH 6 and [Hg]i=0.5 mM on goethite (??-FeOOH), ??-alumina (??-Al2O3), and bayerite (??-Al(OH)3) in the presence of chloride or sulfate, and the sorption products were characterized by extended X-ray absorption fine structure (EXAFS) spectroscopy. The presence of chloride resulted in reduced uptake of Hg(II) on all three substrates over the Cl- concentration ([Cl-]) range 10-5 to 10-2 M, lowering Hg surface coverages on goethite, ??-alumina, and bayerite from 0.42 to 0.07 ??mol/m2, 0.06 to 0.006 ??mol/m2, and 0.55 to 0.39 ??mol/m2 ([Cl -]=10-5 to 10-3 M only), respectively. This reduction in Hg(II) uptake is primarily a result of the formation of stable, nonsorbing aqueous HgCl2 complexes in solution, limiting the amount of free Hg(II) available to sorb. At higher [Cl-] beam reduction of Hg(II) to Hg(I) was observed, resulting in the possible formation of aqueous Hg2Cl2 species and the precipitation of calomel, Hg 2Cl2(s). The presence of sulfate caused enhanced Hg(II) uptake over the sulfate concentration ([SO42-]) range 10-5 to 0.9 M, increasing Hg surface coverages on goethite, ??-alumina, and bayerite from 0.39 to 0.45 ??mol/m2, 0.11 to 0.38 ??mol/m2, and 0.36 to 3.33 ??mol/m2, respectively. This effect is likely due to the direct sorption or accumulation of sulfate ions at the substrate interface, effectively reducing the positive surface charge that electrostatically inhibits Hg(II) sorption. Spectroscopic evidence for ternary surface complexation was observed in isolated cases, specifically in the Hg-goethite-sulfate system at high [SO42-] and in the Hg-goethite-chloride system. ?? 2003 Elsevier Inc. All rights reserved.

Structure of photosystem II and substrate binding at room temperature.

PubMed

Young, Iris D; Ibrahim, Mohamed; Chatterjee, Ruchira; Gul, Sheraz; Fuller, Franklin; Koroidov, Sergey; Brewster, Aaron S; Tran, Rosalie; Alonso-Mori, Roberto; Kroll, Thomas; Michels-Clark, Tara; Laksmono, Hartawan; Sierra, Raymond G; Stan, Claudiu A; Hussein, Rana; Zhang, Miao; Douthit, Lacey; Kubin, Markus; de Lichtenberg, Casper; Long Vo, Pham; Nilsson, Håkan; Cheah, Mun Hon; Shevela, Dmitriy; Saracini, Claudio; Bean, Mackenzie A; Seuffert, Ina; Sokaras, Dimosthenis; Weng, Tsu-Chien; Pastor, Ernest; Weninger, Clemens; Fransson, Thomas; Lassalle, Louise; Bräuer, Philipp; Aller, Pierre; Docker, Peter T; Andi, Babak; Orville, Allen M; Glownia, James M; Nelson, Silke; Sikorski, Marcin; Zhu, Diling; Hunter, Mark S; Lane, Thomas J; Aquila, Andy; Koglin, Jason E; Robinson, Joseph; Liang, Mengning; Boutet, Sébastien; Lyubimov, Artem Y; Uervirojnangkoorn, Monarin; Moriarty, Nigel W; Liebschner, Dorothee; Afonine, Pavel V; Waterman, David G; Evans, Gwyndaf; Wernet, Philippe; Dobbek, Holger; Weis, William I; Brunger, Axel T; Zwart, Petrus H; Adams, Paul D; Zouni, Athina; Messinger, Johannes; Bergmann, Uwe; Sauter, Nicholas K; Kern, Jan; Yachandra, Vittal K; Yano, Junko

2016-12-15

Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn 4 CaO 5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S 0 to S 4 ), in which S 1 is the dark-stable state and S 3 is the last semi-stable state before O-O bond formation and O 2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S 1 ), two-flash illuminated (2F; S 3 -enriched), and ammonia-bound two-flash illuminated (2F-NH 3 ; S 3 -enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S 1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn 4 CaO 5 cluster in the S 2 and S 3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.

Sulfonato-imino copper(ii) complexes: fast and general Chan-Evans-Lam coupling of amines and anilines.

PubMed

Hardouin Duparc, V; Schaper, F

2017-10-14

Sulfonato-imine copper complexes with either chloride or triflate counteranions were prepared in a one-step reaction followed by anion-exchange. They are highly active in Chan-Evans-Lam couplings under mild conditions with a variety of amines or anilines, in particular with sterically hindered substrates. No optimization of reaction conditions other than time and/or temperature is required.

Alpha 2-macroglobulin capture allows detection of mast cell chymase in serum and creates a reservoir of angiotensin II-generating activity.

PubMed

Raymond, Wilfred W; Su, Sharon; Makarova, Anastasia; Wilson, Todd M; Carter, Melody C; Metcalfe, Dean D; Caughey, George H

2009-05-01

Human chymase is a highly efficient angiotensin II-generating serine peptidase expressed by mast cells. When secreted from degranulating cells, it can interact with a variety of circulating antipeptidases, but is mostly captured by alpha(2)-macroglobulin, which sequesters peptidases in a cage-like structure that precludes interactions with large protein substrates and inhibitors, like serpins. The present work shows that alpha(2)-macroglobulin-bound chymase remains accessible to small substrates, including angiotensin I, with activity in serum that is stable with prolonged incubation. We used alpha(2)-macroglobulin capture to develop a sensitive, microtiter plate-based assay for serum chymase, assisted by a novel substrate synthesized based on results of combinatorial screening of peptide substrates. The substrate has low background hydrolysis in serum and is chymase-selective, with minimal cleavage by the chymotryptic peptidases cathepsin G and chymotrypsin. The assay detects activity in chymase-spiked serum with a threshold of approximately 1 pM (30 pg/ml), and reveals native chymase activity in serum of most subjects with systemic mastocytosis. alpha(2)-Macroglobulin-bound chymase generates angiotensin II in chymase-spiked serum, and it appears in native serum as chymostatin-inhibited activity, which can exceed activity of captopril-sensitive angiotensin-converting enzyme. These findings suggest that chymase bound to alpha(2)-macroglobulin is active, that the complex is an angiotensin-converting enzyme inhibitor-resistant reservoir of angiotensin II-generating activity, and that alpha(2)-macroglobulin capture may be exploited in assessing systemic release of secreted peptidases.

α2-Macroglobulin Capture Allows Detection of Mast Cell Chymase in Serum and Creates a Circulating Reservoir of Angiotensin II-generating Activity1

PubMed Central

Raymond, Wilfred W.; Su, Sharon; Makarova, Anastasia; Wilson, Todd M.; Carter, Melody C.; Metcalfe, Dean D.; Caughey, George H.

2009-01-01

Human chymase is a highly efficient angiotensin II-generating serine peptidase expressed by the MCTC subset of mast cells. When secreted from degranulating cells, it can interact with a variety of circulating anti-peptidases, but is mostly captured by α2-macroglobulin, which sequesters peptidases in a cage-like structure that precludes interactions with large protein substrates and inhibitors, like serpins. The present work shows that α2-macroglobulin-bound chymase remains accessible to small substrates, including angiotensin I, with activity in serum that is stable with prolonged incubation. We used α2-macroglobulin capture to develop a sensitive, microtiter plate-based assay for serum chymase, assisted by a novel substrate synthesized based on results of combinatorial screening of peptide substrates. The substrate has low background hydrolysis in serum and is chymase-selective, with minimal cleavage by the chymotryptic peptidases cathepsin G and chymotrypsin. The assay detects activity in chymase-spiked serum with a threshold of ~1 pM (30 pg/ml), and reveals native chymase activity in serum of most subjects with systemic mastocytosis. α2-Macroglobulin-bound chymase generates angiotensin II in chymase-spiked serum, and appears in native serum as chymostatin-inhibited activity, which can exceed activity of captopril-sensitive angiotensin converting enzyme. These findings suggest that chymase bound to α2-macroglobulin is active, that the circulating complex is an angiotensin-converting enzyme inhibitor-resistant reservoir of angiotensin II-generating activity, and that α2-macroglobulin capture may be exploited in assessing systemic release of secreted peptidases. PMID:19380825

Structures of transcription pre-initiation complex with TFIIH and Mediator.

PubMed

Schilbach, S; Hantsche, M; Tegunov, D; Dienemann, C; Wigge, C; Urlaub, H; Cramer, P

2017-11-09

For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the 'E-bridge' helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC-core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II.

Mitochondrial Dysfunction in Schizophrenia: Determination of Mitochondrial Respiratory Activity in a Two-Hit Mouse Model.

PubMed

Monpays, Cécile; Deslauriers, Jessica; Sarret, Philippe; Grignon, Sylvain

2016-08-01

Schizophrenia is a chronic mental illness in which mitochondrial dysfunction has been suggested. Our laboratory recently developed a juvenile murine two-hit model (THM) of schizophrenia based on the combination of gestational inflammation, followed by juvenile restraint stress. We previously reported that relevant behaviors and neurochemical disturbances, including oxidative stress, were reversed by the antioxidant lipoic acid (LA), thereby pointing to the central role played by oxidative abnormalities and prompting us to investigate mitochondrial function. Mitochondrial activity was determined with the MitoXpress® commercial kit in two schizophrenia-relevant regions (prefrontal cortex (PFC) and striatum). Measurements were performed in state 3, with substrates for complex I- and complex II-induced respiratory activity (IRA). We observed an increase in complex I IRA in the PFC and striatum in both sexes but an increase in complex II activity only in males. LA treatment prevented this increase only in complex II IRA in males. Expression levels of the different respiratory chain complexes, as well as fission/fusion proteins and protein carbonylation, were unchanged. In conclusion, our juvenile schizophrenia THM shows an increase in mitochondrial activity reversed by LA, specifically in complex II IRA in males. Further investigations are required to determine the mechanisms of these modifications.

Critical role of mitochondrial ROS is dependent on their site of production on the electron transport chain in ischemic heart.

PubMed

Madungwe, Ngonidzashe B; Zilberstein, Netanel F; Feng, Yansheng; Bopassa, Jean C

2016-01-01

Reactive oxygen species (ROS) generation has been implicated in many pathologies including ischemia/reperfusion (I/R) injury. This led to multiple studies on antioxidant therapies to treat cardiovascular diseases but paradoxically, results have so far been mixed as ROS production can be beneficial as a signaling mechanism and in cardiac protection via preconditioning interventions. We investigated whether the differential impact of increased ROS in injury as well as in protection could be explained by their site of production on the mitochondrial electron transport chain. Using amplex red to measure ROS production, we found that mitochondria isolated from hearts after I/R produced more ROS than non-ischemic when complex I substrate (glutamate/malate) was used. Interestingly, the substrates of complex II (succinate) and ubiquinone (sn-glycerol 3-phosphate, G3P) produced less ROS in mitochondria from I/R hearts compared to normal healthy hearts. The inhibitors of complex I (rotenone) and complex III (antimycin A) increased ROS production when glutamate/malate and G3P were used; in contrast, they reduced ROS production when the complex II substrate was used. Mitochondrial calcium retention capacity required to induce mitochondrial permeability transition pore (mPTP) opening was measured using calcium green fluorescence and was found to be higher when mitochondria were treated with G3P and succinate compared to glutamate/malate. Furthermore, Langendorff hearts treated with glutamate/malate exhibited reduced cardiac functional recovery and increased myocardial infarct size compared to hearts treated with G3P. Thus, ROS production by the stimulated respiratory chain complexes I and III has opposite roles: cardio-deleterious when produced in complex I and cardio-protective when produced in complex III. The mechanism of these ROS involves the inhibition of the mPTP opening, a key event in cell death following ischemia/reperfusion injury.

Storable Arylpalladium(II) Reagents for Alkene Labeling in Aqueous Media

PubMed Central

Simmons, Rebecca L.; Yu, Robert T.; Myers, Andrew G.

2011-01-01

We show that arylpalladium(II) reagents linked to biotin and indocyanine dye residues can be prepared by decarboxylative palladation of appropriately substituted electron-rich benzoic acid derivatives. When prepared under the conditions described, these organometallic intermediates are tolerant of air and water, can be stored for several months in solution in dimethylsulfoxide, and permit biotin- and indocyanine dye-labeling of functionally complex olefinic substrates in water by Heck-type coupling reactions. PMID:21888420

Exosites in the substrate specificity of blood coagulation reactions.

PubMed

Bock, P E; Panizzi, P; Verhamme, I M A

2007-07-01

The specificity of blood coagulation proteinases for substrate, inhibitor, and effector recognition is mediated by exosites on the surfaces of the catalytic domains, physically separated from the catalytic site. Some thrombin ligands bind specifically to either exosite I or II, while others engage both exosites. The involvement of different, overlapping constellations of exosite residues enables binding of structurally diverse ligands. The flexibility of the thrombin structure is central to the mechanism of complex formation and the specificity of exosite interactions. Encounter complex formation is driven by electrostatic ligand-exosite interactions, followed by conformational rearrangement to a stable complex. Exosites on some zymogens are in low affinity proexosite states and are expressed concomitant with catalytic site activation. The requirement for exosite expression controls the specificity of assembly of catalytic complexes on the coagulation pathway, such as the membrane-bound factor Xa*factor Va (prothrombinase) complex, and prevents premature assembly. Substrate recognition by prothrombinase involves a two-step mechanism with initial docking of prothrombin to exosites, followed by a conformational change to engage the FXa catalytic site. Prothrombin and its activation intermediates bind prothrombinase in two alternative conformations determined by the zymogen to proteinase transition that are hypothesized to involve prothrombin (pro)exosite I interactions with FVa, which underpin the sequential activation pathway. The role of exosites as the major source of substrate specificity has stimulated development of exosite-targeted anticoagulants for treatment of thrombosis.

Re-polarization of nuclear spins using selective SABRE-INEPT.

PubMed

Knecht, Stephan; Kiryutin, Alexey S; Yurkovskaya, Alexandra V; Ivanov, Konstantin L

2018-02-01

A method is proposed for significant improvement of NMR pulse sequences used in high-field SABRE (Signal Amplification By Reversible Exchange) experiments. SABRE makes use of spin order transfer from parahydrogen (pH 2 , the H 2 molecule in its singlet spin state) to a substrate in a transient organometallic Ir-based complex. The technique proposed here utilizes "re-polarization", i.e., multiple application of an NMR pulse sequence used for spin order transfer. During re-polarization only the form of the substrate, which is bound to the complex, is excited by selective NMR pulses and the resulting polarization is transferred to the free substrate via chemical exchange. Owing to the fact that (i) only a small fraction of the substrate molecules is in the bound form and (ii) spin relaxation of the free substrate is slow, the re-polarization scheme provides greatly improved NMR signal enhancement, ε. For instance, when pyridine is used as a substrate, single use of the SABRE-INEPT sequence provides ε≈260 for 15 N nuclei, whereas SABRE-INEPT with re-polarization yields ε>2000. We anticipate that the proposed method is useful for achieving maximal NMR enhancement with spin hyperpolarization techniques. Copyright © 2017 Elsevier Inc. All rights reserved.

Re-polarization of nuclear spins using selective SABRE-INEPT

NASA Astrophysics Data System (ADS)

Knecht, Stephan; Kiryutin, Alexey S.; Yurkovskaya, Alexandra V.; Ivanov, Konstantin L.

2018-02-01

A method is proposed for significant improvement of NMR pulse sequences used in high-field SABRE (Signal Amplification By Reversible Exchange) experiments. SABRE makes use of spin order transfer from parahydrogen (pH2, the H2 molecule in its singlet spin state) to a substrate in a transient organometallic Ir-based complex. The technique proposed here utilizes "re-polarization", i.e., multiple application of an NMR pulse sequence used for spin order transfer. During re-polarization only the form of the substrate, which is bound to the complex, is excited by selective NMR pulses and the resulting polarization is transferred to the free substrate via chemical exchange. Owing to the fact that (i) only a small fraction of the substrate molecules is in the bound form and (ii) spin relaxation of the free substrate is slow, the re-polarization scheme provides greatly improved NMR signal enhancement, ε . For instance, when pyridine is used as a substrate, single use of the SABRE-INEPT sequence provides ε ≈ 260 for 15N nuclei, whereas SABRE-INEPT with re-polarization yields ε > 2000 . We anticipate that the proposed method is useful for achieving maximal NMR enhancement with spin hyperpolarization techniques.

Mn(II) Oxidation by the Multicopper Oxidase Complex Mnx: A Binuclear Activation Mechanism.

PubMed

Soldatova, Alexandra V; Tao, Lizhi; Romano, Christine A; Stich, Troy A; Casey, William H; Britt, R David; Tebo, Bradley M; Spiro, Thomas G

2017-08-23

The bacterial protein complex Mnx contains a multicopper oxidase (MCO) MnxG that, unusually, catalyzes the two-electron oxidation of Mn(II) to MnO 2 biomineral, via a Mn(III) intermediate. Although Mn(III)/Mn(II) and Mn(IV)/Mn(III) reduction potentials are expected to be high, we find a low reduction potential, 0.38 V (vs Normal Hydrogen Electrode, pH 7.8), for the MnxG type 1 Cu 2+ , the electron acceptor. Indeed the type 1 Cu 2+ is not reduced by Mn(II) in the absence of molecular oxygen, indicating that substrate oxidation requires an activation step. We have investigated the enzyme mechanism via electronic absorption spectroscopy, using chemometric analysis to separate enzyme-catalyzed MnO 2 formation from MnO 2 nanoparticle aging. The nanoparticle aging time course is characteristic of nucleation and particle growth; rates for these processes followed expected dependencies on Mn(II) concentration and temperature, but exhibited different pH optima. The enzymatic time course is sigmoidal, signaling an activation step, prior to turnover. The Mn(II) concentration and pH dependence of a preceding lag phase indicates weak Mn(II) binding. The activation step is enabled by a pK a > 8.6 deprotonation, which is assigned to Mn(II)-bound H 2 O; it induces a conformation change (consistent with a high activation energy, 106 kJ/mol) that increases Mn(II) affinity. Mnx activation is proposed to decrease the Mn(III/II) reduction potential below that of type 1 Cu(II/I) by formation of a hydroxide-bridged binuclear complex, Mn(II)(μ-OH)Mn(II), at the substrate site. Turnover is found to depend cooperatively on two Mn(II) and is enabled by a pK a 7.6 double deprotonation. It is proposed that turnover produces a Mn(III)(μ-OH) 2 Mn(III) intermediate that proceeds to the enzyme product, likely Mn(IV)(μ-O) 2 Mn(IV) or an oligomer, which subsequently nucleates MnO 2 nanoparticles. We conclude that Mnx exploits manganese polynuclear chemistry in order to facilitate an otherwise difficult oxidation reaction, as well as biomineralization. The mechanism of the Mn(III/IV) conversion step is elucidated in an accompanying paper .

Synthesis, characterization, computational studies, antimicrobial activities and carbonic anhydrase inhibitor effects of 2-hydroxy acetophenone-N-methyl p-toluenesulfonylhydrazone and its Co(II), Pd(II), Pt(II) complexes

NASA Astrophysics Data System (ADS)

Özbek, Neslihan; Alyar, Saliha; Memmi, Burcu Koçak; Gündüzalp, Ayla Balaban; Bahçeci, Zafer; Alyar, Hamit

2017-01-01

2-Hydroxyacetophenone-N-methyl p-toluenesulfonylhydrazone (afptsmh) derived from p-toluenesulfonicacid-1-methylhydrazide (ptsmh) and its Co(II), Pd(II), Pt(II) complexes were synthesized for the first time. Synthesized compounds were characterized by spectroscopic methods (FT-IR, 1Hsbnd 13C NMR, LC-MS, UV-vis), magnetic susceptibility and conductivity measurements. 1H and 13C shielding tensors for crystal structure of ligand were calculated with GIAO/DFT/B3LYP/6-311++G(d,p) methods in CDCl3. The vibrational band assignments were performed at B3LYP/6-311++G(d,p) theory level combined with scaled quantum mechanics force field (SQMFF) methodology. The antibacterial activities of synthesized compounds were studied against some Gram positive and Gram negative bacteria by using microdilution and disc diffusion methods. In vitro enzyme inhibitory effects of the compounds were measured by UV-vis spectrophotometer. The enzyme activities against human carbonic anhydrase II (hCA II) were evaluated as IC50 (the half maximal inhibitory concentration) values. It was found that afptsmh and its metal complexes have inhibitory effects on hCA II isoenzyme. General esterase activities were determined using alpha and beta naphtyl acetate substrates (α- and β-NAs) of Drosophila melanogaster (D. melanogaster). Activity results show that afptsmh does not strongly affect the bacteria strains and also shows poor inhibitory activity against hCAII isoenzyme whereas all complexes posses higher biological activities.

Inhibition Kinetics and Emodin Cocrystal Structure of a Type II Polyketide Ketoreductase†,‡

PubMed Central

Korman, Tyler Paz; Tan, Yuhong; Wong, Justin; Luo, Rui; Tsai, Shiou-Chuan

2008-01-01

Type II polyketides are a class of natural products that include pharmaceutically important aromatic compounds such as the antibiotic tetracycline and antitumor compound doxorubicin. The type II polyketide synthase (PKS) is a complex consisting of 5–10 standalone domains homologous to fatty acid synthase (FAS). Polyketide ketoreductase (KR) provides regio- and stereochemical diversity during the reduction. How the type II polyketide KR specifically reduces only the C9 carbonyl group is not well understood. The cocrystal structures of actinorhodin polyketide ketoreductase (actKR) bound with NADPH or NADP+ and the inhibitor emodin were solved with the wild type and P94L mutant of actKR, revealing the first observation of a bent p-quinone in an enzyme active site. Molecular dynamics simulation help explain the origin of the bent geometry. Extensive screening for in vitro substrates shows that unlike FAS KR, the actKR prefers bicyclic substrates. Inhibition kinetics indicate that actKR follows an ordered Bi Bi mechanism. Together with docking simulations that identified a potential phosphopantetheine binding groove, the structural and functional studies reveal that the C9 specificity is a result of active site geometry and substrate ring constraints. The results lay the foundation for the design of novel aromatic polyketide natural products with different reduction patterns. PMID:18205400

Inhibition Kinetics And Emodin Cocrystal Structure of a Type II Polyketide Ketoreductase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Korman, T.P.; Tan, Y.-H.; Wong, J.

Type II polyketides are a class of natural products that include pharmaceutically important aromatic compounds such as the antibiotic tetracycline and antitumor compound doxorubicin. The type II polyketide synthase (PKS) is a complex consisting of 5-10 standalone domains homologous to fatty acid synthase (FAS). Polyketide ketoreductase (KR) provides regio- and stereochemical diversity during the reduction. How the type II polyketide KR specifically reduces only the C9 carbonyl group is not well understood. The cocrystal structures of actinorhodin polyketide ketoreductase (actKR) bound with NADPH or NADP{sup +} and the inhibitor emodin were solved with the wild type and P94L mutant ofmore » actKR, revealing the first observation of a bent p-quinone in an enzyme active site. Molecular dynamics simulation help explain the origin of the bent geometry. Extensive screening for in vitro substrates shows that unlike FAS KR, the actKR prefers bicyclic substrates. Inhibition kinetics indicate that actKR follows an ordered Bi Bi mechanism. Together with docking simulations that identified a potential phosphopantetheine binding groove, the structural and functional studies reveal that the C9 specificity is a result of active site geometry and substrate ring constraints. The results lay the foundation for the design of novel aromatic polyketide natural products with different reduction patterns.« less

Novel Substrate-Based Inhibitors of Human Glutamate Carboxypeptidase II with Enhanced Lipophilicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plechanovová, Anna; Byun, Youngjoo; Alquicer, Glenda

2012-10-09

Virtually all low molecular weight inhibitors of human glutamate carboxypeptidase II (GCPII) are highly polar compounds that have limited use in settings where more lipophilic molecules are desired. Here we report the identification and characterization of GCPII inhibitors with enhanced liphophilicity that are derived from a series of newly identified dipeptidic GCPII substrates featuring nonpolar aliphatic side chains at the C-terminus. To analyze the interactions governing the substrate recognition by GCPII, we determined crystal structures of the inactive GCPII(E424A) mutant in complex with selected dipeptides and complemented the structural data with quantum mechanics/molecular mechanics calculations. Results reveal the importance ofmore » nonpolar interactions governing GCPII affinity toward novel substrates as well as formerly unnoticed plasticity of the S1' specificity pocket. On the basis of those data, we designed, synthesized, and evaluated a series of novel GCPII inhibitors with enhanced lipophilicity, with the best candidates having low nanomolar inhibition constants and clogD > -0.3. Our findings offer new insights into the design of more lipophilic inhibitors targeting GCPII.« less

Radiochemical studies of 99mTc complexes of modified cysteine ligands and bifunctional chelating agents.

PubMed

Pillai, M R; Kothari, K; Banerjee, S; Samuel, G; Suresh, M; Sarma, H D; Jurisson, S

1999-07-01

The synthesis of four novel ligands using the amino-acid cysteine and its ethyl carboxylate derivative is described. The synthetic method involves a two-step procedure, wherein the intermediate Schiff base formed by the condensation of the amino group of the cysteine substrate and salicylaldehyde is reduced to give the target ligands. The intermediates and the final products were characterized by high resolution nuclear magnetic resonance spectroscopy. Complexation studies of the ligands with 99mTc were optimized using stannous tartrate as the reducing agent under varying reaction conditions. The complexes were characterized using standard quality control techniques such as thin layer chromatography, paper electrophoresis, and paper chromatography. Lipophilicities of the complexes were estimated by solvent extraction into chloroform. Substantial changes in net charge and lipophilicity of the 99mTc complexes were observed on substituting the carboxylic acid functionality in ligands I and II with the ethyl carboxylate groups (ligands II and IV). All the ligands formed 99mTc complexes in high yield. Whereas the complexes with ligands I and II were observed to be hydrophilic in nature and not extractable into CHCl3, ligands III and IV resulted in neutral and lipophilic 99mTc complexes. The 99mTc complex with ligand II was not stable and on storage formed a hydrophilic and nonextractable species. The biodistribution of the complexes of ligands I and II showed that they cleared predominantly through the kidneys, whereas the complexes with ligands III and IV were excreted primarily through the hepatobiliary system. No significant brain uptake was observed with the 99mTc complexes with ligands III and IV despite their favorable properties of neutrality, lipophilicity, and conversion into a hydrophilic species. These ligands offer potential for use as bifunctional chelating agents.

What does the Sr-substituted 2.1 Å resolution crystal structure of photosystem II reveal about the water oxidation mechanism?

PubMed

Terrett, Richard; Petrie, Simon; Pace, Ron J; Stranger, Robert

2014-03-25

A density functional study of the Sr-substituted photosystem II water oxidising complex demonstrates that its recent X-ray crystal structure is consistent with a (Mn(III))4 oxidation state pattern, and with a Sr-bound hydroxide ion. The Sr-water-hydroxide interactions rationalize differences in the exchange rates of substrate water and kinetics of dioxygen bond formation relative to the Ca-containing structure.

D-Amino acid oxidase bio-functionalized platforms: Toward an enhanced enzymatic bio-activity

NASA Astrophysics Data System (ADS)

Herrera, Elisa; Valdez Taubas, Javier; Giacomelli, Carla E.

2015-11-01

The purpose of this work is to study the adsorption process and surface bio-activity of His-tagged D-amino acid oxidase (DAAO) from Rhodotorula gracilis (His6-RgDAAO) as the first step for the development of an electrochemical bio-functionalized platform. With such a purpose this work comprises: (a) the His6-RgDAAO bio-activity in solution determined by amperometry, (b) the adsorption mechanism of His6-RgDAAO on bare gold and carboxylated modified substrates in the absence (substrate/COO-) and presence of Ni(II) (substrate/COO- + Ni(II)) determined by reflectometry, and (c) the bio-activity of the His6-RgDAAO bio-functionalized platforms determined by amperometry. Comparing the adsorption behavior and bio-activity of His6-RgDAAO on these different solid substrates allows understanding the contribution of the diverse interactions responsible for the platform performance. His6-RgDAAO enzymatic performance in solution is highly improved when compared to the previously used pig kidney (pk) DAAO. His6-RgDAAO exhibits an amperometrically detectable bio-activity at concentrations as low as those expected on a bio-functional platform; hence, it is a viable bio-recognition element of D-amino acids to be coupled to electrochemical platforms. Moreover, His6-RgDAAO bio-functionalized platforms exhibit a higher surface activity than pkDAAO physically adsorbed on gold. The platform built on Ni(II) modified substrates present enhanced bio-activity because the surface complexes histidine-Ni(II) provide with site-oriented, native-like enzymes. The adsorption mechanism responsible of the excellent performance of the bio-functionalized platform takes place in two steps involving electrostatic and bio-affinity interactions whose prevalence depends on the degree of surface coverage.

Analysis of the interaction mode between hyperthermophilic archaeal group II chaperonin and prefoldin using a platform of chaperonin oligomers of various subunit arrangements.

PubMed

Sahlan, Muhamad; Kanzaki, Taro; Zako, Tamotsu; Maeda, Mizuo; Yohda, Masafumi

2010-09-01

Prefoldin is a co-chaperone that captures an unfolded protein substrate and transfers it to the group II chaperonin for completion of protein folding. Group II chaperonin of a hyperthermophilic archaeon, Thermococcus strain KS-1, interacts and cooperates with archaeal prefoldins. Although the interaction sites within chaperonin and prefoldin have been analyzed, the binding mode between jellyfish-like hexameric prefoldin and the double octameric ring group II chaperonin remains unclear. As prefoldin binds the chaperonin beta subunit more strongly than the alpha subunit, we analyzed the binding mode between prefoldin and chaperonin in the context of Thermococcus group II chaperonin complexes of various subunit compositions and arrangements. The oligomers exhibited various affinities for prefoldins according to the number and order of subunits. Binding affinity increased with the number of Cpnbeta subunits. Interestingly, chaperonin complexes containing two beta subunits adjacently exhibited stronger affinities than other chaperonin complexes containing the same number of beta subunits. The result suggests that all four beta tentacles of prefoldin interact with the helical protrusions of CPN in the PFD-CPN complex as the previously proposed model that two adjacent PFD beta subunits seem to interact with two CPN adjacent subunits. Copyright © 2010 Elsevier B.V. All rights reserved.

Indirect electroreductive cyclization and electrohydrocyclization using catalytic reduced nickel(II) salen.

PubMed

Miranda, James A; Wade, Carolyn J; Little, R Daniel

2005-09-30

[Chemical reaction: See text] We describe efforts to achieve the electroreductive cyclization (ERC) and the electrohydrocyclization (EHC) reactions using catalytic nickel(II) salen as a mediator. While nickel(II) salen proved effective, the analogous cobalt complex as well as nickel(II) cyclam were not. The transformations were achieved in yields ranging from 60 to 94% using either a mercury pool or an environmentally preferable reticulated vitreous carbon (RVC) cathode. These examples represent the first instances wherein a nickel salen complex has been used in this manner. Clear differences between the voltammetric behavior of the ERC and EHC substrates were observed. The bisenoate 14, for example, displays a substantially larger catalytic current. When the structurally modified mediator 31 was used, the electron-transfer pathway shuts down. Instead, the reduced form of 31 behaves as an electrogenerated base, leading to the formation of the intramolecular Michael adduct 23. Presumably, the methyl groups of the modified ligand diminish the ability of the reduced form of the complex to serve as a nucleophile but not as a base. Aldehyde 23 was also characterized as a side product of the nickel(II) salen mediated electroreductive cyclization of 11. Given that it is absent from nonmediated processes, its formation is linked to the presence of the mediator. To account for the results, we favor the existence of a mechanistic continuum involving an equilibrium between nickel(II) salen (15) and two reduced forms, one being the metal-centered species 16, the other being a ligand-centered species 17. We postulate that one form may be more prominently involved with the chemistry than another, depending upon the electronic properties/requirements of the substrate, and suggest that the equilibrium will shift to accommodate the need. Thus, for a hard electrophile like an alkyl halide, the properties of 16 ought to dominate, whereas 17 ought to predominate as the reactive species accounting for the chemistry described herein since it properly matches a soft ligand-centered nucleophile with a soft electron deficient alkene.

The coupling of carbon dioxide and epoxides by phenanthroline derivatives containing different Cu(II) complexes as catalyst

NASA Astrophysics Data System (ADS)

Kilic, Ahmet; Palali, Ahmet Arif; Durgun, Mustafa; Tasci, Zeynep; Ulusoy, Mahmut

2013-09-01

A series of the mononuclear Cu(II) metal complexes containing the ligand Bdppz [(9a,13a-dihydro-4,5,9,14-tetraaza-benzo[b]triphenylene-11-yl)-phenyl-methanone] (L1) and Aqphen [(12,17-dihydronaphthol[2,3-h]dipyrido[3,2-a:2‧,3‧-c]-phenazine-12,17-dione)] (L2) were synthesized and used as catalyst for the coupling of carbon dioxide (CO2) and liquid epoxide which served as both reactant and solvent. Dimethylamino pyridine (DMAP) was used as co-catalyst. The yields of epoxides to corresponding cyclic carbonates were determined by comparing the ratio of product to substrate in the 1H NMR spectrum of an aliquot of the reaction mixture. The mononuclear Cu(II) complexes of these ligands were synthesized by treating an ethanol solvent of the appropriate ligand with a different molar amount of CuCl2·2H2O. The Cu(II) complexes were characterized by FT-IR, UV-Vis, elemental analysis, melting point analysis, mass spectra, molar conductivity measurements and magnetic susceptibility techniques. The reaction of the Bdppz and Aqphen ligands in a 1:1, 1:2 or 1:3 mole ratio with CuCl2·2H2O afforded ionic Cu(II) complexes in the presence of Et3N.

A photofunctional bottom-up bis(dipyrrinato)zinc(II) complex nanosheet

PubMed Central

Sakamoto, Ryota; Hoshiko, Ken; Liu, Qian; Yagi, Toshiki; Nagayama, Tatsuhiro; Kusaka, Shinpei; Tsuchiya, Mizuho; Kitagawa, Yasutaka; Wong, Wai-Yeung; Nishihara, Hiroshi

2015-01-01

Two-dimensional polymeric nanosheets have recently gained much attention, particularly top-down nanosheets such as graphene and metal chalcogenides originating from bulk-layered mother materials. Although molecule-based bottom-up nanosheets manufactured directly from molecular components can exhibit greater structural diversity than top-down nanosheets, the bottom-up nanosheets reported thus far lack useful functionalities. Here we show the design and synthesis of a bottom-up nanosheet featuring a photoactive bis(dipyrrinato)zinc(II) complex motif. A liquid/liquid interfacial synthesis between a three-way dipyrrin ligand and zinc(II) ions results in a multi-layer nanosheet, whereas an air/liquid interfacial reaction produces a single-layer or few-layer nanosheet with domain sizes of >10 μm on one side. The bis(dipyrrinato)zinc(II) metal complex nanosheet is easy to deposit on various substrates using the Langmuir–Schäfer process. The nanosheet deposited on a transparent SnO2 electrode functions as a photoanode in a photoelectric conversion system, and is thus the first photofunctional bottom-up nanosheet. PMID:25831973

An Artificial Enzyme Made by Covalent Grafting of an Fe(II) Complex into β-Lactoglobulin: Molecular Chemistry, Oxidation Catalysis, and Reaction-Intermediate Monitoring in a Protein.

PubMed

Buron, Charlotte; Sénéchal-David, Katell; Ricoux, Rémy; Le Caër, Jean-Pierre; Guérineau, Vincent; Méjanelle, Philippe; Guillot, Régis; Herrero, Christian; Mahy, Jean-Pierre; Banse, Frédéric

2015-08-17

An artificial metalloenzyme based on the covalent grafting of a nonheme Fe(II) polyazadentate complex into bovine β-lactoglobulin has been prepared and characterized by using various spectroscopic techniques. Attachment of the Fe(II) catalyst to the protein scaffold is shown to occur specifically at Cys121. In addition, spectrophotometric titration with cyanide ions based on the spin-state conversion of the initial high spin (S=2) Fe(II) complex into a low spin (S=0) one allows qualitative and quantitative characterization of the metal center's first coordination sphere. This biohybrid catalyst activates hydrogen peroxide to oxidize thioanisole into phenylmethylsulfoxide as the sole product with an enantiomeric excess of up to 20 %. Investigation of the reaction between the biohybrid system and H2 O2 reveals the generation of a high spin (S=5/2) Fe(III) (η(2) -O2 ) intermediate, which is proposed to be responsible for the catalytic sulfoxidation of the substrate. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure and Function of p97 and Pex1/6 Type II AAA+ Complexes.

PubMed

Saffert, Paul; Enenkel, Cordula; Wendler, Petra

2017-01-01

Protein complexes of the Type II AAA+ (ATPases associated with diverse cellular activities) family are typically hexamers of 80-150 kDa protomers that harbor two AAA+ ATPase domains. They form double ring assemblies flanked by associated domains, which can be N-terminal, intercalated or C-terminal to the ATPase domains. Most prominent members of this family include NSF (N-ethyl-maleimide sensitive factor), p97/VCP (valosin-containing protein), the Pex1/Pex6 complex and Hsp104 in eukaryotes and ClpB in bacteria. Tremendous efforts have been undertaken to understand the conformational dynamics of protein remodeling type II AAA+ complexes. A uniform mode of action has not been derived from these works. This review focuses on p97/VCP and the Pex1/6 complex, which both structurally remodel ubiquitinated substrate proteins. P97/VCP plays a role in many processes, including ER- associated protein degradation, and the Pex1/Pex6 complex dislocates and recycles the transport receptor Pex5 from the peroxisomal membrane during peroxisomal protein import. We give an introduction into existing knowledge about the biochemical and cellular activities of the complexes before discussing structural information. We particularly emphasize recent electron microscopy structures of the two AAA+ complexes and summarize their structural differences.

Annexin II is associated with mRNAs which may constitute a distinct subpopulation.

PubMed Central

Vedeler, A; Hollås, H

2000-01-01

Protein-mRNA interactions affect mRNA transport, anchorage, stability and translatability in the cytoplasm. During the purification of three subpopulations of polysomes, it was observed that a 36-kDa protein, identified as annexin II, is associated with only one specific population of polysomes, namely cytoskeleton-associated polysomes. This association appears to be calcium-dependent since it was sensitive to EGTA and could be reconstituted in vitro. UV irradiation resulted in partial, EGTA-resistant cross-linking of annexin II to the polysomes. Binding of (32)P-labelled total RNA to proteins isolated from the cytoskeleton-bound polysomes on a NorthWestern blot resulted in a radioactive band having the same mobility as annexin II and, most importantly, purified native annexin II immobilized on nitrocellulose specifically binds mRNA. The mRNA population isolated from cytoskeleton-bound polysomes binds to annexin II with the highest affinity as compared with those isolated from free or membrane-bound polysomes. Interestingly, the annexin II complex, isolated from porcine small intestinal microvilli was a far better substrate for mRNA binding than the complex derived from transformed Krebs II ascites cells. When cytoskeleton-associated polysomes were split into 60 S and 40 S ribosomal subunits, and a peak containing mRNA complexes, annexin II fractionated with the mRNAs. Finally, using affinity purification of mRNA on poly(A)(+)-coupled magnetic beads, annexin II was only detected in association with messenger ribonucleoproteins (mRNPs) present in the cytoskeletal fraction (non-polysomal mRNPs). These results, derived from both in vitro experiments and cell fractionation, suggest that annexin II binds directly to the RNA moiety of mRNP complexes containing a specific population of mRNAs. PMID:10839987

Partial Reconstruction of Flavonoid and Isoflavonoid Biosynthesis in Yeast Using Soybean Type I and Type II Chalcone Isomerases1[w

PubMed Central

Ralston, Lyle; Subramanian, Senthil; Matsuno, Michiyo; Yu, Oliver

2005-01-01

Flavonoids and isoflavonoids are major plant secondary metabolites that mediate diverse biological functions and exert significant ecological impacts. These compounds play important roles in many essential physiological processes. In addition, flavonoids and isoflavonoids have direct but complex effects on human health, ranging from reducing cholesterol levels and preventing certain cancers to improving women's health. In this study, we cloned and functionally characterized five soybean (Glycine max) chalcone isomerases (CHIs), key enzymes in the phenylpropanoid pathway that produces flavonoids and isoflavonoids. Gene expression and kinetics analysis suggest that the soybean type I CHI, which uses naringenin chalcone as substrate, is coordinately regulated with other flavonoid-specific genes, while the type II CHIs, which use a variety of chalcone substrates, are coordinately regulated with an isoflavonoid-specific gene and specifically activated by nodulation signals. Furthermore, we found that some of the newly identified soybean CHIs do not require the 4′-hydroxy moiety on the substrate for high enzyme activity. We then engineered yeast (Saccharomyces cerevisiae) to produce flavonoid and isoflavonoid compounds. When one of the type II CHIs was coexpressed with an isoflavone synthase, the enzyme catalyzing the first committed step of isoflavonoid biosynthesis, various chalcone substrates added to the culture media were converted to an assortment of isoflavanones and isoflavones. We also reconstructed the flavonoid pathway by coexpressing CHI with either flavanone 3β-hydroxylase or flavone synthase II. The in vivo reconstruction of the flavonoid and isoflavonoid pathways in yeast provides a unique platform to study enzyme interactions and metabolic flux. PMID:15778463

Structure of photosystem II and substrate binding at room temperature

PubMed Central

Gul, Sheraz; Fuller, Franklin; Koroidov, Sergey; Brewster, Aaron S.; Tran, Rosalie; Alonso-Mori, Roberto; Kroll, Thomas; Michels-Clark, Tara; Laksmono, Hartawan; Sierra, Raymond G.; Stan, Claudiu A.; Hussein, Rana; Zhang, Miao; Douthit, Lacey; Kubin, Markus; de Lichtenberg, Casper; Long Vo, Pham; Nilsson, Håkan; Cheah, Mun Hon; Shevela, Dmitriy; Saracini, Claudio; Bean, Mackenzie A.; Seuffert, Ina; Sokaras, Dimosthenis; Weng, Tsu-Chien; Pastor, Ernest; Weninger, Clemens; Fransson, Thomas; Lassalle, Louise; Bräuer, Philipp; Aller, Pierre; Docker, Peter T.; Andi, Babak; Orville, Allen M.; Glownia, James M.; Nelson, Silke; Sikorski, Marcin; Zhu, Diling; Hunter, Mark S.; Lane, Thomas J.; Aquila, Andy; Koglin, Jason E.; Robinson, Joseph; Liang, Mengning; Boutet, Sébastien; Lyubimov, Artem Y.; Uervirojnangkoorn, Monarin; Moriarty, Nigel W.; Liebschner, Dorothee; Afonine, Pavel V.; Waterman, David G.; Evans, Gwyndaf; Wernet, Philippe; Dobbek, Holger; Weis, William I.; Brunger, Axel T.; Zwart, Petrus H.; Adams, Paul D.; Zouni, Athina; Messinger, Johannes; Bergmann, Uwe; Sauter, Nicholas K.; Kern, Jan; Yachandra, Vittal K.; Yano, Junko

2016-01-01

Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment-protein complex, couples the one-electron photochemistry at the reaction center with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC) (Fig. 1a, Extended Data Fig. 1). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4)1, where S1 is the dark stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution2,3. A detailed understanding of the O-O bond formation mechanism remains a challenge, and elucidating the structures of the OEC in the different S-states, as well as the binding of the two substrate waters to the catalytic site4-6, is a prerequisite for this purpose. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage free, room temperature (RT) structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å structure of PS II7 at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, RT measurements are required to study the structural landscape of proteins under functional conditions8,9, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analog, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states10. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site10-13. Thus, this approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms. PMID:27871088

Mn(II) Oxidation by the Multicopper Oxidase Complex Mnx: A Coordinated Two-Stage Mn(II)/(III) and Mn(III)/(IV) Mechanism.

PubMed

Soldatova, Alexandra V; Romano, Christine A; Tao, Lizhi; Stich, Troy A; Casey, William H; Britt, R David; Tebo, Bradley M; Spiro, Thomas G

2017-08-23

The bacterial manganese oxidase MnxG of the Mnx protein complex is unique among multicopper oxidases (MCOs) in carrying out a two-electron metal oxidation, converting Mn(II) to MnO 2 nanoparticles. The reaction occurs in two stages: Mn(II) → Mn(III) and Mn(III) → MnO 2 . In a companion study , we show that the electron transfer from Mn(II) to the low-potential type 1 Cu of MnxG requires an activation step, likely forming a hydroxide bridge at a dinuclear Mn(II) site. Here we study the second oxidation step, using pyrophosphate (PP) as a Mn(III) trap. PP chelates Mn(III) produced by the enzyme and subsequently allows it to become a substrate for the second stage of the reaction. EPR spectroscopy confirms the presence of Mn(III) bound to the enzyme. The Mn(III) oxidation step does not involve direct electron transfer to the enzyme from Mn(III), which is shown by kinetic measurements to be excluded from the Mn(II) binding site. Instead, Mn(III) is proposed to disproportionate at an adjacent polynuclear site, thereby allowing indirect oxidation to Mn(IV) and recycling of Mn(II). PP plays a multifaceted role, slowing the reaction by complexing both Mn(II) and Mn(III) in solution, and also inhibiting catalysis, likely through binding at or near the active site. An overall mechanism for Mnx-catalyzed MnO 2 production from Mn(II) is presented.

Single Turnover Kinetics of Tryptophan Hydroxylase: Evidence for a New Intermediate in the Reaction of the Aromatic Amino Acid Hydroxylases

PubMed Central

Pavon, Jorge Alex; Eser, Bekir; Huynh, Michaela T.; Fitzpatrick, Paul F.

2010-01-01

Tryptophan hydroxylase (TrpH) uses a non-heme mononuclear iron center to catalyze the tetrahydropterin-dependent hydroxylation of tryptophan to 5-hydroxytryptophan. The reactions of the TrpH·Fe(II), TrpH·Fe(II)·tryptophan, TrpH·Fe(II)·6MePH4·tryptophan, and TrpH·Fe(II)·6MePH4·phenylalanine complexes with O2 were monitored by stopped-flow absorbance spectroscopy and rapid quench methods. The second-order rate constant for the oxidation of TrpH·Fe(II) has a value of 104 M−1s−1 irrespective of the presence of tryptophan. Stopped-flow absorbance analyses of the reaction of the TrpH·Fe(II)·6MePH4·tryptophan complex with oxygen are consistent with the initial step being reversible binding of oxygen, followed by the formation with a rate constant of 65 s−1 of an intermediate I that has maximal absorbance at 420 nm. The rate constant for decay of I, 4.4 s−1, matches that for formation of the 4a-hydroxypterin product monitored at 248 nm. Chemical-quench analyses show that 5-hydroxytryptophan forms with a rate constant of 1.3 s−1, and that overall turnover is limited by a subsequent slow step, presumably product release, with a rate constant of 0.2 s−1. All of the data with tryptophan as substrate can be described by a five-step mechanism. In contrast, with phenylalanine as substrate, the reaction can be described by three steps: a second-order reaction with oxygen to form I, decay of I as tyrosine forms, and slow product release. PMID:20687613

Prefoldin, a jellyfish-like molecular chaperone: functional cooperation with a group II chaperonin and beyond.

PubMed

Sahlan, Muhamad; Zako, Tamotsu; Yohda, Masafumi

2018-04-01

Prefoldin is a hexameric molecular chaperone found in the cytosol of archaea and eukaryotes. Its hexameric complex is built from two related classes of subunits and has the appearance of a jellyfish: its body consists of a double beta-barrel assembly with six long tentacle-like coiled coils protruding from it. Using the tentacles, prefoldin captures an unfolded protein substrate and transfers it to a group II chaperonin. The prefoldin-group II chaperonin system is thought to be important for the folding of newly synthesized proteins and for their maintenance, or proteostasis, in the cytosol. Based on structural information of archaeal prefoldins, the mechanisms of substrate recognition and prefoldin-chaperonin cooperation have been investigated. In contrast, the role and mechanism of eukaryotic PFDs remain unknown. Recent studies have shown that prefoldin plays an important role in proteostasis and is involved in various diseases. In this paper, we review a series of studies on the molecular mechanisms of archaeal prefoldins and introduce recent findings about eukaryotic prefoldin.

The reaction mechanism of methyl-coenzyme M reductase: How an enzyme enforces strict binding order

DOE PAGES

Wongnate, Thanyaporn; Ragsdale, Stephen W.

2015-02-17

Methyl-coenzyme M reductase (MCR) is a nickel tetrahydrocorphinoid (coenzyme F430) containing enzyme involved in the biological synthesis and anaerobic oxidation of methane. MCR catalyzes the conversion of methyl-2-mercaptoethanesulfonate (methyl-SCoM) and N-7-mercaptoheptanoylthreonine phosphate (CoB 7SH) to CH 4 and the mixed disulfide CoBS-SCoM. In this study, the reaction of MCR from Methanothermobacter marburgensis, with its native substrates was investigated using static binding, chemical quench, and stopped-flow techniques. Rate constants were measured for each step in this strictly ordered ternary complex catalytic mechanism. Surprisingly, in the absence of the other substrate, MCR can bind either substrate; however, only one binary complex (MCR·methyl-SCoM)more » is productive whereas the other (MCR·CoB 7SH) is inhibitory. Moreover, the kinetic data demonstrate that binding of methyl-SCoM to the inhibitory MCR·CoB 7SH complex is highly disfavored ( Kd = 56 mM). However, binding of CoB 7SH to the productive MCR·methyl-SCoM complex to form the active ternary complex (CoB 7SH·MCR(Ni I)·CH 3SCoM) is highly favored ( Kd = 79 μM). Only then can the chemical reaction occur ( kobs = 20 s -1 at 25 °C), leading to rapid formation and dissociation of CH 4 leaving the binary product complex (MCR(Ni II)·CoB 7S -·SCoM), which undergoes electron transfer to regenerate Ni(I) and the final product CoBS-SCoM. In conclusion, this first rapid kinetics study of MCR with its natural substrates describes how an enzyme can enforce a strictly ordered ternary complex mechanism and serves as a template for identification of the reaction intermediates.« less

Investigating the Impact of Asp181 Point Mutations on Interactions between PTP1B and Phosphotyrosine Substrate

NASA Astrophysics Data System (ADS)

Liu, Mengyuan; Wang, Lushan; Sun, Xun; Zhao, Xian

2014-05-01

Protein tyrosine phosphatase 1B (PTP1B) is a key negative regulator of insulin and leptin signaling, which suggests that it is an attractive therapeutic target in type II diabetes and obesity. The aim of this research is to explore residues which interact with phosphotyrosine substrate can be affected by D181 point mutations and lead to increased substrate binding. To achieve this goal, molecular dynamics simulations were performed on wild type (WT) and two mutated PTP1B/substrate complexes. The cross-correlation and principal component analyses show that point mutations can affect the motions of some residues in the active site of PTP1B. Moreover, the hydrogen bond and energy decomposition analyses indicate that apart from residue 181, point mutations have influence on the interactions of substrate with several residues in the active site of PTP1B.

Substrate water exchange in photosystem II depends on the peripheral proteins.

PubMed

Hillier, W; Hendry, G; Burnap, R L; Wydrzynski, T

2001-12-14

The (18)O exchange rates for the substrate water bound in the S(3) state were determined in different photosystem II sample types using time-resolved mass spectrometry. The samples included thylakoid membranes, salt-washed Triton X-100-prepared membrane fragments, and purified core complexes from spinach and cyanobacteria. For each sample type, two kinetically distinct isotopic exchange rates could be resolved, indicating that the biphasic exchange behavior for the substrate water is inherent to the O(2)-evolving catalytic site in the S(3) state. However, the fast phase of exchange became somewhat slower (by a factor of approximately 2) in NaCl-washed membrane fragments and core complexes from spinach in which the 16- and 23-kDa extrinsic proteins have been removed, compared with the corresponding rate for the intact samples. For CaCl(2)-washed membrane fragments in which the 33-kDa manganese stabilizing protein (MSP) has also been removed, the fast phase of exchange slowed down even further (by a factor of approximately 3). Interestingly, the slow phase of exchange was little affected in the samples from spinach. For core complexes prepared from Synechocystis PCC 6803 and Synechococcus elongatus, the fast and slow exchange rates were variously affected. Nevertheless, within the experimental error, nearly the same exchange rates were measured for thylakoid samples made from wild type and an MSP-lacking mutant of Synechocystis PCC 6803. This result could indicate that the MSP has a slightly different function in eukaryotic organisms compared with prokaryotic organisms. In all samples, however, the differences in the exchange rates are relatively small. Such small differences are unlikely to arise from major changes in the metal-ligand structure at the catalytic site. Rather, the observed differences may reflect subtle long range effects in which the exchange reaction coordinates become slightly altered. We discuss the results in terms of solvent penetration into photosystem II and the regional dielectric around the catalytic site.

Electrochemical Water Oxidation and Stereoselective Oxygen Atom Transfer Mediated by a Copper Complex.

PubMed

Kafentzi, Maria-Chrysanthi; Papadakis, Raffaello; Gennarini, Federica; Kochem, Amélie; Iranzo, Olga; Le Mest, Yves; Le Poul, Nicolas; Tron, Thierry; Faure, Bruno; Simaan, A Jalila; Réglier, Marius

2018-04-06

Water oxidation by copper-based complexes to form dioxygen has attracted attention in recent years, with the aim of developing efficient and cheap catalysts for chemical energy storage. In addition, high-valent metal-oxo species produced by the oxidation of metal complexes in the presence of water can be used to achieve substrate oxygenation with the use of H 2 O as an oxygen source. To date, this strategy has not been reported for copper complexes. Herein, a copper(II) complex, [(RPY2)Cu(OTf) 2 ] (RPY2=N-substituted bis[2-pyridyl(ethylamine)] ligands; R=indane; OTf=triflate), is used. This complex, which contains an oxidizable substrate moiety (indane), is used as a tool to monitor an intramolecular oxygen atom transfer reaction. Electrochemical properties were investigated and, upon electrolysis at 1.30 V versus a normal hydrogen electrode (NHE), both dioxygen production and oxygenation of the indane moiety were observed. The ligand was oxidized in a highly diastereoselective manner, which indicated that the observed reactivity was mediated by metal-centered reactive species. The pH dependence of the reactivity was monitored and correlated with speciation deduced from different techniques, ranging from potentiometric titrations to spectroscopic studies and DFT calculations. Water oxidation for dioxygen production occurs at neutral pH and is probably mediated by the oxidation of a mononuclear copper(II) precursor. It is achieved with a rather low overpotential (280 mV at pH 7), although with limited efficiency. On the other hand, oxygenation is maximum at pH 8-8.5 and is probably mediated by the electrochemical oxidation of an antiferromagnetically coupled dinuclear bis(μ-hydroxo) copper(II) precursor. This constitutes the first example of copper-centered oxidative water activation for a selective oxygenation reaction. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A model of EcoRII restriction endonuclease action: the active complex is most likely formed by one protein subunit and one DNA recognition site

NASA Technical Reports Server (NTRS)

Karpova, E. A.; Kubareva, E. A.; Shabarova, Z. A.

1999-01-01

To elucidate the mechanism of interaction of restriction endonuclease EcoRII with DNA, we studied by native gel electrophoresis the binding of this endonuclease to a set of synthetic DNA-duplexes containing the modified or canonical recognition sequence 5'-d(CCA/TGG)-3'. All binding substrate or substrate analogues tested could be divided into two major groups: (i) duplexes that, at the interaction with endonuclease EcoRII, form two types of stable complexes on native gel in the absence of Mg2+ cofactor; (ii) duplexes that form only one type of complex, observed both in the presence and absence of Mg2+. Unlike the latter, duplexes under the first group can be hydrolyzed by endonuclease. Data obtained suggest that the active complex is most likely formed by one protein subunit and one DNA recognition sequence. A model of EcoRII endonuclease action is presented.

Mechanism and enantioselectivity in palladium-catalyzed conjugate addition of arylboronic acids to β-substituted cyclic enones: insights from computation and experiment.

PubMed

Holder, Jeffrey C; Zou, Lufeng; Marziale, Alexander N; Liu, Peng; Lan, Yu; Gatti, Michele; Kikushima, Kotaro; Houk, K N; Stoltz, Brian M

2013-10-09

Enantioselective conjugate additions of arylboronic acids to β-substituted cyclic enones have been previously reported from our laboratories. Air- and moisture-tolerant conditions were achieved with a catalyst derived in situ from palladium(II) trifluoroacetate and the chiral ligand (S)-t-BuPyOx. We now report a combined experimental and computational investigation on the mechanism, the nature of the active catalyst, the origins of the enantioselectivity, and the stereoelectronic effects of the ligand and the substrates of this transformation. Enantioselectivity is controlled primarily by steric repulsions between the t-Bu group of the chiral ligand and the α-methylene hydrogens of the enone substrate in the enantiodetermining carbopalladation step. Computations indicate that the reaction occurs via formation of a cationic arylpalladium(II) species, and subsequent carbopalladation of the enone olefin forms the key carbon-carbon bond. Studies of nonlinear effects and stoichiometric and catalytic reactions of isolated (PyOx)Pd(Ph)I complexes show that a monomeric arylpalladium-ligand complex is the active species in the selectivity-determining step. The addition of water and ammonium hexafluorophosphate synergistically increases the rate of the reaction, corroborating the hypothesis that a cationic palladium species is involved in the reaction pathway. These additives also allow the reaction to be performed at 40 °C and facilitate an expanded substrate scope.

Mechanism and Enantioselectivity in Palladium-Catalyzed Conjugate Addition of Arylboronic Acids to β-Substituted Cyclic Enones: Insights from Computation and Experiment

PubMed Central

Holder, Jeffrey C.; Zou, Lufeng; Marziale, Alexander N.; Liu, Peng; Lan, Yu; Gatti, Michele; Kikushima, Kotaro; Houk, K. N.; Stoltz, Brian M.

2013-01-01

Enantioselective conjugate additions of arylboronic acids to β-substituted cyclic enones have been reported previously from our laboratories. Air and moisture tolerant conditions were achieved with a catalyst derived in situ from palladium(II) trifluoroacetate and the chiral ligand (S)-t-BuPyOx. We now report a combined experimental and computational investigation on the mechanism, the nature of the active catalyst, the origins of the enantioselectivity, and the stereoelectronic effects of the ligand and the substrates of this transformation. Enantioselectivity is controlled primarily by steric repulsions between the t-Bu group of the chiral ligand and the α-methylene hydrogens of the enone substrate in the enantiodetermining carbopalladation step. Computations indicate that the reaction occurs via formation of a cationic arylpalladium(II) species, and subsequent carbopalladation of the enone olefin forms the key carbon-carbon bond. Studies of non-linear effects and stoichiometric and catalytic reactions of isolated (PyOx)Pd(Ph)I complexes show that a monomeric arylpalladium-ligand complex is the active species in the selectivity-determining step. The addition of water and ammonium hexafluorophosphate synergistically increases the rate of the reaction, corroborating the hypothesis that a cationic palladium species is involved in the reaction pathway. These additives also allow the reaction to be performed at 40 °C and facilitate an expanded substrate scope. PMID:24028424

Second-Sphere Effects in Dinuclear FeIIIZnII Hydrolase Biomimetics: Tuning Binding and Reactivity Properties.

PubMed

Camargo, Tiago Pacheco; Neves, Ademir; Peralta, Rosely A; Chaves, Cláudia; Maia, Elene C P; Lizarazo-Jaimes, Edgar H; Gomes, Dawidson A; Bortolotto, Tiago; Norberto, Douglas R; Terenzi, Hernán; Tierney, David L; Schenk, Gerhard

2018-01-02

Herein, we report the synthesis and characterization of two dinuclear Fe III Zn II complexes [Fe III Zn II LP1] (1) and [Fe III Zn II LP2] (2), in which LP1 and LP2 are conjugated systems containing one and two pyrene groups, respectively, connected via the diamine -HN(CH 2 ) 4 NH- spacer to the well-known N 5 O 2 -donor H 2 L ligand (H 2 L = 2-bis{[(2-pyridylmethyl)aminomethyl]-6-[(2-hydroxybenzyl)(2-pyridylmethyl)]aminomethyl}-4-methylphenol). The complex [Fe III Zn II L1] (3), in which H 2 L was modified to H 2 L1, with a carbonyl group attached to the terminal phenol group, was included in this study for comparison purposes. 1 Both complexes 1 and 2 were satisfactorily characterized in the solid state and in solution. Extended X-ray absorption fine structure data for 1 and 3 in an acetonitrile solution show that the multiply bridged structure seen in the solid state of 3 is retained in solution. Potentiometric and UV-vis titration of 1 and 2 show that electrostatic interaction between the protonated amino groups and coordinated water molecules significantly decreases the pK a of the iron(III)-bound water compared to those of 3. On the other hand, catalytic activity studies using 1 and 2 in the hydrolysis of the activated substrate bis(2,4-dinitrophenyl)phosphate (BDNPP) resulted in a significant increase in the association of the substrate (K ass ≅ 1/K M ) compared to that of 3 because of electrostatic and hydrophobic interactions between BDNPP and the side-chain diaminopyrene of the ligands H 2 LP1 and H 2 LP2. In addition, the introduction of the pyrene motifs in 1 and 2 enhanced their activity toward DNA and as effective antitumor drugs, although the biochemical mechanism of the latter effect is currently under investigation. These complexes represent interesting examples of how to promote an increase in the activity of traditional artificial metal nucleases by introducing second-coordination-sphere effects.

Molecular recognition in protein modification with rhodium metallopeptides

PubMed Central

Ball, Zachary T.

2015-01-01

Chemical manipulation of natural, unengineered proteins is a daunting challenge which tests the limits of reaction design. By combining transition-metal or other catalysts with molecular recognition ideas, it is possible to achieve site-selective protein reactivity without the need for engineered recognition sequences or reactive sites. Some recent examples in this area have used ruthenium photocatalysis, pyridine organocatalysis, and rhodium(II) metallocarbene catalysis, indicating that the fundamental ideas provide opportunities for using diverse reactivity on complex protein substrates and in complex cell-like environments. PMID:25588960

Substrate-Triggered Addition of Dioxygen to the Diferrous Cofactor of Aldehyde-Deformylating Oxygenase to form a Diferric-Peroxide Intermediate†

PubMed Central

Nørgaard, Hanne; Warui, Douglas M.; Rajakovich, Lauren J.; Chang, Wei-chen; Booker, Squire J.; Krebs, Carsten; Bollinger, J. Martin

2013-01-01

Cyanobacterial aldehyde-deformylating oxygenases (ADOs) belong to the ferritin-like diiron-carboxylate superfamily of dioxygen-activating proteins. They catalyze conversion of saturated or mono-unsaturated Cn fatty aldehydes to formate and the corresponding Cn-1 alkanes or alkenes, respectively. This unusual, apparently redox-neutral transformation actually requires four electrons per turnover to reduce the O2 co-substrate to the oxidation state of water and incorporates one O-atom from O2 into the formate co-product. We show here that the complex of the diiron(II/II) form of ADO from Nostoc punctiforme (Np) with an aldehyde substrate reacts with O2 to form a colored intermediate with spectroscopic properties suggestive of a Fe2III/III complex with a bound peroxide. Its Mössbauer spectra reveal that the intermediate possesses an antiferromagnetically (AF) coupled Fe2III/III center with resolved sub-sites. The intermediate is long-lived in the absence of a reducing system, decaying slowly (t1/2 ~ 400 s at 5 °C) to produce a very modest yield of formate (< 0.15 enzyme equivalents), but reacts rapidly with the fully reduced form of 1-methoxy-5-methylphenazine (MeOPMS) to yield product, albeit at only ~ 50% of the maximum theoretical yield (owing to competition from one or more unproductive pathway). The results represent the most definitive evidence to date that ADO can use a diiron cofactor (rather than a homo- or hetero-dinuclear cluster involving another transition metal) and provide support for a mechanism involving attack on the carbonyl of the bound substrate by the reduced O2 moiety to form a Fe2III/III-peroxyhemiacetal complex, which undergoes reductive O-O-bond cleavage, leading to C1–C2 radical fragmentation and formation of the alk(a/e)ne and formate products. PMID:23987523

Preliminary results of human PrPC protein studied by spectroscopic techniques

NASA Astrophysics Data System (ADS)

Nowakowski, Michał; Czapla-Masztafiak, Joanna; Kozak, Maciej; Zhukov, Igor; Zhukova, Lilia; Szlachetko, Jakub; Kwiatek, Wojciech M.

2017-11-01

Neurodegenerative diseases are one of the malfunctions of human nervous system, being a class of complex and prominent pathologies. The human prion Protease Resistant Protein (PrP) is protein regulating copper metabolism in mammalian cells through binding of Cu(II) ions to specific fragments. Nowadays misfolding of this protein is associated with development of prion diseases. Therefore, it is crucial to obtain structural information about coordination of Cu(II) by PrP protein. Herein, we report X-ray absorption spectroscopy (XAS) measurements, carried out on SuperXAS beamline (SLS, PSI Villigen) on PrPC-Cu(II) complexes. Obtained results were compared with theoretical predictions done by FEFF 9.6 software. Complementary to XAS data, Atomic Force Microscopy (AFM) measurements were conducted to obtain low resolution structural information about prepared sample that allow to develop protocol of fixing PrPC molecules on solid substrate used for further experiments. It has been established that folded C-terminal domain of PrPC protein has around 5 nm in diameter. Presented results showed that both XAS and AFM methods are useful tools in detailed examination of complexes of human PrPC either with Cu(II) or with other divalent metal ions.

Reactivity of Hydride Bridges in High-Spin [3M-3(μ-H)] Clusters (M = FeII, CoII).

PubMed

Lee, Yousoon; Anderton, Kevin J; Sloane, Forrest T; Ermert, David M; Abboud, Khalil A; García-Serres, Ricardo; Murray, Leslie J

2015-08-26

The designed [3M-3(μ-H)] clusters (M = Fe(II), Co(II)) Fe3H3L (1-H) and Co3H3L (2-H) [where L(3-) is a tris(β-diketiminate) cyclophane] were synthesized by treating the corresponding M3Br3L complexes with KBEt3H. From single-crystal X-ray analysis, the hydride ligands are sterically protected by the cyclophane ligand, and these complexes selectively react with CO2 over other unsaturated substrates (e.g., CS2, Me3SiCCH, C2H2, and CH3CN). The reaction of 1-H or 2-H with CO2 at room temperature yielded Fe3(OCHO)(H)2L (1-CO2) or Co3(OCHO)(H)2L (2-CO2), respectively, which evidence the differential reactivity of the hydride ligands within these complexes. The analogous reactions at elevated temperatures revealed a distinct difference in the reactivity pattern for 2-H as compared to 1-H; Fe3(OCHO)3L (1-3CO2) was generated from 1-H, while 2-H afforded only 2-CO2.

Ama1p-activated anaphase-promoting complex regulates the destruction of Cdc20p during meiosis II

PubMed Central

Tan, Grace S.; Magurno, Jennifer; Cooper, Katrina F.

2011-01-01

The execution of meiotic divisions in Saccharomyces cerevisiae is regulated by anaphase-promoting complex/cyclosome (APC/C)–mediated protein degradation. During meiosis, the APC/C is activated by association with Cdc20p or the meiosis-specific activator Ama1p. We present evidence that, as cells exit from meiosis II, APC/CAma1 mediates Cdc20p destruction. APC/CAma1 recognizes two degrons on Cdc20p, the destruction box and destruction degron, with either domain being sufficient to mediate Cdc20p destruction. Cdc20p does not need to associate with the APC/C to bind Ama1p or be destroyed. Coimmunoprecipitation analyses showed that the diverged amino-terminal region of Ama1p recognizes both Cdc20p and Clb1p, a previously identified substrate of APC/CAma1. Domain swap experiments revealed that the C-terminal WD region of Cdh1p, when fused to the N-terminal region of Ama1p, could direct most of Ama1p functions, although at a reduced level. In addition, this fusion protein cannot complement the spore wall defect in ama1Δ strains, indicating that substrate specificity is also derived from the WD repeat domain. These findings provide a mechanism to temporally down-regulate APC/CCdc20 activity as the cells complete meiosis II and form spores. PMID:21118994

Ammonia binding to the oxygen-evolving complex of photosystem II identifies the solvent-exchangeable oxygen bridge (μ-oxo) of the manganese tetramer

PubMed Central

Pérez Navarro, Montserrat; Ames, William M.; Nilsson, Håkan; Lohmiller, Thomas; Pantazis, Dimitrios A.; Rapatskiy, Leonid; Nowaczyk, Marc M.; Neese, Frank; Boussac, Alain; Messinger, Johannes; Lubitz, Wolfgang; Cox, Nicholas

2013-01-01

The assignment of the two substrate water sites of the tetra-manganese penta-oxygen calcium (Mn4O5Ca) cluster of photosystem II is essential for the elucidation of the mechanism of biological O-O bond formation and the subsequent design of bio-inspired water-splitting catalysts. We recently demonstrated using pulsed EPR spectroscopy that one of the five oxygen bridges (μ-oxo) exchanges unusually rapidly with bulk water and is thus a likely candidate for one of the substrates. Ammonia, a water analog, was previously shown to bind to the Mn4O5Ca cluster, potentially displacing a water/substrate ligand [Britt RD, et al. (1989) J Am Chem Soc 111(10):3522–3532]. Here we show by a combination of EPR and time-resolved membrane inlet mass spectrometry that the binding of ammonia perturbs the exchangeable μ-oxo bridge without drastically altering the binding/exchange kinetics of the two substrates. In combination with broken-symmetry density functional theory, our results show that (i) the exchangable μ-oxo bridge is O5 {using the labeling of the current crystal structure [Umena Y, et al. (2011) Nature 473(7345):55–60]}; (ii) ammonia displaces a water ligand to the outer manganese (MnA4-W1); and (iii) as W1 is trans to O5, ammonia binding elongates the MnA4-O5 bond, leading to the perturbation of the μ-oxo bridge resonance and to a small change in the water exchange rates. These experimental results support O-O bond formation between O5 and possibly an oxyl radical as proposed by Siegbahn and exclude W1 as the second substrate water. PMID:24023065

Probes of eukaryotic DNA-dependent RNA polymerase II-I. Binding of 9-beta-D-arabinofuranosyl-6-mercaptopurine to the elongation subsite.

PubMed

Cho, J M; Kimball, A P

1982-08-15

9-beta-D-Arabinofuranosyl-6-mercaptopurine (ara-6-MP) was used to affinity-label wheat germ DNA-dependent RNA polymerase II (or B) (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6). This nucleoside analogue was found to be a competitive inhibitor with respect to [3H]UMP incorporation. Natural substrates protected the enzyme from inactivation by ara-6-MP when the enzyme was preincubated with excess concentrations of substrates, suggesting that the inhibitor binds at the elongation subsite. The inhibitor bound the catalytic center of the enzyme with a stoichiometry of 0.6:1. The sulfhydryl reagent, dithiothreitol, reversed the inhibition by ara-6-MP, suggesting that the 6-thiol group of the inhibitor was interacting closely with an essential cysteine residue in the catalytic center of the enzyme. Chromatographic analysis of the pronase-digestion products of the RNA polymerase II-ara-6-MP complex also showed that ara-6-MP had bound a cysteine residue. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the denatured [6-35S]ara-6-MP-labeled RNA polymerase II revealed that over 80% of the radioactivity was associated with the IIb subunit of the enzyme.

Impaired mitochondrial oxidative phosphorylation and supercomplex assembly in rectus abdominis muscle of diabetic obese individuals.

PubMed

Antoun, Ghadi; McMurray, Fiona; Thrush, A Brianne; Patten, David A; Peixoto, Alyssa C; Slack, Ruth S; McPherson, Ruth; Dent, Robert; Harper, Mary-Ellen

2015-12-01

Skeletal muscle mitochondrial dysfunction has been documented in patients with type 2 diabetes mellitus; however, specific respiratory defects and their mechanisms are poorly understood. The aim of the current study was to examine oxidative phosphorylation and electron transport chain (ETC) supercomplex assembly in rectus abdominis muscles of 10 obese diabetic and 10 obese non-diabetic individuals. Twenty obese women undergoing Roux-en-Y gastric bypass surgery were recruited for this study. Muscle samples were obtained intraoperatively and subdivided for multiple analyses, including high-resolution respirometry and assessment of supercomplex assembly. Clinical data obtained from referring physicians were correlated with laboratory findings. Participants in both groups were of a similar age, weight and BMI. Mitochondrial respiration rates were markedly reduced in diabetic vs non-diabetic patients. This defect was observed during maximal ADP-stimulated respiration in the presence of complex I-linked substrates and complex I- and II-linked substrates, and during maximal uncoupled respiration. There were no differences in fatty acid (octanoyl carnitine) supported respiration, leak respiration or isolated activity of cytochrome c oxidase. Intriguingly, significant correlations were found between glycated haemoglobin (HbA1c) levels and maximal respiration or respiration supported by complex I, complex I and II or fatty acid. In the muscle of diabetic patients, blue native gel electrophoresis revealed a striking decrease in complex I, III and IV containing ETC supercomplexes. These findings support the hypothesis that ETC supercomplex assembly may be an important underlying mechanism of muscle mitochondrial dysfunction in type 2 diabetes mellitus.

Chemical Equilibrium Models for the S3 State of the Oxygen-Evolving Complex of Photosystem II.

PubMed

Isobe, Hiroshi; Shoji, Mitsuo; Shen, Jian-Ren; Yamaguchi, Kizashi

2016-01-19

We have performed hybrid density functional theory (DFT) calculations to investigate how chemical equilibria can be described in the S3 state of the oxygen-evolving complex in photosystem II. For a chosen 340-atom model, 1 stable and 11 metastable intermediates have been identified within the range of 13 kcal mol(-1) that differ in protonation, charge, spin, and conformational states. The results imply that reversible interconversion of these intermediates gives rise to dynamic equilibria that involve processes with relocations of protons and electrons residing in the Mn4CaO5 cluster, as well as bound water ligands, with concomitant large changes in the cluster geometry. Such proton tautomerism and redox isomerism are responsible for reversible activation/deactivation processes of substrate oxygen species, through which Mn-O and O-O bonds are transiently ruptured and formed. These results may allow for a tentative interpretation of kinetic data on substrate water exchange on the order of seconds at room temperature, as measured by time-resolved mass spectrometry. The reliability of the hybrid DFT method for the multielectron redox reaction in such an intricate system is also addressed.

The crystal structures of native hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 and of substrate and inhibitor complexes.

PubMed

Ferraroni, Marta; Da Vela, Stefano; Kolvenbach, Boris A; Corvini, Philippe F X; Scozzafava, Andrea

2017-05-01

The crystal structure of hydroquinone 1,2-dioxygenase, a Fe(II) ring cleaving dioxygenase from Sphingomonas sp. strain TTNP3, which oxidizes a wide range of hydroquinones to the corresponding 4-hydroxymuconic semialdehydes, has been solved by Molecular Replacement, using the coordinates of PnpCD from Pseudomonas sp. strain WBC-3. The enzyme is a heterotetramer, constituted of two subunits α and two β of 19 and 38kDa, respectively. Both the two subunits fold as a cupin, but that of the small α subunit lacks a competent metal binding pocket. Two tetramers are present in the asymmetric unit. Each of the four β subunits in the asymmetric unit binds one Fe(II) ion. The iron ion in each β subunit is coordinated to three protein residues, His258, Glu264, and His305 and a water molecule. The crystal structures of the complexes with the substrate methylhydroquinone, obtained under anaerobic conditions, and with the inhibitors 4-hydroxybenzoate and 4-nitrophenol were also solved. The structures of the native enzyme and of the complexes present significant differences in the active site region compared to PnpCD, the other hydroquinone 1,2-dioxygenase of known structure, and in particular they show a different coordination at the metal center. Copyright © 2017 Elsevier B.V. All rights reserved.

A structural and functional model for the 1-aminocyclopropane-1-carboxylic acid oxidase.

PubMed

Sallmann, Madleen; Oldenburg, Fabio; Braun, Beatrice; Réglier, Marius; Simaan, A Jalila; Limberg, Christian

2015-10-12

The hitherto most realistic low-molecular-weight analogue for the 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO) is reported. The ACCOs 2-His-1-carboxylate iron(II) active site was mimicked by a TpFe moiety, to which the natural substrate ACC could be bound. The resulting complex [Tp(Me,Ph) FeACC] (1), according to X-ray diffraction analysis performed for the nickel analogue, represents an excellent structural model, featuring ACC coordinated in a bidentate fashion-as proposed for the enzymatic substrate complex-as well as a vacant coordination site that forms the basis for the first successful replication also of the ACCO function: 1 is the first known ACC complex that reacts with O2 to produce ethylene. As a FeOOH species had been suggested as intermediate in the catalytic cycle, H2 O2 was tested as the oxidant, too, and indeed evolution of ethylene proceeded even more rapidly to give 65 % yield. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evidence for Alkene cis-Aminocupration, an Aminooxygenation Case Study: Kinetics, EPR Spectroscopy, and DFT Calculations

PubMed Central

Paderes, Monissa C.; Belding, Lee; Fanovic, Branden; Dudding, Travis; Keister, Jerome B.

2012-01-01

Alkene difunctionalization reactions are important in organic synthesis. We have recently shown that copper(II) complexes can promote and catalyze intramolecular alkene aminooxygenation, carboamination, and diamination reactions. In this contribution, we report a combined experimental and theoretical examination of the mechanism of the copper(II)-promoted olefin aminooxygenation reaction. Kinetics experiments revealed a mechanistic pathway involving an equilibrium reaction between a copper(II) carboxylate complex and the γ-alkenyl sulfonamide substrate and a rate-limiting intramolecular cis-addition of N–Cu across the olefin. Kinetic isotope effect studies support that the cis-aminocupration is the rate-determining step. UV/Vis spectra support a role for the base in the break-up of copper(II) carboxylate dimer to monomeric species. Electron paramagnetic resonance (EPR) spectra provide evidence for a kinetically competent N–Cu intermediate with a CuII oxidation state. Due to the highly similar stereochemical and reactivity trends among the CuII-promoted and catalyzed alkene difunctionalization reactions we have developed, the cis-aminocupration mechanism can reasonably be generalized across the reaction class. The methods and findings disclosed in this report should also prove valuable to the mechanism analysis and optimization of other copper(-II) carboxylate promoted reactions, especially those that take place in aprotic organic solvents. PMID:22237868

Hydrolysis mechanisms of BNPP mediated by facial copper(II) complexes bearing single alkyl guanidine pendants: cooperation between the metal centers and the guanidine pendants.

PubMed

Zhang, Xuepeng; Liu, Xueping; Phillips, David Lee; Zhao, Cunyuan

2016-01-28

The hydrolysis mechanisms of DNA dinucleotide analogue BNPP(-) (bis(p-nitrophenyl) phosphate) catalyzed by mononuclear/dinuclear facial copper(ii) complexes bearing single alkyl guanidine pendants were investigated using density functional theory (DFT) calculations. Active catalyst forms have been investigated and four different reaction modes are proposed accordingly. The [Cu2(L(1))2(μ-OH)](3+) (L(1) is 1-(2-guanidinoethyl)-1,4,7-triazacyclononane) complex features a strong μ-hydroxo mediated antiferromagnetic coupling between the bimetallic centers and the corresponding more stable open-shell singlet state. Three different reaction modes involving two catalysts and a substrate were proposed for L(1) entries and the mode 1 in which an inter-complex nucleophilic attack by a metal bound hydroxide was found to be more favorable. In the L(3)-involved reactions (L(3) is 1-(4-guanidinobutyl)-1,4,7-triazacyclononane), the reaction mode in which an in-plane intracomplex scissoring-like nucleophilic attack by a Cu(ii)-bound hydroxide was found to be more competitive. The protonated guanidine pendants in each proposed mechanism were found to play crucial roles in stabilizing the reaction structures via hydrogen bonds and in facilitating the departure of the leaving group via electrostatic attraction. The calculated results are consistent with the experimental observations that the Cu(ii)-L(3) complexes are hydrolytically more favorable than their L(1)-involved counterparts.

Electrocatalytic reduction of CO2 with CCC-NHC pincer nickel complexes.

PubMed

Cope, James D; Liyanage, Nalaka P; Kelley, Paul J; Denny, Jason A; Valente, Edward J; Webster, Charles Edwin; Delcamp, Jared H; Hollis, T Keith

2017-08-22

A CCC-NHC pincer Ni(ii)Cl complex was prepared according to the metallation/transmetallation methodology. It was fully characterized by electrochemical, NMR spectroscopic, theoretical, and X-ray crystallographic methods. The complex and its cation were evaluated for electrocatalytic reduction of CO 2 under a variety of conditions and found to provide some of the fastest catalytic rates and highest substrate selectivities (CO 2 vs. H + ) reported. Rates improved in the presence of water and, significantly, catalysis occurred at the first reduction potential, presumably at the Ni(i) state. Controlled potential electrolysis (CPE) was found to yield CO at 34% and formate at 47% Faradaic efficiency (FE).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Romano, Keith P.; Laine, Jennifer M.; Deveau, Laura M.

Hepatitis C NS3/4A protease is a prime therapeutic target that is responsible for cleaving the viral polyprotein at junctions 3-4A, 4A4B, 4B5A, and 5A5B and two host cell adaptor proteins of the innate immune response, TRIF and MAVS. In this study, NS3/4A crystal structures of both host cell cleavage sites were determined and compared to the crystal structures of viral substrates. Two distinct protease conformations were observed and correlated with substrate specificity: (i) 3-4A, 4A4B, 5A5B, and MAVS, which are processed more efficiently by the protease, form extensive electrostatic networks when in complex with the protease, and (ii) TRIF andmore » 4B5A, which contain polyproline motifs in their full-length sequences, do not form electrostatic networks in their crystal complexes. These findings provide mechanistic insights into NS3/4A substrate recognition, which may assist in a more rational approach to inhibitor design in the face of the rapid acquisition of resistance.« less

Saturation kinetics in phenolic O-H bond oxidation by a mononuclear Mn(III)-OH complex derived from dioxygen.

PubMed

Wijeratne, Gayan B; Corzine, Briana; Day, Victor W; Jackson, Timothy A

2014-07-21

The mononuclear hydroxomanganese(III) complex, [Mn(III)(OH)(dpaq)](+), which is supported by the amide-containing N5 ligand dpaq (dpaq = 2-[bis(pyridin-2-ylmethyl)]amino-N-quinolin-8-yl-acetamidate) was generated by treatment of the manganese(II) species, [Mn(II)(dpaq)](OTf), with dioxygen in acetonitrile solution at 25 °C. This oxygenation reaction proceeds with essentially quantitative yield (greater than 98% isolated yield) and represents a rare example of an O2-mediated oxidation of a manganese(II) complex to generate a single product. The X-ray diffraction structure of [Mn(III)(OH)(dpaq)](+) reveals a short Mn-OH distance of 1.806(13) Å, with the hydroxo moiety trans to the amide function of the dpaq ligand. No shielding of the hydroxo group is observed in the solid-state structure. Nonetheless, [Mn(III)(OH)(dpaq)](+) is remarkably stable, decreasing in concentration by only 10% when stored in MeCN at 25 °C for 1 week. The [Mn(III)(OH)(dpaq)](+) complex participates in proton-coupled electron transfer reactions with substrates with relatively weak O-H and C-H bonds. For example, [Mn(III)(OH)(dpaq)](+) oxidizes TEMPOH (TEMPOH = 2,2'-6,6'-tetramethylpiperidine-1-ol), which has a bond dissociation free energy (BDFE) of 66.5 kcal/mol, in MeCN at 25 °C. The hydrogen/deuterium kinetic isotope effect of 1.8 observed for this reaction implies a concerted proton-electron transfer pathway. The [Mn(III)(OH)(dpaq)](+) complex also oxidizes xanthene (C-H BDFE of 73.3 kcal/mol in dimethylsulfoxide) and phenols, such as 2,4,6-tri-t-butylphenol, with BDFEs of less than 79 kcal/mol. Saturation kinetics were observed for phenol oxidation, implying an initial equilibrium prior to the rate-determining step. On the basis of a collective body of evidence, the equilibrium step is attributed to the formation of a hydrogen-bonding complex between [Mn(III)(OH)(dpaq)](+) and the phenol substrates.

Direct observation of the influence of cardiolipin and antibiotics on lipid II binding to MurJ

NASA Astrophysics Data System (ADS)

Bolla, Jani Reddy; Sauer, Joshua B.; Wu, Di; Mehmood, Shahid; Allison, Timothy M.; Robinson, Carol V.

2018-03-01

Translocation of lipid II across the cytoplasmic membrane is essential in peptidoglycan biogenesis. Although most steps are understood, identifying the lipid II flippase has yielded conflicting results, and the lipid II binding properties of two candidate flippases—MurJ and FtsW—remain largely unknown. Here we apply native mass spectrometry to both proteins and characterize lipid II binding. We observed lower levels of lipid II binding to FtsW compared to MurJ, consistent with MurJ having a higher affinity. Site-directed mutagenesis of MurJ suggests that mutations at A29 and D269 attenuate lipid II binding to MurJ, whereas chemical modification of A29 eliminates binding. The antibiotic ramoplanin dissociates lipid II from MurJ, whereas vancomycin binds to form a stable complex with MurJ:lipid II. Furthermore, we reveal cardiolipins associate with MurJ but not FtsW, and exogenous cardiolipins reduce lipid II binding to MurJ. These observations provide insights into determinants of lipid II binding to MurJ and suggest roles for endogenous lipids in regulating substrate binding.

Inter-ring rotations of AAA ATPase p97 revealed by electron cryomicroscopy

PubMed Central

Yeung, Heidi O.; Förster, Andreas; Bebeacua, Cecilia; Niwa, Hajime; Ewens, Caroline; McKeown, Ciarán; Zhang, Xiaodong; Freemont, Paul S.

2014-01-01

The type II AAA+ protein p97 is involved in numerous cellular activities, including endoplasmic reticulum-associated degradation, transcription activation, membrane fusion and cell-cycle control. These activities are at least in part regulated by the ubiquitin system, in which p97 is thought to target ubiquitylated protein substrates within macromolecular complexes and assist in their extraction or disassembly. Although ATPase activity is essential for p97 function, little is known about how ATP binding or hydrolysis is coupled with p97 conformational changes and substrate remodelling. Here, we have used single-particle electron cryomicroscopy (cryo-EM) to study the effect of nucleotides on p97 conformation. We have identified conformational heterogeneity within the cryo-EM datasets from which we have resolved two major p97 conformations. A comparison of conformations reveals inter-ring rotations upon nucleotide binding and hydrolysis that may be linked to the remodelling of target protein complexes. PMID:24598262

The RNA Polymerase II Trigger Loop Functions in Substrate Selection and is Directly Targeted by α-amanitin

PubMed Central

Kaplan, Craig D.; Larsson, Karl-Magnus; Kornberg, Roger D.

2008-01-01

Summary Structural, biochemical and genetic studies have led to proposals that a mobile element of multi-subunit RNA polymerases, the Trigger Loop (TL), plays a critical role in catalysis and can be targeted by antibiotic inhibitors. Here we present evidence that the Saccharomyces cerevisiae RNA Polymerase II (Pol II) TL participates in substrate selection. Amino acid substitutions within the Pol II TL preferentially alter substrate usage and enzyme fidelity, as does inhibition of transcription by α-amanitin. Finally, substitution of His1085 in the TL specifically renders Pol II highly resistant to α-amanitin, indicating a functional interaction between His1085 and α-amanitin that is supported by re-refinement of an α-amanitin-Pol II crystal structure. We propose that α-amanitin inhibited Pol II elongation, which is slow and exhibits reduced substrate selectivity, results from direct α-amanitin interference with the TL. PMID:18538653

Low-valent group 14 element hydride chemistry: towards catalysis.

PubMed

Hadlington, Terrance J; Driess, Matthias; Jones, Cameron

2018-06-05

The chemistry of group 14 element(ii) hydride complexes has rapidly expanded since the first stable example of such a compound was reported in 2000. Since that time it has become apparent that these systems display remarkable reactivity patterns, in some cases mimicking those of late transition-metal (TM) hydride compounds. This is especially so for the hydroelementation of unsaturated organic substrates. Recently, this aspect of their reactivity has been extended to the use of group 14 element(ii) hydrides as efficient, "TM-like" catalysts in organic synthesis. This review will detail how the chemistry of these hydride compounds has advanced since their early development. Throughout, there is a focus on the importance of ligand effects in these systems, and how ligand design can greatly modify a coordinated complex's electronic structure, reactivity, and catalytic efficiency.

Evaporation of liquid droplets on solid substrates. II. Periodic substrates with moving contact lines

NASA Astrophysics Data System (ADS)

Amini, Amirhossein; Homsy, G. M.

2017-04-01

Experiments on evaporating droplets on structured surfaces have shown that the contact line does not move with constant speed, but rather in a steplike "stick-slip" fashion. As a first step in understanding such behavior, we study the evaporation of a two-dimensional volatile liquid droplet on a nonplanar heated solid substrate with a moving contact line and fixed contact angle. The model for the flat case is adapted to include curved substrates, numerical solutions are achieved for various periodic and quasiperiodic substrate profiles, and the dynamics of the contact line and the apparent contact angle are studied. In contrast with our results for a flat substrate, for which the contact line recedes in a nearly constant speed, we observe that the contact line speed and position show significant time variation and that the contact line moves in an approximate steplike fashion on relatively steep substrates. For the simplest case of a periodic substrate, we find that the apparent contact angle is periodic in time. For doubly periodic substrates, we find that the apparent contact angle is periodic and that the problem exhibits a phase-locking behavior. For multimode quasiperiodic substrates, we find the contact line behavior to be temporally complex and not only limited to a stick-slip motion. In all cases, we find that the overall evaporation is increased relative to the flat substrate.

Krebs cycle metabolites and preferential succinate oxidation following neonatal hypoxic-ischemic brain injury in mice

PubMed Central

Sahni, Prateek V.; Zhang, Jimmy; Sosunov, Sergey; Galkin, Alexander; Niatsetskaya, Zoya; Starkov, Anatoly; Brookes, Paul S.; Ten, Vadim S.

2017-01-01

Background Reverse electron transport (RET) driven by the oxidation of succinate has been proposed as the mechanism of accelerated production of reactive oxygen species (ROS) in post-ischemic mitochondria. However, it remains unclear whether upon reperfusion, mitochondria preferentially oxidase succinate. Methods Neonatal mice were subjected to Rice-Vannucci model of hypoxicischemic brain injury (HI) followed by assessment of Krebs cycle metabolites, mitochondrial substrate preference, and H2O2 generation rate in the ischemic brain. Results While brain mitochondria from control mice exhibited a rotenonesensitive complex-I-dependent respiration, HI-brain mitochondria, at the initiation of reperfusion, demonstrated complex-II-dependent respiration, as rotenone minimally affected, but inhibition of complex-II ceased respiration. This was associated with a 30-fold increase of cerebral succinate concentration and significantly elevated H2O2 emission rate in HI-mice compared to controls. At sixty minutes of reperfusion, cerebral succinate content and the mitochondrial response to rotenone did not differ from that in controls. Conclusion These data are the first ex-vivo evidence, that at the initiation of reperfusion, brain mitochondria transiently shift their metabolism from complex-I-dependent oxidation of NADH toward complex II-linked oxidation of succinate. Our study provides a critical piece of support for existence of the RET-dependent mechanism of elevated ROS production in reperfusion. PMID:29211056

Krebs cycle metabolites and preferential succinate oxidation following neonatal hypoxic-ischemic brain injury in mice.

PubMed

Sahni, Prateek V; Zhang, Jimmy; Sosunov, Sergey; Galkin, Alexander; Niatsetskaya, Zoya; Starkov, Anatoly; Brookes, Paul S; Ten, Vadim S

2018-02-01

BackgroundReverse electron transport (RET) driven by the oxidation of succinate has been proposed as the mechanism of accelerated production of reactive oxygen species (ROS) in post-ischemic mitochondria. However, it remains unclear whether upon reperfusion, mitochondria preferentially oxidase succinate.MethodsNeonatal mice were subjected to Rice-Vannucci model of hypoxic-ischemic brain injury (HI) followed by assessment of Krebs cycle metabolites, mitochondrial substrate preference, and H 2 O 2 generation rate in the ischemic brain.ResultsWhile brain mitochondria from control mice exhibited a rotenone-sensitive complex-I-dependent respiration, HI-brain mitochondria, at the initiation of reperfusion, demonstrated complex-II-dependent respiration, as rotenone minimally affected, but inhibition of complex-II ceased respiration. This was associated with a 30-fold increase of cerebral succinate concentration and significantly elevated H 2 O 2 emission rate in HI-mice compared to controls. At 60 min of reperfusion, cerebral succinate content and the mitochondrial response to rotenone did not differ from that in controls.ConclusionThese data are the first ex vivo evidence, that at the initiation of reperfusion, brain mitochondria transiently shift their metabolism from complex-I-dependent oxidation of NADH toward complex II-linked oxidation of succinate. Our study provides a critical piece of support for existence of the RET-dependent mechanism of elevated ROS production in reperfusion.

Chaperonins: The hunt for the Group II mechanism.

PubMed

Bigotti, Maria Giulia; Clarke, Anthony R

2008-06-15

Chaperonins are multi-subunit complexes that enhance the efficiency of protein-folding reactions by capturing protein substrates in their central cavities. They occur in all prokaryotic and eukaryotic cell types and, alone amongst molecular chaperones, chaperonin knockouts are always lethal. Chaperonins come in two forms; the Group I are found in bacteria, mitochondria and plastids [W.A. Fenton, A.L. Horwich, Q. Rev. Biophys. 36 (2003) 229-256, [1

Proton NMR spectroscopic characterization of binary and ternary complexes of cobalt(II) carboxypeptidase A with inhibitors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bertini, I.; Luchinat, C.; Messori, L.

The binding of L- and D-phenylalanine and carboxylate inhibitors to cobalt(II)-substituted carboxypeptidase A, Co(II)CPD (E), in the presence and absence of pseudohalogens (X = N/sub 3//sup -/, NCO/sup -/, and NCS/sup -/) has been studied by /sup 1/H NMR spectroscopy. This technique monitors the proton signals of histidine residues bound to cobalt(II) and is therefore sensitive to the interactions of inhibitors that perturb the coordination sphere of the metal. Enzyme-inhibitor complexes, E/times/I, E/times/I/sub 2/, and E/times/I/times/X, each with characteristic NMR features, have been identified. The NMR data suggest that when the carboxylate group of a substrate of inhibitor binds atmore » the active site, a conformational change occurs that allows a second ligand molecule to bind to the metal ion, altering its coordination sphere and thereby attenuating the bidentate behavior of Glu-72. The /sup 1/H NMR signals also reflect alterations in the histidine interactions with the metal upon inhibitor binding. Isotropic shifts in the signals for the C-4 (c) and N protons (a) of one of the histidine ligands are readily observed in all of these complexes. These signals are relatively constant for all E/times/I and E/times/I/times/X complexes, indicating that this ligand is in a relatively fixed or buried conformation. However in the 2:1 carboxylate inhibitor (E/times/I/sub 2/) complexes, both signals are shifted upfield, suggesting a disturbance in the interaction of this histidine with the metal.« less

Synthesis, structure and catalytic activities of nickel(II) complexes bearing N4 tetradentate Schiff base ligand

NASA Astrophysics Data System (ADS)

Sarkar, Saikat; Nag, Sanat Kumar; Chattopadhyay, Asoke Prasun; Dey, Kamalendu; Islam, Sk. Manirul; Sarkar, Avijit; Sarkar, Sougata

2018-05-01

Two new nickel(II) complexes [Ni(L)Cl2] (1) and [Ni(L)(NCS)2] (2) of a neutral tetradentate mono-condensed Schiff base ligand, 3-(2-(2-aminoethylamino)ethylimino)butan-2-one oxime (L) have been synthesized and characterized using different physicochemical techniques e.g. elemental analyses, spectroscopic (IR, Electronic, NMR) methods, conductivity and molecular measurements. The crystal structure of complex (2) has been determined by using single crystal X-ray diffraction method and it suggests a distorted octahedral geometry around nickel(II) having a NiN6 coordinating atmosphere. The non-coordinated Osbnd H group on the ligand L remain engaged in H-bonding interactions with the S end of the coordinated thiocyanate moiety. These H-bonding interactions lead to Osbnd S separations of 3.132 Å and play prominent role in crystal packing. It is observed that the mononuclear units are glued together with such Osbnd H…S interactions and finally results in an 1D supramolecular sheet-like arrangement. DFT/TDDFT based theoretical calculations were also performed on the ligand and the complexes aiming at the accomplishment of idea regarding their optimized geometry, electronic transitions and the molecular energy levels. Finally the catalytic behavior of the complexes for oxidation of styrene has also been carried out. A variety of reaction conditions like the effect of solvent, effect of temperature and time as well as the effect of ratio of substrate to oxidant were thoroughly studied to judge the catalytic efficiency of the Ni(II) coordination entity.

The mechanism of catalysis by type-II NADH:quinone oxidoreductases

PubMed Central

Blaza, James N.; Bridges, Hannah R.; Aragão, David; Dunn, Elyse A.; Heikal, Adam; Cook, Gregory M.; Nakatani, Yoshio; Hirst, Judy

2017-01-01

Type II NADH:quinone oxidoreductase (NDH-2) is central to the respiratory chains of many organisms. It is not present in mammals so may be exploited as an antimicrobial drug target or used as a substitute for dysfunctional respiratory complex I in neuromuscular disorders. NDH-2 is a single-subunit monotopic membrane protein with just a flavin cofactor, yet no consensus exists on its mechanism. Here, we use steady-state and pre-steady-state kinetics combined with mutagenesis and structural studies to determine the mechanism of NDH-2 from Caldalkalibacillus thermarum. We show that the two substrate reactions occur independently, at different sites, and regardless of the occupancy of the partner site. We conclude that the reaction pathway is determined stochastically, by the substrate/product concentrations and dissociation constants, and can follow either a ping-pong or ternary mechanism. This mechanistic versatility provides a unified explanation for all extant data and a new foundation for the development of therapeutic strategies. PMID:28067272

Energetic Limitations on Microbial Respiration of Organic Compounds using Aqueous Fe(III) Complexes

NASA Astrophysics Data System (ADS)

Naughton, H.; Fendorf, S. E.

2015-12-01

Soil organic matter constitutes up to 75% of the terrestrial carbon stock. Microorganisms mediate the breakdown of organic compounds and the return of carbon to the atmosphere, predominantly through respiration. Microbial respiration requires an electron acceptor and an electron donor such as small fatty acids, organic acids, alcohols, sugars, and other molecules that differ in oxidation state of carbon. Carbon redox state affects how much energy is required to oxidize a molecule through respiration. Therefore, different organic compounds should offer a spectrum of energies to respiring microorganisms. However, microbial respiration has traditionally focused on the availability and reduction potential of electron acceptors, ignoring the organic electron donor. We found through incubation experiments that the organic compound serving as electron donor determined how rapidly Shewanella putrefaciens CN32 respires organic substrate and the extent of reduction of the electron acceptor. We simulated a range of energetically favorable to unfavorable electron acceptors using organic chelators bound to Fe(III) with equilibrium stability constants ranging from log(K) of 11.5 to 25.0 for the 1:1 complex, where more stable complexes are less favorable for microbial respiration. Organic substrates varied in nominal oxidation state of carbon from +2 to -2. The most energetically favorable substrate, lactate, promoted up to 30x more rapid increase in percent Fe(II) compared to less favorable substrates such as formate. This increased respiration on lactate was more substantial with less stable Fe(III)-chelate complexes. Intriguingly, this pattern contradicts respiration rate predicted by nominal oxidation state of carbon. Our results suggest that organic substrates will be consumed so long as the energetic toll corresponding to the electron donor half reaction is counterbalanced by the energy available from the electron accepting half reaction. We propose using the chemical structure of organic matter, elucidated with techniques such as FT-ICR MS, to improve microbial decomposition and carbon cycling models by incorporating energetic limitations due to carbon oxidation.

Heterobimetallic dinuclear lanthanide alkoxide complexes as acid-base difunctional catalysts for transesterification.

PubMed

Zeng, Ruijie; Sheng, Hongting; Zhang, Yongcang; Feng, Yan; Chen, Zhi; Wang, Junfeng; Chen, Man; Zhu, Manzhou; Guo, Qingxiang

2014-10-03

A practical lanthanide(III)-catalyzed transesterification of carboxylic esters, weakly reactive carbonates, and much less-reactive ethyl silicate with primary and secondary alcohols was developed. Heterobimetallic dinuclear lanthanide alkoxide complexes [Ln2Na8{(OCH2CH2NMe2)}12(OH)2] (Ln = Nd (I), Sm (II), and Yb (III)) were used as highly active catalysts for this reaction. The mild reaction conditions enabled the transesterification of various substrates to proceed in good to high yield. Efficient activation of transesterification may be endowed by the above complexes as cooperative acid-base difunctional catalysts, which is proposed to be responsible for the higher reactivity in comparison with simple acid/base catalysts.

RNA polymerase II trigger loop residues stabilize and position the incoming nucleotide triphosphate in transcription

PubMed Central

Huang, Xuhui; Wang, Dong; Weiss, Dahlia R.; Bushnell, David A.; Kornberg, Roger D.; Levitt, Michael

2010-01-01

A structurally conserved element, the trigger loop, has been suggested to play a key role in substrate selection and catalysis of RNA polymerase II (pol II) transcription elongation. Recently resolved X-ray structures showed that the trigger loop forms direct interactions with the β-phosphate and base of the matched nucleotide triphosphate (NTP) through residues His1085 and Leu1081, respectively. In order to understand the role of these two critical residues in stabilizing active site conformation in the dynamic complex, we performed all-atom molecular dynamics simulations of the wild-type pol II elongation complex and its mutants in explicit solvent. In the wild-type complex, we found that the trigger loop is stabilized in the “closed” conformation, and His1085 forms a stable interaction with the NTP. Simulations of point mutations of His1085 are shown to affect this interaction; simulations of alternative protonation states, which are inaccessible through experiment, indicate that only the protonated form is able to stabilize the His1085-NTP interaction. Another trigger loop residue, Leu1081, stabilizes the incoming nucleotide position through interaction with the nucleotide base. Our simulations of this Leu mutant suggest a three-component mechanism for correctly positioning the incoming NTP in which (i) hydrophobic contact through Leu1081, (ii) base stacking, and (iii) base pairing work together to minimize the motion of the incoming NTP base. These results complement experimental observations and provide insight into the role of the trigger loop on transcription fidelity. PMID:20798057

New copper complexes with bipyrazolic ligands: Synthesis, characterization and evaluation of the antibacterial and catalytic properties

NASA Astrophysics Data System (ADS)

Harit, Tarik; Abouloifa, Houssam; Tillard, Monique; Eddike, Driss; Asehraou, Abdeslam; Malek, Fouad

2018-07-01

The synthesis of new bipyrazolic ligands functionalized by carboxyl groups, namely 3-Bis(3‧-carboxyl-5‧-methyl-l'-pyrazolyl) propan-2-ol (L1) and 1,3-Bis(3‧-carboxyl-5‧-methyl-l '-pyrazolyl),2-methyl propane (L2) is reported. Their corresponding [C13H15CuN4O5] (CuL1) and [C14H16CuN4O4] (CuL2) copper (II) complexes are also elaborated and characterized by elemental analysis, FTIR an UV-visible spectroscopy. The crystal structure of the CuL1 complex confirms that copper atom is 4-coordinated, in a distorted square planar geometry within the molecule, and achieves its coordination through weak intermolecular interactions leading to two dimensional slabs. This geometry is in agreement with UV-visible results which also evidence that structure of complexes are affected in DMSO in contrast to methanol. No antibacterial activity against all the tested bacterial strains has been found for the Cu (II) complexes. By contrast, CuL1 is characterized with good catalytic properties in the air-oxidation of catechol substrate to quinone.

Crystal structures of the structure-selective nuclease Mus81-Eme1 bound to flap DNA substrates

PubMed Central

Gwon, Gwang Hyeon; Jo, Aera; Baek, Kyuwon; Jin, Kyeong Sik; Fu, Yaoyao; Lee, Jong-Bong; Kim, YoungChang; Cho, Yunje

2014-01-01

The Mus81-Eme1 complex is a structure-selective endonuclease with a critical role in the resolution of recombination intermediates during DNA repair after interstrand cross-links, replication fork collapse, or double-strand breaks. To explain the molecular basis of 3′ flap substrate recognition and cleavage mechanism by Mus81-Eme1, we determined crystal structures of human Mus81-Eme1 bound to various flap DNA substrates. Mus81-Eme1 undergoes gross substrate-induced conformational changes that reveal two key features: (i) a hydrophobic wedge of Mus81 that separates pre- and post-nick duplex DNA and (ii) a “5′ end binding pocket” that hosts the 5′ nicked end of post-nick DNA. These features are crucial for comprehensive protein-DNA interaction, sharp bending of the 3′ flap DNA substrate, and incision strand placement at the active site. While Mus81-Eme1 unexpectedly shares several common features with members of the 5′ flap nuclease family, the combined structural, biochemical, and biophysical analyses explain why Mus81-Eme1 preferentially cleaves 3′ flap DNA substrates with 5′ nicked ends. PMID:24733841

The Crystal Structure Analysis of Group B Streptococcus Sortase C1: A Model for the ;Lid; Movement upon Substrate Binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khare, Baldeep; Fu, Zheng-Qing; Huang, I-Hsiu

2012-02-07

A unique feature of the class-C-type sortases, enzymes essential for Gram-positive pilus biogenesis, is the presence of a flexible 'lid' anchored in the active site. However, the mechanistic details of the 'lid' displacement, suggested to be a critical prelude for enzyme catalysis, are not yet known. This is partly due to the absence of enzyme-substrate and enzyme-inhibitor complex crystal structures. We have recently described the crystal structures of the Streptococcus agalactiae SAG2603 V/R sortase SrtC1 in two space groups (type II and type III) and that of its 'lid' mutant and proposed a role of the 'lid' as a protectormore » of the active-site hydrophobic environment. Here, we report the crystal structures of SAG2603 V/R sortase C1 in a different space group (type I) and that of its complex with a small-molecule cysteine protease inhibitor. We observe that the catalytic Cys residue is covalently linked to the small-molecule inhibitor without lid displacement. However, the type I structure provides a view of the sortase SrtC1 lid displacement while having structural elements similar to a substrate sorting motif suitably positioned in the active site. We propose that these major conformational changes seen in the presence of a substrate mimic in the active site may represent universal features of class C sortase substrate recognition and enzyme activation.« less

Pb, Cu, and Zn distributions at humic acid-coated metal-oxide surfaces

DOE PAGES

Wang, Yingge; Michel, F. Marc; Choi, Yongseong; ...

2016-05-09

Here, mineral surfaces are often coated by natural organic matter (NOM), which has a major influence on metal-ion sorption and sequestration because of the abundance of binding sites in such coatings and the changes they cause in local nanoscale environments. The effects of NOM coatings on mineral surfaces are, however, still poorly understood at the molecular level due to the complexity of these systems. In this study, we have applied long-period X-ray standing wave-fluorescence yield (LP-XSW-FY) spectroscopy to measure the partitioning of naturally present Cu(II) (0.0226%), Zn(II) (0.009%), and Pb(II) ( 0.0004%) between Elliott Soil Humic Acid (ESHA) coatings andmore » three model single-crystal metal-oxide substrates: α-Al 2O 3 (0 0 0 1), α-Al 2O 3 (1 1 0 2), and α-Fe 2O 3 (0 0 0 1). The competitive sorption effects among these metal ions for binding sites in the ESHA coatings and on the metal-oxide surfaces were investigated as a function of reaction time, calcium content, and solution pH. Pb(II) ions present in the ESHA coatings were found to redistribute to reactive α-Al 2O 3 (1 1 0 2) and α-Fe 2O 3 (0 0 0 1) surfaces after 3 h of reaction (pH = 6.0, [Ca(II)] = 2 mM). Pb(II) partitioning onto these reactive metal-oxide surfaces increased with increasing reaction time (up to 7 d). In addition, the partitioning of Cu(II) and Zn(II) from the ESHA coating to the α-Fe 2O 3 (0 0 0 1) substrate increased slightly with reaction time (2.4% and 3.7% for Cu(II) and Zn(II), respectively, after 3 h and 6.4% and 7.7% for Cu(II) and Zn(II), respectively, after 72 h of reaction time).« less

The role of glutamine and other alternate substrates as energy sources in the fetal rat lung type II cell.

PubMed

Fox, R E; Hopkins, I B; Cabacungan, E T; Tildon, J T

1996-07-01

Glucose has been thought to be the primary substrate for energy metabolism in the developing lung; however, alternate substrates are used for energy metabolism in other organs. To examine the role of alternate substrates in the lung, we measured rates of oxidation of glutamine, glucose, lactate, and 3-hydroxybutyrate in type II pneumocytes isolated from d 19 fetal rat lungs by measuring the production of 14CO2 from labeled substrates. Glutamine had a rate of 24.36 +/- 4.51 nmol 14CO2 produced/ h/mg of protein (mean +/- SEM), whereas lactate had a significantly higher rate, 40.29 +/- 4.42. 3-Hydroxybutyrate had a rate of 14.91 +/- 1.93. The rate of glucose oxidation was 2.13 +/- 0.36, significantly lower than that of glutamine. To examine the interactions of substrates normally found in the intracellular milieu, we measured the effect of unlabeled substrates as competitors on labeled substrate. This identifies multiple metabolic compartments of energy metabolism. Glucose, but not lactate, inhibited the oxidation of glutamine, suggesting a compartmentation of tricarboxylic acid cycle activity, rather than simple dilution by glucose. Glucose and lactate had reciprocal inhibition. Our data suggest at least two separate compartments in the type II cells for substrate oxidation, one for glutamine metabolism and a second for glucose metabolism. In summary, we have documented that glutamine and other alternate substrates are oxidized preferentially over glucose for energy metabolism in the d 19 fetal rat lung type II pneumocyte. In addition, we have delineated some of the compartmentation that occurs within the developing type II cell, which may determine how these substrates are used.

Phenoxo bridged dinuclear Zn(II) Schiff base complex as new precursor for preparation zinc oxide nanoparticles: Synthesis, characterization, crystal structures and photoluminescence studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saeednia, S., E-mail: sami_saeednia@yahoo.com; Iranmanesh, P.; Ardakani, M. Hatefi

Highlights: • A novel nano-scale Zn(II) complex was synthesized by solvothermal method. • Chemical structure of the nanostructures was characterized as well as bulk complex. • The photoluminescence property of the complex was investigated at room temperature. • The thermogravimetry and differential thermal analysis were carried out. • Thermal decomposition of the nanostructures was prepared zinc oxide nanoparticles. - Abstract: Nanoparticles of a novel Zn(II) Schiff base complex, [Zn(HL)NO{sub 3}]{sub 2} (1), (H{sub 2}L = 2-[(2-hydroxy-propylimino) methyl] phenol), was synthesized by using solvothermal method. Shape, morphology and chemical structure of the synthesized nanoparticles were characterized by scanning electron microscopy (SEM),more » X-ray powder diffraction (XRD), Fourier Transform Infrared Spectoscopy (FT-IR) and UV–vis spectroscopy. Structural determination of compound 1 was determined by single-crystal X-ray diffraction. The results were revealed that the zinc complex is a centrosymmetric dimer in which deprotonated phenolates bridge the two five-coordinate metal atoms and link the two halves of the dimer. The thermal stability of compound 1 was analyzed by thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC). The effect of the initial substrates concentration and reaction time on size and morphology of compound 1 nanostructure was investigated as well. Furthermore, the luminescent properties of the complex 1 were examined. ZnO nanoparticles with diameter between 15 and 20 nm were simply synthesized by solid-state transformation of compound 1 at 700 °C.« less

Substrate-triggered addition of dioxygen to the diferrous cofactor of aldehyde-deformylating oxygenase to form a diferric-peroxide intermediate.

PubMed

Pandelia, Maria E; Li, Ning; Nørgaard, Hanne; Warui, Douglas M; Rajakovich, Lauren J; Chang, Wei-Chen; Booker, Squire J; Krebs, Carsten; Bollinger, J Martin

2013-10-23

Cyanobacterial aldehyde-deformylating oxygenases (ADOs) belong to the ferritin-like diiron-carboxylate superfamily of dioxygen-activating proteins. They catalyze conversion of saturated or monounsaturated C(n) fatty aldehydes to formate and the corresponding C(n-1) alkanes or alkenes, respectively. This unusual, apparently redox-neutral transformation actually requires four electrons per turnover to reduce the O2 cosubstrate to the oxidation state of water and incorporates one O-atom from O2 into the formate coproduct. We show here that the complex of the diiron(II/II) form of ADO from Nostoc punctiforme (Np) with an aldehyde substrate reacts with O2 to form a colored intermediate with spectroscopic properties suggestive of a Fe2(III/III) complex with a bound peroxide. Its Mössbauer spectra reveal that the intermediate possesses an antiferromagnetically (AF) coupled Fe2(III/III) center with resolved subsites. The intermediate is long-lived in the absence of a reducing system, decaying slowly (t(1/2) ~ 400 s at 5 °C) to produce a very modest yield of formate (<0.15 enzyme equivalents), but reacts rapidly with the fully reduced form of 1-methoxy-5-methylphenazinium methylsulfate ((MeO)PMS) to yield product, albeit at only ~50% of the maximum theoretical yield (owing to competition from one or more unproductive pathway). The results represent the most definitive evidence to date that ADO can use a diiron cofactor (rather than a homo- or heterodinuclear cluster involving another transition metal) and provide support for a mechanism involving attack on the carbonyl of the bound substrate by the reduced O2 moiety to form a Fe2(III/III)-peroxyhemiacetal complex, which undergoes reductive O-O-bond cleavage, leading to C1-C2 radical fragmentation and formation of the alk(a/e)ne and formate products.

Substrate Topography Induces a Crossover from 2D to 3D Behavior in Fibroblast Migration

PubMed Central

Ghibaudo, Marion; Trichet, Léa; Le Digabel, Jimmy; Richert, Alain; Hersen, Pascal; Ladoux, Benoît

2009-01-01

Abstract In a three-dimensional environment, cells migrate through complex topographical features. Using microstructured substrates, we investigate the role of substrate topography in cell adhesion and migration. To do so, fibroblasts are plated on chemically identical substrates composed of microfabricated pillars. When the dimensions of the pillars (i.e., the diameter, length, and spacing) are varied, migrating cells encounter alternating flat and rough surfaces that depend on the spacing between the pillars. Consequently, we show that substrate topography affects cell shape and migration by modifying cell-to-substrate interactions. Cells on micropillar substrates exhibit more elongated and branched shapes with fewer actin stress fibers compared with cells on flat surfaces. By analyzing the migration paths in various environments, we observe different mechanisms of cell migration, including a persistent type of migration, that depend on the organization of the topographical features. These responses can be attributed to a spatial reorganization of the actin cytoskeleton due to physical constraints and a preferential formation of focal adhesions on the micropillars, with an increased lifetime compared to that observed on flat surfaces. By changing myosin II activity, we show that actomyosin contractility is essential in the cellular response to micron-scale topographic signals. Finally, the analysis of cell movements at the frontier between flat and micropillar substrates shows that cell transmigration through the micropillar substrates depends on the spacing between the pillars. PMID:19580774

Rational Design Synthesis and Evaluation of New Selective Inhibitors of Microbial Class II (Zinc Dependent) Fructose Bis-phosphate Aldolases

DOE Office of Scientific and Technical Information (OSTI.GOV)

R Daher; M Coincon; M Fonvielle

2011-12-31

We report the synthesis and biochemical evaluation of several selective inhibitors of class II (zinc dependent) fructose bis-phosphate aldolases (Fba). The products were designed as transition-state analogues of the catalyzed reaction, structurally related to the substrate fructose bis-phosphate (or sedoheptulose bis-phosphate) and based on an N-substituted hydroxamic acid, as a chelator of the zinc ion present in active site. The compounds synthesized were tested on class II Fbas from various pathogenic microorganisms and, by comparison, on a mammalian class I Fba. The best inhibitor shows Ki against class II Fbas from various pathogens in the nM range, with very highmore » selectivity (up to 105). Structural analyses of inhibitors in complex with aldolases rationalize and corroborate the enzymatic kinetics results. These inhibitors represent lead compounds for the preparation of new synthetic antibiotics, notably for tuberculosis prophylaxis.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Zhenzhou, E-mail: jiangcpu@yahoo.com.cn; Bao, Qingli, E-mail: bao_ql@126.com; Sun, Lixin, E-mail: slxcpu@126.com

This report describes an investigation of the pathological mechanism of acute renal failure caused by toxic tubular necrosis after treatment with aristolochic acid I (AAI) in Sprague–Dawley (SD) rats. The rats were gavaged with AAI at 0, 5, 20, or 80 mg/kg/day for 7 days. The pathologic examination of the kidneys showed severe acute tubular degenerative changes primarily affecting the proximal tubules. Supporting these results, we detected significantly increased concentrations of blood urea nitrogen (BUN) and creatinine (Cr) in the rats treated with AAI, indicating damage to the kidneys. Ultrastructural examination showed that proximal tubular mitochondria were extremely enlarged andmore » dysmorphic with loss and disorientation of their cristae. Mitochondrial function analysis revealed that the two indicators for mitochondrial energy metabolism, the respiratory control ratio (RCR) and ATP content, were reduced in a dose-dependent manner after AAI treatment. The RCR in the presence of substrates for complex I was reduced more significantly than in the presence of substrates for complex II. In additional experiments, the activity of respiratory complex I, which is partly encoded by mitochondrial DNA (mtDNA), was more significantly impaired than that of respiratory complex II, which is completely encoded by nuclear DNA (nDNA). A real-time PCR assay revealed a marked reduction of mtDNA in the kidneys treated with AAI. Taken together, these results suggested that mtDNA depletion and respiratory chain defects play critical roles in the pathogenesis of kidney injury induced by AAI, and that the same processes might contribute to aristolochic acid-induced nephrotoxicity in humans. -- Highlights: ► AAI-induced acute renal failure in rats and the proximal tubule was the target. ► Tubular mitochondria were morphologically aberrant in ultrastructural examination. ► AAI impair mitochondrial bioenergetic function and mtDNA replication.« less

Synthesis and characterization of para-pyridine linked NHC palladium complexes and their studies for the Heck-Mizoroki coupling reaction.

PubMed

Liu, Ya-Ming; Lin, Yi-Chun; Chen, Wen-Ching; Cheng, Jen-Hao; Chen, Yi-Lin; Yap, Glenn P A; Sun, Shih-Sheng; Ong, Tiow-Gan

2012-06-28

This paper describes the synthesis of 1-(pyridine-4-ylmethyl) NHC and their Pd(II) and Ag(I) complexes, which are fully characterized. Interestingly, we have also synthesized a Pd complex 3a-CO(3) using a more direct treatment of K(2)CO(3) with PdCl(2). 3a-CO(3) represents the first reported solid structure of a Pd η(2)-carbonato complex stabilized by an NHC framework. 3a-CO(3) can be easily converted to a PdCl(2) derivative by treating it with chloroform. We have found these palladium complexes mediate the Heck-Mizoroki coupling with a low catalyst loading. Furthermore, we also expand such catalytic manifold toward constructing fused polyaromatic substrates, a highly useful class of compounds in optoelectronic chemistry.

New ruthenium(II) carbonyl complexes bearing disulfide Schiff base ligands and their applications as catalyst for some organic transformations

NASA Astrophysics Data System (ADS)

Prakash, Govindan; Viswanathamurthi, Periasamy

2014-08-01

Schiff base disulfide ligands (H2L1-6) were synthesized from the condensation of cystamine with salicylaldehyde(H2L1), 5-chlorosalicylaldehyde(H2L2), o-vanillin(H2L3), 2-hydroxyacetophenone(H2L4), 3-methyl-2-hydroxyacetophenone(H2L5), and 2-hydroxy-1-naphthaldehyde(H2L6). H2L1-6 reacts with the ruthenium precursor complex [RuHCl(CO)(PPh3)3] in benzene giving rise to six new ruthenium(II) complexes of general formula [Ru(CO)L1-6]. Characterization of the new complexes was carried out by using elemental and spectral (IR, UV-Vis, NMR (1H and 13C) and Mass) techniques. An octahedral geometry was assigned for all the complexes based on the spectral data obtained. The catalytic efficiency of the new complexes in aldehyde to amide conversion in the presence of NaHCO3, N-alkylation of aniline in the presence of t-BuOK, and transfer hydrogenation of ketones in the presence of iPrOH/KOH reactions were studied. Furthermore, the effect of solvents and catalyst/substrate ratio on the catalytic aldehyde to amide conversion were also discussed.

New ruthenium(II) carbonyl complexes bearing disulfide Schiff base ligands and their applications as catalyst for some organic transformations.

PubMed

Prakash, Govindan; Viswanathamurthi, Periasamy

2014-08-14

Schiff base disulfide ligands (H2L(1-6)) were synthesized from the condensation of cystamine with salicylaldehyde(H2L(1)), 5-chlorosalicylaldehyde(H2L(2)), o-vanillin(H2L(3)), 2-hydroxyacetophenone(H2L(4)), 3-methyl-2-hydroxyacetophenone(H2L(5)), and 2-hydroxy-1-naphthaldehyde(H2L(6)). H2L(1-6) reacts with the ruthenium precursor complex [RuHCl(CO)(PPh3)3] in benzene giving rise to six new ruthenium(II) complexes of general formula [Ru(CO)L(1-6)]. Characterization of the new complexes was carried out by using elemental and spectral (IR, UV-Vis, NMR ((1)H and (13)C) and Mass) techniques. An octahedral geometry was assigned for all the complexes based on the spectral data obtained. The catalytic efficiency of the new complexes in aldehyde to amide conversion in the presence of NaHCO3, N-alkylation of aniline in the presence of t-BuOK, and transfer hydrogenation of ketones in the presence of iPrOH/KOH reactions were studied. Furthermore, the effect of solvents and catalyst/substrate ratio on the catalytic aldehyde to amide conversion were also discussed. Copyright © 2014 Elsevier B.V. All rights reserved.

The Chemical Vapor Deposition of Thin Metal Oxide Films

NASA Astrophysics Data System (ADS)

Laurie, Angus Buchanan

1990-01-01

Chemical vapor deposition (CVD) is an important method of preparing thin films of materials. Copper (II) oxide is an important p-type semiconductor and a major component of high T_{rm c} superconducting oxides. By using a volatile copper (II) chelate precursor, copper (II) bishexafluoroacetylacetonate, it has been possible to prepare thin films of copper (II) oxide by low temperature normal pressure metalorganic chemical vapor deposition. In the metalorganic CVD (MOCVD) production of oxide thin films, oxygen gas saturated with water vapor has been used mainly to reduce residual carbon and fluorine content. This research has investigated the influence of water-saturated oxygen on the morphology of thin films of CuO produced by low temperature chemical vapor deposition onto quartz, magnesium oxide and cubic zirconia substrates. ZnO is a useful n-type semiconductor material and is commonly prepared by the MOCVD method using organometallic precursors such as dimethyl or diethylzinc. These compounds are difficult to handle under atmospheric conditions. In this research, thin polycrystalline films of zinc oxide were grown on a variety of substrates by normal pressure CVD using a zinc chelate complex with zinc(II) bishexafluoroacetylacetonate dihydrate (Zn(hfa)_2.2H _2O) as the zinc source. Zn(hfa) _2.2H_2O is not moisture - or air-sensitive and is thus more easily handled. By operating under reduced-pressure conditions (20-500 torr) it is possible to substantially reduce deposition times and improve film quality. This research has investigated the reduced-pressure CVD of thin films of CuO and ZnO. Sub-micron films of tin(IV) oxide (SnO _2) have been grown by normal pressure CVD on quartz substrates by using tetraphenyltin (TPT) as the source of tin. All CVD films were characterized by X-ray powder diffraction (XRPD), scanning electron microscopy (SEM) and electron probe microanalysis (EPMA).

Batch and fixed-bed biosorption of Cd(II) from aqueous solution using immobilized Pleurotus ostreatus spent substrate.

PubMed

Jin, Yu; Teng, Chunying; Yu, Sumei; Song, Tao; Dong, Liying; Liang, Jinsong; Bai, Xin; Liu, Xuesheng; Hu, Xiaojing; Qu, Juanjuan

2018-01-01

To prevent the blockage in a continuous fix-bed system, Pleurotus Ostreatus spent substrate (POSS), a composite agricultural waste, was immobilized into granular adsorbents (IPOSS) with polymeric matrix, and used to remove Cd(II) from synthetic wastewater in batch experiment as well as in continuous fixed-bed column system. In batch experiment, higher pH, temperature and Cd(II) initial concentration were conducive to a higher biosorption capacity, and the maximum biosorption capacity reached up to 87.2 mg/g at Cd(II) initial concentration of 200 mg/L, pH 6 and 25 °C. The biosorption of Cd(II) onto IPOSS followed the Langmuir isotherm model with the maximum adsorption capacity(q max ) of 100 mg/g. The biosorption was an endothermic reaction and a spontaneous process based on positive value of ΔH 0 and negative value of ΔG 0 . In fixed-bed column system, higher bed depth, lower flow rate and influent Cd(II) concentration led to a longer breakthrough and exhaustion time, and the best performance (equilibrium uptake (q e ) of 14.4 mg, breakthrough time at 31 h and exhaustion time at 78 h) was achieved at a bed depth of 110 cm, a flow rate of 1.2 L/h and an influent concentration of 100 mg/L. Furthermore, regeneration experiment revealed a good reusability of IPOSS with 0.1 M HNO 3 as eluting agent during three cycles of adsorption and desorption. Cd(II) biosorption onto IPOSS mainly relied on a chemical process including ion exchange and complexation or coordination revealed by SEM-EDX, FTIR and XRD analysis. Copyright © 2017. Published by Elsevier Ltd.

Method of manufacturing semiconductor having group II-group VI compounds doped with nitrogen

DOEpatents

Compaan, Alvin D.; Price, Kent J.; Ma, Xianda; Makhratchev, Konstantin

2005-02-08

A method of making a semiconductor comprises depositing a group II-group VI compound onto a substrate in the presence of nitrogen using sputtering to produce a nitrogen-doped semiconductor. This method can be used for making a photovoltaic cell using sputtering to apply a back contact layer of group II-group VI compound to a substrate in the presence of nitrogen, the back coating layer being doped with nitrogen. A semiconductor comprising a group II-group VI compound doped with nitrogen, and a photovoltaic cell comprising a substrate on which is deposited a layer of a group II-group VI compound doped with nitrogen, are also included.

Reaction of an Iron(IV) Nitrido Complex with Cyclohexadienes: Cycloaddition and Hydrogen-Atom Abstraction

PubMed Central

2015-01-01

The iron(IV) nitrido complex PhB(MesIm)3Fe≡N reacts with 1,3-cyclohexadiene to yield the iron(II) pyrrolide complex PhB(MesIm)3Fe(η5-C4H4N) in high yield. The mechanism of product formation is proposed to involve sequential [4 + 1] cycloaddition and retro Diels–Alder reactions. Surprisingly, reaction with 1,4-cyclohexadiene yields the same iron-containing product, albeit in substantially lower yield. The proposed reaction mechanism, supported by electronic structure calculations, involves hydrogen-atom abstraction from 1,4-cyclohexadiene to provide the cyclohexadienyl radical. This radical is an intermediate in substrate isomerization to 1,3-cyclohexadiene, leading to formation of the pyrrolide product. PMID:25068927

Structure of a Clostridium botulinum C143S thiaminase I/thiamin complex reveals active site architecture .

PubMed

Sikowitz, Megan D; Shome, Brateen; Zhang, Yang; Begley, Tadhg P; Ealick, Steven E

2013-11-05

Thiaminases are responsible for the degradation of thiamin and its metabolites. Two classes of thiaminases have been identified based on their three-dimensional structures and their requirements for a nucleophilic second substrate. Although the reactions of several thiaminases have been characterized, the physiological role of thiamin degradation is not fully understood. We have determined the three-dimensional X-ray structure of an inactive C143S mutant of Clostridium botulinum (Cb) thiaminase I with bound thiamin at 2.2 Å resolution. The C143S/thiamin complex provides atomic level details of the orientation of thiamin upon binding to Cb-thiaminase I and the identity of active site residues involved in substrate binding and catalysis. The specific roles of active site residues were probed by using site directed mutagenesis and kinetic analyses, leading to a detailed mechanism for Cb-thiaminase I. The structure of Cb-thiaminase I is also compared to the functionally similar but structurally distinct thiaminase II.

Tandem catalysis of ring-closing metathesis/atom transfer radical reactions with homobimetallic ruthenium–arene complexes

PubMed Central

Borguet, Yannick; Sauvage, Xavier; Zaragoza, Guillermo; Demonceau, Albert

2010-01-01

Summary The tandem catalysis of ring-closing metathesis/atom transfer radical reactions was investigated with the homobimetallic ruthenium–indenylidene complex [(p-cymene)Ru(μ-Cl)3RuCl(3-phenyl-1-indenylidene)(PCy3)] (1) to generate active species in situ. The two catalytic processes were first carried out independently in a case study before the whole sequence was optimized and applied to the synthesis of several polyhalogenated bicyclic γ-lactams and lactones from α,ω-diene substrates bearing trihaloacetamide or trichloroacetate functionalities. The individual steps were carefully monitored by 1H and 31P NMR spectroscopies in order to understand the intimate details of the catalytic cycles. Polyhalogenated substrates and the ethylene released upon metathesis induced the clean transformation of catalyst precursor 1 into the Ru(II)–Ru(III) mixed-valence compound [(p-cymene)Ru(μ-Cl)3RuCl2(PCy3)], which was found to be an efficient promoter for atom transfer radical reactions under the adopted experimental conditions. PMID:21160564

Enantioselective photochemistry via Lewis acid catalyzed triplet energy transfer

PubMed Central

Blum, Travis R.; Miller, Zachary D.; Bates, Desiree M.; Guzei, Ilia A.; Yoon, Tehshik P.

2017-01-01

Relatively few catalytic systems are able to control the stereochemistry of electronically excited organic intermediates. Here we report the discovery that a chiral Lewis acid complex can catalyze triplet energy transfer from an electronically excited photosensitizer. This strategy is applied to asymmetric [2+2] photocycloadditions of 2′-hydroxychalcones using tris(bipyridyl) ruthenium(II) as a sensitizer. A variety of electrochemical, computational, and spectroscopic data rule out substrate activation via photoinduced electron transfer and instead support a mechanism in which Lewis acid coordination dramatically lowers the triplet energy of the chalcone substrate. We expect that this approach will enable chemists to more broadly apply their detailed understanding of chiral Lewis acid catalysis to stereocontrol in reactions of electronically excited states. PMID:27980203

A miniaturized assay for measuring small molecule phosphorylation in the presence of complex matrices.

PubMed

Spry, Christina; Saliba, Kevin J; Strauss, Erick

2014-04-15

We describe here a simple, miniaturized radiation-based phosphorylation assay that can be used to monitor phosphorylation of a diverse range of small molecule substrates in the presence of purified and crude enzyme preparations. Ba(OH)2 and ZnSO4 are used to terminate phosphoryl transfer and to precipitate selectively the phosphorylated reaction product in a single step; non-phosphorylated substrate is removed by filtration prior to quantification. The key advantages over alternative radiation-based assays are that: (i) high-energy/short-lived radioactive emitters are not required; (ii) high-quality data can be obtained without the need for high radioactivity concentrations; and (iii) the assay is compatible with high-throughput applications. Copyright © 2013 Elsevier Inc. All rights reserved.

Structural changes in the S 3 state of the oxygen evolving complex in photosystem II

DOE PAGES

Hatakeyama, Makoto; Ogata, Koji; Fujii, Katsushi; ...

2016-03-19

The S 3 state of the Mn 4CaO 5-cluster in photosystem II was investigated by DFT calculations and compared with EXAFS data. Considering previously proposed mechanism; a water molecule is inserted into an open coordination site of Mn upon S 2 to S 3 transition that becomes a substrate water, we examined if the water insertion is essential for the S 3 formation, or if one cannot eliminate other possible routes that do not require a water insertion at the S 3 stage. The novel S 3 state structure consisting of only short 2.7–2.8 Å MnMn distances was discussed.

Structural changes in the S 3 state of the oxygen evolving complex in photosystem II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hatakeyama, Makoto; Ogata, Koji; Fujii, Katsushi

The S 3 state of the Mn 4CaO 5-cluster in photosystem II was investigated by DFT calculations and compared with EXAFS data. Considering previously proposed mechanism; a water molecule is inserted into an open coordination site of Mn upon S 2 to S 3 transition that becomes a substrate water, we examined if the water insertion is essential for the S 3 formation, or if one cannot eliminate other possible routes that do not require a water insertion at the S 3 stage. The novel S 3 state structure consisting of only short 2.7–2.8 Å MnMn distances was discussed.

Diastereoselective sp2-sp3 coupling of sugar enol ethers with unactivated cycloalkenes: new entries to C-branched sugars.

PubMed

Hussain, Nazar; Tatina, Madhu Babu; Rasool, Faheem; Mukherjee, Debaraj

2016-10-25

Sugar enol ethers undergo efficient coupling at C-2 with unactivated cycloalkenes under a low Pd loading affording allylic substitution products. High diastereoselectivity was observed at the allylic centre with sterically hindered substrates. Generation of a π-allyl complex by the Pd(ii) catalyst via cleavage of the allylic C-H bond of the cycloalkene may be responsible for the formation of sp 2 -sp 3 coupling products.

Propagation failures, breathing pulses, and backfiring in an excitable reaction-diffusion system.

PubMed

Manz, Niklas; Steinbock, Oliver

2006-09-01

We report results from experiments with a pseudo-one-dimensional Belousov-Zhabotinsky reaction that employs 1,4-cyclohexanedione as its organic substrate. This excitable system shows traveling oxidation pulses and pulse trains that can undergo complex sequences of propagation failures. Moreover, we present examples for (i) breathing pulses that undergo periodic changes in speed and size and (ii) backfiring pulses that near their back repeatedly generate new pulses propagating in opposite direction.

Conversion of the sensor kinase DcuS of Escherichia coli of the DcuB/DcuS sensor complex to the C4 -dicarboxylate responsive form by the transporter DcuB.

PubMed

Wörner, Sebastian; Strecker, Alexander; Monzel, Christian; Zeltner, Matthias; Witan, Julian; Ebert-Jung, Andrea; Unden, Gottfried

2016-12-01

The sensor kinase DcuS of Escherichia coli co-operates under aerobic conditions with the C 4 -dicarboxylate transporter DctA to form the DctA/DcuS sensor complex. Under anaerobic conditions C 4 -dicarboxylate transport in fumarate respiration is catalyzed by C 4 -dicarboxylate/fumarate antiporter DcuB. (i) DcuB interacted with DcuS as demonstrated by a bacterial two-hybrid system (BACTH) and by co-chromatography of the solubilized membrane-proteins (mHPINE assay). (ii) In the DcuB/DcuS complex only DcuS served as the sensor since mutations in the substrate site of DcuS changed substrate specificity of sensing, and substrates maleate or 3-nitropropionate induced DcuS response without affecting the fumarate site of DcuB. (iii) The half-maximal concentration for induction of DcuS by fumarate (1 to 2 mM) and the corresponding K m for transport (50 µM) differ by a factor of 20 to 40. Therefore, the fumarate sites are different in transport and sensing. (iv) Increasing levels of DcuB converted DcuS from the permanent ON (DcuB deficient) state to the fumarate responsive form. Overall, the data show that DcuS and DcuB form a DcuB/DcuS complex representing the C 4 -dicarboxylate responsive form, and that the sensory site of the complex is located in DcuS whereas DcuB is required for converting DcuS to the sensory competent state. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Crystallization and preliminary crystallographic analysis of human Atg4B–LC3 complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Satoo, Kenji; Suzuki, Nobuo N.; Fujioka, Yuko

2007-02-01

Human Atg4B and LC3 were expressed, purified and crystallized as a complex. Diffraction data were collected to a resolution of 1.9 Å. The reversible modification of Atg8 with phosphatidylethanolamine (PE) is crucial for autophagy, the bulk degradation process of cytoplasmic components by the vacuolar/lysosomal system. Atg4 is a cysteine protease that is responsible for the processing and deconjugation of Atg8. Human Atg4B (HsAtg4B; a mammalian orthologue of yeast Atg4) and LC3 (a mammalian orthologue of yeast Atg8) were expressed and purified and two complexes, one consisting of HsAtg4B(1–354) and LC3(1–120) (complex I; the product complex) and the other consisting ofmore » HsAtg4B(1–354) and LC3(1–124) (complex II; the substrate complex), were crystallized using polyethylene glycol 3350 as a precipitant. In both complexes His280 of HsAtg4B was mutated to alanine. The crystals belong to the same space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 47.5, b = 91.8, c = 102.6 Å for complex I and a = 46.9, b = 90.9, c = 102.5 Å for complex II. Diffraction data were collected to a resolution of 1.9 Å from both crystals.« less

High Intensity Interval Training (HIIT) Induces Specific Changes in Respiration and Electron Leakage in the Mitochondria of Different Rat Skeletal Muscles

PubMed Central

de-Souza-Ferreira, Eduardo; Guerra Martinez, Camila; Kurtenbach, Eleonora; Casimiro-Lopes, Gustavo; Galina, Antonio

2015-01-01

High intensity interval training (HIIT) is characterized by vigorous exercise with short rest intervals. Hydrogen peroxide (H2O2) plays a key role in muscle adaptation. This study aimed to evaluate whether HIIT promotes similar H2O2 formation via O2 consumption (electron leakage) in three skeletal muscles with different twitch characteristics. Rats were assigned to two groups: sedentary (n=10) and HIIT (n=10, swimming training). We collected the tibialis anterior (TA-fast), gastrocnemius (GAST-fast/slow) and soleus (SOL-slow) muscles. The fibers were analyzed for mitochondrial respiration, H2O2 production and citrate synthase (CS) activity. A multi-substrate (glycerol phosphate (G3P), pyruvate, malate, glutamate and succinate) approach was used to analyze the mitochondria in permeabilized fibers. Compared to the control group, oxygen flow coupled to ATP synthesis, complex I and complex II was higher in the TA of the HIIT group by 1.5-, 3.0- and 2.7-fold, respectively. In contrast, oxygen consumed by mitochondrial glycerol phosphate dehydrogenase (mGPdH) was 30% lower. Surprisingly, the oxygen flow coupled to ATP synthesis was 42% lower after HIIT in the SOL. Moreover, oxygen flow coupled to ATP synthesis and complex II was higher by 1.4- and 2.7-fold in the GAST of the HIIT group. After HIIT, CS activity increased 1.3-fold in the TA, and H2O2 production was 1.3-fold higher in the TA at sites containing mGPdH. No significant differences in H2O2 production were detected in the SOL. Surprisingly, HIIT increased H2O2 production in the GAST via complex II, phosphorylation, oligomycin and antimycin by 1.6-, 1.8-, 2.2-, and 2.2-fold, respectively. Electron leakage was 3.3-fold higher in the TA with G3P and 1.8-fold higher in the GAST with multiple substrates. Unexpectedly, the HIIT protocol induced different respiration and electron leakage responses in different types of muscle. PMID:26121248

High Intensity Interval Training (HIIT) Induces Specific Changes in Respiration and Electron Leakage in the Mitochondria of Different Rat Skeletal Muscles.

PubMed

Ramos-Filho, Dionizio; Chicaybam, Gustavo; de-Souza-Ferreira, Eduardo; Guerra Martinez, Camila; Kurtenbach, Eleonora; Casimiro-Lopes, Gustavo; Galina, Antonio

2015-01-01

High intensity interval training (HIIT) is characterized by vigorous exercise with short rest intervals. Hydrogen peroxide (H2O2) plays a key role in muscle adaptation. This study aimed to evaluate whether HIIT promotes similar H2O2 formation via O2 consumption (electron leakage) in three skeletal muscles with different twitch characteristics. Rats were assigned to two groups: sedentary (n=10) and HIIT (n=10, swimming training). We collected the tibialis anterior (TA-fast), gastrocnemius (GAST-fast/slow) and soleus (SOL-slow) muscles. The fibers were analyzed for mitochondrial respiration, H2O2 production and citrate synthase (CS) activity. A multi-substrate (glycerol phosphate (G3P), pyruvate, malate, glutamate and succinate) approach was used to analyze the mitochondria in permeabilized fibers. Compared to the control group, oxygen flow coupled to ATP synthesis, complex I and complex II was higher in the TA of the HIIT group by 1.5-, 3.0- and 2.7-fold, respectively. In contrast, oxygen consumed by mitochondrial glycerol phosphate dehydrogenase (mGPdH) was 30% lower. Surprisingly, the oxygen flow coupled to ATP synthesis was 42% lower after HIIT in the SOL. Moreover, oxygen flow coupled to ATP synthesis and complex II was higher by 1.4- and 2.7-fold in the GAST of the HIIT group. After HIIT, CS activity increased 1.3-fold in the TA, and H2O2 production was 1.3-fold higher in the TA at sites containing mGPdH. No significant differences in H2O2 production were detected in the SOL. Surprisingly, HIIT increased H2O2 production in the GAST via complex II, phosphorylation, oligomycin and antimycin by 1.6-, 1.8-, 2.2-, and 2.2-fold, respectively. Electron leakage was 3.3-fold higher in the TA with G3P and 1.8-fold higher in the GAST with multiple substrates. Unexpectedly, the HIIT protocol induced different respiration and electron leakage responses in different types of muscle.

Cellulose Microfibril Formation by Surface-Tethered Cellulose Synthase Enzymes.

PubMed

Basu, Snehasish; Omadjela, Okako; Gaddes, David; Tadigadapa, Srinivas; Zimmer, Jochen; Catchmark, Jeffrey M

2016-02-23

Cellulose microfibrils are pseudocrystalline arrays of cellulose chains that are synthesized by cellulose synthases. The enzymes are organized into large membrane-embedded complexes in which each enzyme likely synthesizes and secretes a β-(1→4) glucan. The relationship between the organization of the enzymes in these complexes and cellulose crystallization has not been explored. To better understand this relationship, we used atomic force microscopy to visualize cellulose microfibril formation from nickel-film-immobilized bacterial cellulose synthase enzymes (BcsA-Bs), which in standard solution only form amorphous cellulose from monomeric BcsA-B complexes. Fourier transform infrared spectroscopy and X-ray diffraction techniques show that surface-tethered BcsA-Bs synthesize highly crystalline cellulose II in the presence of UDP-Glc, the allosteric activator cyclic-di-GMP, as well as magnesium. The cellulose II cross section/diameter and the crystal size and crystallinity depend on the surface density of tethered enzymes as well as the overall concentration of substrates. Our results provide the correlation between cellulose microfibril formation and the spatial organization of cellulose synthases.

A Balancing Act: Stability versus Reactivity of Mn(O) Complexes.

PubMed

Neu, Heather M; Baglia, Regina A; Goldberg, David P

2015-10-20

A large class of heme and non-heme metalloenzymes utilize O2 or its derivatives (e.g., H2O2) to generate high-valent metal-oxo intermediates for performing challenging and selective oxidations. Due to their reactive nature, these intermediates are often short-lived and very difficult to characterize. Synthetic chemists have sought to prepare analogous metal-oxo complexes with ligands that impart enough stability to allow for their characterization and an examination of their inherent reactivity. The challenge in designing these molecules is to achieve a balance between their stability, which should allow for their in situ characterization or isolation, and their reactivity, in which they can still participate in interesting chemical transformations. This Account focuses on our recent efforts to generate and stabilize high-valent manganese-oxo porphyrinoid complexes and tune their reactivity in the oxidation of organic substrates. Dioxygen can be used to generate a high-valent Mn(V)(O) corrolazine (Mn(V)(O)(TBP8Cz)) by irradiation of Mn(III)(TBP8Cz) with visible light in the presence of a C-H substrate. Quantitative formation of the Mn(V)(O) complex occurs with concomitant selective hydroxylation of the benzylic substrate hexamethylbenzene. Addition of a strong H(+) donor converted this light/O2/substrate reaction from a stoichiometric to a catalytic process with modest turnovers. The addition of H(+) likely activates a transient Mn(V)(O) complex to achieve turnover, whereas in the absence of H(+), the Mn(V)(O) complex is an unreactive "dead-end" complex. Addition of anionic donors to the Mn(V)(O) complex also leads to enhanced reactivity, with a large increase in the rate of two-electron oxygen atom transfer (OAT) to thioether substrates. Spectroscopic characterization (Mn K-edge X-ray absorption and resonance Raman spectroscopies) revealed that the anionic donors (X(-)) bind to the Mn(V) ion to form six-coordinate [Mn(V)(O)(X)](-) complexes. An unusual "V-shaped" Hammett plot for the oxidation of para-substituted thioanisole derivatives suggested that six-coordinate [Mn(V)(O)(X)](-) complexes can act as both electrophiles and nucleophiles, depending on the nature of the substrate. Oxidation of the Mn(V)(O) corrolazine resulted in the in situ generation of a Mn(V)(O) π-radical cation complex, [Mn(V)(O)(TBP8Cz(•+))](+), which exhibited more than a 100-fold rate increase in the oxidation of thioethers. The addition of Lewis acids (LA; Zn(II), B(C6F5)3) to the closed-shell, diamagnetic Mn(V)(O)(TBP8Cz) stabilized a paramagnetic valence tautomer Mn(IV)(O)(TBP8Cz(•+))(LA), which was characterized as a second π-radical cation complex by NMR, EPR, UV-vis, and high resolution cold spray ionization MS. The Mn(IV)(O)(TBP8Cz(•+))(LA) complexes are able to abstract H(•) from phenols and exhibit a rate enhancement of up to ∼100-fold over the parent Mn(V)(O) valence tautomer. In contrast, a large decrease in rate is observed for OAT for the Mn(IV)(O)(TBP8Cz(•+))(LA) complexes. The rate enhancement for hydrogen atom transfer (HAT) may derive from the higher redox potential for the π-radical cation complex, while the large rate decrease seen for OAT may come from a decrease in electrophilicity for an Mn(IV)(O) versus Mn(V)(O) complex.

Experimental and Theoretical Studies on the Nazarov Cyclization/Wagner-Meerwein Rearrangement Sequence

PubMed Central

Lebœuf, David; Ciesielski, Jennifer

2012-01-01

Highly functionalized cyclopentenones can be generated stereospecifically by a chemoselective copper(II)-mediated Nazarov/Wagner-Meerwein rearrangement sequence of divinyl ketones. A detailed investigation of this sequence is described including a study of substrate scope and limitations. After the initial 4π electrocyclization, this reaction proceeds via two different sequential [1,2]-shifts, with selectivity that depends upon either migratory ability or the steric bulkiness of the substituents at C1 and C5. This methodology allows the creation of vicinal stereogenic centers, including adjacent quaternary centers. This sequence can also be achieved by using a catalytic amount of copper(II) in combination with NaBAr4f, a weak Lewis acid. During the study of the scope of the reaction, a partial or complete E / Z isomerization of the enone moiety was observed in some cases prior to the cyclization, which resulted in a mixture of diastereomeric products. Use of a Cu(II)-bisoxazoline complex prevented the isomerization, allowing high diastereoselectivity to be obtained in all substrate types. In addition, the reaction sequence was studied by DFT computations at the UB3LYP/6-31G(d,p) level, which are consistent with the proposed sequences observed, including E / Z isomerizations and chemoselective Wagner-Meerwein shifts. PMID:22471833

Age-dependent reductions in mitochondrial respiration are exacerbated by calcium in the female rat heart.

PubMed

Hunter, J Craig; Machikas, Alexandra M; Korzick, Donna H

2012-06-01

Cardiovascular disease mortality increases rapidly after menopause by poorly defined mechanisms. Because mitochondrial function and Ca(2+) sensitivity are important regulators of cell death after myocardial ischemia, we sought to determine whether aging and/or estrogen deficiency (ovariectomy) increased mitochondrial Ca(2+) sensitivity. Mitochondrial respiration was measured in ventricular mitochondria isolated from adult (6 months; n = 26) and aged (24 months; n = 25), intact or ovariectomized female rats using the substrates α-ketoglutarate/malate (complex I); succinate/rotenone (complex II); ascorbate/N,N,N',N'-tetramethyl-p-phenylenediamine/antimycin (complex IV). State 2 and 3 respiration was initiated by sequential addition of mitochondria and adenosine diphosphate. Ca(2+) sensitivity was assessed by Ca(2+)-induced swelling of de-energized mitochondria and reduction in state 3 respiration. Propylpyrazole triol (PPT) was administered intraperitoneally 45 minutes before euthanasia to assess mitochondrial protective effects through estrogen receptor (ER) α activation. Aging decreased the respiratory control index (RCI; state 3/state 2) for complexes I and II by 12% and 8%, respectively, independent of ovary status (P < 0.05). Of interest, Ca(2+) induced a greater decrease (18%-30%; P < 0.05) in complex I state 3 respiration in aged and ovariectomized animals, and mitochondrial swelling occurred twice as quickly in aged (vs adult) female rats (P < 0.05). Pretreatment with PPT increased RCI by 8% and 7% at complexes I and II, respectively (P < 0.05) but surprisingly increased Ca(2+) sensitivity. Age-dependent decreases in RCI and sensitization to Ca(2+) may explain in part the age-associated reductions in female ischemic tolerance; however, protection afforded by ER agonism involves more complex mechanisms. Copyright © 2012 Elsevier HS Journals, Inc. All rights reserved.

Age-Dependent Reductions in Mitochondrial Respiration are Exacerbated by Calcium in the Female Rat Heart

PubMed Central

Hunter, J. Craig; Machikas, Alexandra M.; Korzick, Donna H.

2012-01-01

Cardiovascular disease mortality increases rapidly following menopause by poorly defined mechanisms. Since mitochondrial function and Ca2+ sensitivity are important regulators of cell death following myocardial ischemia, we sought to determine if aging and/or estrogen deficiency (ovx) increased mitochondrial Ca2+ sensitivity. Mitochondrial respiration was measured in ventricular mitochondria isolated from adult (6mo; n=26) and aged (24mo; n=25), intact or ovariectomized female rats using the substrates: α-ketoglutarate/malate (Complex I); succinate/rotenone (Complex II); ascorbate/TMPD/Antimycin (Complex IV). State 2 and State 3 respiration was initiated by sequential addition of mitochondria and ADP. Ca2+ sensitivity was assessed by Ca2+-induced swelling of de-energized mitochondria and reduction in state 3 respiration. Propylpyrazole triol (PPT) was administered i.p. 45 min prior to euthanasia to assess mitochondrial protective effects through estrogen receptor (ER) α activation. Aging decreased the respiratory control index (RCI; state 3/state 2) for Complexes I and II by 12% and 8%, respectively, independent of ovary status (p<0.05). Of interest, Ca2+ induced a greater decrease (18–30%; p<0.05) in Complex I state 3 respiration in aged and ovx animals, and mitochondrial swelling occurred twice as quickly in aged (vs. adult) female rats (p<0.05). Pretreatment with PPT increased RCI by 8% and 7% at Complexes I and II, respectively (p<0.05) but surprisingly increased Ca2+ sensitivity. Age-dependent decreases in RCI and sensitization to Ca2+ may explain in part the age-associated reductions in female ischemic tolerance; however protection afforded by ER agonism involves more complex mechanisms. PMID:22555015

Host regulation of lysogenic decision in bacteriophage lambda: transmembrane modulation of FtsH (HflB), the cII degrading protease, by HflKC (HflA).

PubMed

Kihara, A; Akiyama, Y; Ito, K

1997-05-27

The cII gene product of bacteriophage lambda is unstable and required for the establishment of lysogenization. Its intracellular amount is important for the decision between lytic growth and lysogenization. Two genetic loci of Escherichia coli are crucial for these commitments of infecting lambda genome. One of them, hflA encodes the HflKC membrane protein complex, which has been believed to be a protease degrading the cII protein. However, both its absence and overproduction stabilized cII in vivo and the proposed serine protease-like sequence motif in HflC was dispensable for the lysogenization control. Moreover, the HflKC protein was found to reside on the periplasmic side of the plasma membrane. In contrast, the other host gene, ftsH (hflB) encoding an integral membrane ATPase/protease, is positively required for degradation of cII, since loss of its function stabilized cII and its overexpression accelerated the cII degradation. In vitro, purified FtsH catalyzed ATP-dependent proteolysis of cII and HflKC antagonized the FtsH action. These results, together with our previous finding that FtsH and HflKC form a complex, suggest that FtsH is the cII degrading protease and HflKC is a modulator of the FtsH function. We propose that this transmembrane modulation differentiates the FtsH actions to different substrate proteins such as the membrane-bound SecY protein and the cytosolic cII protein. This study necessitates a revision of the prevailing view about the host control over lambda lysogenic decision.

Substrate specificity of the cdk-activating kinase (CAK) is altered upon association with TFIIH.

PubMed Central

Rossignol, M; Kolb-Cheynel, I; Egly, J M

1997-01-01

The transcription/DNA repair factor TFIIH consists of nine subunits, several exhibiting known functions: helicase/ATPase, kinase activity and DNA binding. Three subunits of TFIIH, cdk7, cyclin H and MAT1, form a ternary complex, cdk-activating kinase (CAK), found either on its own or as part of TFIIH. In the present work, we demonstrate that purified human CAK complex (free CAK) and recombinant CAK (rCAK) produced in insect cells exhibit a strong preference for the cyclin-dependent kinase 2 (cdk2) over a ctd oligopeptide substrate (which mimics the carboxy-terminal domain of the RNA polymerase II). In contrast, TFIIH preferentially phosphorylates the ctd as well as TFIIE alpha, but not cdk2. TFIIH was resolved into four subcomplexes: the kinase complex composed of cdk7, cyclin H and MAT1; the core TFIIH which contains XPB, p62, p52, p44 and p34; and two other subcomplexes in which XPD is found associated with either the kinase complex or with the core TFIIH. Using these fractions, we demonstrate that TFIIH lacking the CAK subcomplex completely recovers its transcriptional activity in the presence of free CAK. Furthermore, studies examining the interactions between TFIIH subunits provide evidence that CAK is integrated within TFIIH via XPB and XPD. PMID:9130708

A sensitive plasmonic copper(II) sensor based on gold nanoparticles deposited on ITO glass substrate.

PubMed

Ding, Lijun; Gao, Yan; Di, Junwei

2016-09-15

Gold nanoparticles (Au NPs) based plasmonic probe was developed for sensitive and selective detection of Cu(2+) ion. The Au NPs were self-assembled on transparent indium tin oxide (ITO) film coated glass substrate using poly dimethyl diallyl ammonium chloride (PDDA) as a linker and then calcined at 400°C to obtain pure Au NPs on ITO surface (ITO/Au NPs). The probe was fabricated by functionalizing l-cysteine (Cys) on to gold surface (ITO/Au NPs/Cys). The strong chelation of Cu(2+) with Cys formed a stable Cys-Cu complex, and resulted in the red-shift of localized surface plasmon resonance (LSPR) peak of the Au NPs. The introduction of bovine serum albumin (BSA) as the second complexant could form complex of Cys-Cu-BAS and further markedly enhanced the red-shift of the LSPR peak. This plasmonic probe provided a highly sensitive and selective detection towards Cu(2+) ions, with a wide linear detection range (10(-11)-10(-5)M) over 6 orders of magnitude. The simple and cost-effective probe was successfully applied to the determination of Cu(2+) in real samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase

NASA Astrophysics Data System (ADS)

Werther, Tobias; Wahlefeld, Stefan; Salewski, Johannes; Kuhlmann, Uwe; Zebger, Ingo; Hildebrandt, Peter; Dobbek, Holger

2017-07-01

How an enzyme activates its substrate for turnover is fundamental for catalysis but incompletely understood on a structural level. With redox enzymes one typically analyses structures of enzyme-substrate complexes in the unreactive oxidation state of the cofactor, assuming that the interaction between enzyme and substrate is independent of the cofactors oxidation state. Here, we investigate the Michaelis complex of the flavoenzyme xenobiotic reductase A with the reactive reduced cofactor bound to its substrates by X-ray crystallography and resonance Raman spectroscopy and compare it to the non-reactive oxidized Michaelis complex mimics. We find that substrates bind in different orientations to the oxidized and reduced flavin, in both cases flattening its structure. But only authentic Michaelis complexes display an unexpected rich vibrational band pattern uncovering a strong donor-acceptor complex between reduced flavin and substrate. This interaction likely activates the catalytic ground state of the reduced flavin, accelerating the reaction within a compressed cofactor-substrate complex.

Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase

PubMed Central

Werther, Tobias; Wahlefeld, Stefan; Salewski, Johannes; Kuhlmann, Uwe; Zebger, Ingo; Hildebrandt, Peter; Dobbek, Holger

2017-01-01

How an enzyme activates its substrate for turnover is fundamental for catalysis but incompletely understood on a structural level. With redox enzymes one typically analyses structures of enzyme–substrate complexes in the unreactive oxidation state of the cofactor, assuming that the interaction between enzyme and substrate is independent of the cofactors oxidation state. Here, we investigate the Michaelis complex of the flavoenzyme xenobiotic reductase A with the reactive reduced cofactor bound to its substrates by X-ray crystallography and resonance Raman spectroscopy and compare it to the non-reactive oxidized Michaelis complex mimics. We find that substrates bind in different orientations to the oxidized and reduced flavin, in both cases flattening its structure. But only authentic Michaelis complexes display an unexpected rich vibrational band pattern uncovering a strong donor–acceptor complex between reduced flavin and substrate. This interaction likely activates the catalytic ground state of the reduced flavin, accelerating the reaction within a compressed cofactor–substrate complex.

When lithography meets self-assembly: a review of recent advances in the directed assembly of complex metal nanostructures on planar and textured surfaces

NASA Astrophysics Data System (ADS)

Hughes, Robert A.; Menumerov, Eredzhep; Neretina, Svetlana

2017-07-01

One of the foremost challenges in nanofabrication is the establishment of a processing science that integrates wafer-based materials, techniques, and devices with the extraordinary physicochemical properties accessible when materials are reduced to nanoscale dimensions. Such a merger would allow for exacting controls on nanostructure positioning, promote cooperative phenomenon between adjacent nanostructures and/or substrate materials, and allow for electrical contact to individual or groups of nanostructures. With neither self-assembly nor top-down lithographic processes being able to adequately meet this challenge, advancements have often relied on a hybrid strategy that utilizes lithographically-defined features to direct the assembly of nanostructures into organized patterns. While these so-called directed assembly techniques have proven viable, much of this effort has focused on the assembly of periodic arrays of spherical or near-spherical nanostructures comprised of a single element. Work directed toward the fabrication of more complex nanostructures, while still at a nascent stage, has nevertheless demonstrated the possibility of forming arrays of nanocubes, nanorods, nanoprisms, nanoshells, nanocages, nanoframes, core-shell structures, Janus structures, and various alloys on the substrate surface. In this topical review, we describe the progress made in the directed assembly of periodic arrays of these complex metal nanostructures on planar and textured substrates. The review is divided into three broad strategies reliant on: (i) the deterministic positioning of colloidal structures, (ii) the reorganization of deposited metal films at elevated temperatures, and (iii) liquid-phase chemistry practiced directly on the substrate surface. These strategies collectively utilize a broad range of techniques including capillary assembly, microcontact printing, chemical surface modulation, templated dewetting, nanoimprint lithography, and dip-pen nanolithography and employ a wide scope of chemical processes including redox reactions, alloying, dealloying, phase separation, galvanic replacement, preferential etching, template-mediated reactions, and facet-selective capping agents. Taken together, they highlight the diverse toolset available when fabricating organized surfaces of substrate-supported nanostructures.

Novel Co(II) phthalocyanines of extended periphery and their water-soluble derivatives. Synthesis, spectral properties and catalytic activity

NASA Astrophysics Data System (ADS)

Filippova, Anna; Vashurin, Artur; Znoyko, Serafima; Kuzmin, Ilya; Razumov, Mikhail; Chernova, Alena; Shaposhnikov, Gennady; Koifman, Oscar

2017-12-01

Novel complexes of cobalt and copper with substituted phthalocyanines were synthesized and characterized. Their water-soluble derivatives were obtained by sulfonation under mild conditions and structurally proved. Aggregation equilibrium in water mediums was shown and influence of geometrical and electron parameters of macroheterocycle peripheral substituents on these processes was established. Catalytic activity upon liquid-phase oxidation of N,N-diethylcarbamodithiolate to thiuram E was studied. Kinetic parameters of substrate oxidation in presence of cobalt phthalocyanines were considered.

Pd-Catalyzed Asymmetric β-Hydride Elimination En Route to Chiral Allenes

PubMed Central

Crouch, Ian T.; Neff, Robynne K.; Frantz, Doug E.

2013-01-01

We wish to report our preliminary results on the discovery and development of a catalytic, asymmetric β-hydride elimination from vinyl Pd(II)-complexes derived from enol triflates to access chiral allenes. To achieve this, we developed a class of chiral phosphite ligands that demonstrate high enantioselectivity, allow access of either allene enantiomer, and are readily synthesized. The methodology is demonstrated on over 20 substrates and application to the formal asymmetric total synthesis of the natural product, (+)-epibatidine, is also provided. PMID:23488914

Ablation of multi-wavelet re-entry: general principles and in silico analyses.

PubMed

Spector, Peter S; Correa de Sa, Daniel D; Tischler, Ethan S; Thompson, Nathaniel C; Habel, Nicole; Stinnett-Donnelly, Justin; Benson, Bryce E; Bielau, Philipp; Bates, Jason H T

2012-11-01

Catheter ablation strategies for treatment of cardiac arrhythmias are quite successful when targeting spatially constrained substrates. Complex, dynamic, and spatially varying substrates, however, pose a significant challenge for ablation, which delivers spatially fixed lesions. We describe tissue excitation using concepts of surface topology which provides a framework for addressing this challenge. The aim of this study was to test the efficacy of mechanism-based ablation strategies in the setting of complex dynamic substrates. We used a computational model of propagation through electrically excitable tissue to test the effects of ablation on excitation patterns of progressively greater complexity, from fixed rotors to multi-wavelet re-entry. Our results indicate that (i) focal ablation at a spiral-wave core does not result in termination; (ii) termination requires linear lesions from the tissue edge to the spiral-wave core; (iii) meandering spiral-waves terminate upon collision with a boundary (linear lesion or tissue edge); (iv) the probability of terminating multi-wavelet re-entry is proportional to the ratio of total boundary length to tissue area; (v) the efficacy of linear lesions varies directly with the regional density of spiral-waves. We establish a theoretical framework for re-entrant arrhythmias that explains the requirements for their successful treatment. We demonstrate the inadequacy of focal ablation for spatially fixed spiral-waves. Mechanistically guided principles for ablating multi-wavelet re-entry are provided. The potential to capitalize upon regional heterogeneity of spiral-wave density for improved ablation efficacy is described.

Reductive Activation of O2 by Non-Heme Iron(II) Benzilate Complexes of N4 Ligands: Effect of Ligand Topology on the Reactivity of O2-Derived Oxidant.

PubMed

Chakraborty, Biswarup; Jana, Rahul Dev; Singh, Reena; Paria, Sayantan; Paine, Tapan Kanti

2017-01-03

A series of iron(II) benzilate complexes (1-7) with general formula [(L)Fe II (benzilate)] + have been isolated and characterized to study the effect of supporting ligand (L) on the reactivity of metal-based oxidant generated in the reaction with dioxygen. Five tripodal N 4 ligands (tris(2-pyridylmethyl)amine (TPA in 1), tris(6-methyl-2-pyridylmethyl)amine (6-Me 3 -TPA in 2), N 1 ,N 1 -dimethyl-N 2 ,N 2 -bis(2-pyridylmethyl)ethane-1,2-diamine (iso-BPMEN in 3), N 1 ,N 1 -dimethyl-N 2 ,N 2 -bis(6-methyl-2-pyridylmethyl)ethane-1,2-diamine (6-Me 2 -iso-BPMEN in 4), and tris(2-benzimidazolylmethyl)amine (TBimA in 7)) along with two linear tetradentate amine ligands (N 1 ,N 2 -dimethyl-N 1 ,N 2 -bis(2-pyridylmethyl)ethane-1,2-diamine (BPMEN in 5) and N 1 ,N 2 -dimethyl-N 1 ,N 2 -bis(6-methyl-2-pyridylmethyl)ethane-1,2-diamine (6-Me 2 -BPMEN in 6)) were employed in the study. Single-crystal X-ray structural studies reveal that each of the complex cations of 1-3 and 5 contains a mononuclear six-coordinate iron(II) center coordinated by a monoanionic benzilate, whereas complex 7 contains a mononuclear five-coordinate iron(II) center. Benzilate binds to the iron center in a monodentate fashion via one of the carboxylate oxygens in 1 and 7, but it coordinates in a bidentate chelating mode through carboxylate oxygen and neutral hydroxy oxygen in 2, 3, and 5. All of the iron(II) complexes react with dioxygen to exhibit quantitative decarboxylation of benzilic acid to benzophenone. In the decarboxylation pathway, dioxygen becomes reduced on the iron center and the resulting iron-oxygen oxidant shows versatile reactivity. The oxidants are nucleophilic in nature and oxidize sulfide to sulfoxide and sulfone. Furthermore, complexes 2 and 4-6 react with alkenes to produce cis-diols in moderate yields with the incorporation of both the oxygen atoms of dioxygen. The oxygen atoms of the nucleophilic oxidants do not exchange with water. On the basis of interception studies, nucleophilic iron(II) hydroperoxides are proposed to generate in situ in the reaction pathways. The difference in reactivity of the complexes toward external substrates could be attributed to the geometry of the O 2 -derived iron-oxygen oxidant. DFT calculations suggest that, among all possible geometries and spin states, high-spin side-on iron(II) hydroperoxides are energetically favorable for the complexes of 6-Me 3 -TPA, 6-Me 2 -iso-BPMEN, BPMEN, and 6-Me 2 -BPMEN ligands, while high spin end-on iron(II) hydroperoxides are favorable for the complexes of TPA, iso-BPMEN, and TBimA ligands.

Attenuation of drug-stimulated topoisomerase II-DNA cleavable complex formation in wild-type HL-60 cells treated with an intracellular calcium buffer is correlated with decreased cytotoxicity and site-specific hypophosphorylation of topoisomerase IIalpha.

PubMed Central

Aoyama, M; Grabowski, D R; Dubyak, G R; Constantinou, A I; Rybicki, L A; Bukowski, R M; Ganapathi, M K; Hickson, I D; Ganapathi, R

1998-01-01

Topoisomerase II (topo II), an essential enzyme for cell viability, is also the target for clinically important anti-neoplastic agents that stimulate topo II-mediated DNA scission. The role of alterations in topo IIalpha phosphorylation and its effect on drug-induced DNA damage and cytotoxicity were investigated. Following loading of HL-60 cells with the calcium buffer 1, 2-bis-(o-aminophenoxy)ethane-N,N,N',N'-tetra-acetic acid tetra(acetoxymethyl) ester (BAPTA-AM), which abrogates intracellular Ca2+ transients, a significant decrease in etoposide (VP-16)- or amsacrine (m-AMSA)-stabilized topo II-DNA cleavable complex formation and a corresponding decrease in cytotoxicity was observed. In a cell-free system, nuclear extracts from BAPTA-AM-treated cells exhibited markedly less activity when assayed for VP-16-stabilized topo II-DNA complex formation, but not decatenation of kinetoplast DNA. In contrast, the loading of HL-60 cells with N,N,N', N'-tetrakis-(2-pyridyl)ethylenediamine (TPEN), which binds heavy metals without disturbing calcium or magnesium concentrations, did not significantly affect VP-16-stimulated topo II-DNA cleavable complex formation or cytotoxicity. In HL-60 cells the accumulation of BAPTA, but not TPEN, also led to the hypophosphorylation of topo IIalpha. Tryptic phosphopeptide mapping of topo IIalpha protein from HL-60 cells revealed: (a) eight major phosphorylation sites in untreated cells; (b) hypophosphorylation of two out of eight sites in BAPTA-AM-treated cells; and (c) hypophosphorylation of between two and four out of eight sites in topo II-poison-resistant HL-60 cells. The two hypophosphorylated sites present following BAPTA-AM treatment of wild-type cells were identical with the hypophosphorylated sites in the resistant cells, but were not the same as the sites that are substrates for casein kinase II [Wells, Addison, Fry, Ganapathi and Hickson (1994) J. Biol. Chem. 269, 29746-29751]. In summary, changes in intracellular Ca2+ transients that lead to the site-specific hypophosphorylation of topo IIalpha are possibly involved in regulating the DNA damage caused by and the cytotoxic potential of topo II poisons. PMID:9841887

Policing starter unit selection of the enterocin type II polyketide synthase by the type II thioesterase EncL.

PubMed

Kalaitzis, John A; Cheng, Qian; Meluzzi, Dario; Xiang, Longkuan; Izumikawa, Miho; Dorrestein, Pieter C; Moore, Bradley S

2011-11-15

Enterocin is an atypical type II polyketide synthase (PKS) product from the marine actinomycete 'Streptomyces maritimus'. The enterocin biosynthesis gene cluster (enc) codes for proteins involved in the assembly and attachment of the rare benzoate primer that initiates polyketide assembly with the addition of seven malonate molecules and culminates in a Favorskii-like rearrangement of the linear poly-β-ketone to give its distinctive non-aromatic, caged core structure. Fundamental to enterocin biosynthesis, which utilizes a single acyl carrier protein (ACP), EncC, for both priming with benzoate and elongating with malonate, involves maintaining the correct balance of acyl-EncC substrates for efficient polyketide assembly. Here, we report the characterization of EncL as a type II thioesterase that functions to edit starter unit (mis)priming of EncC. We performed a series of in vivo mutational studies, heterologous expression experiments, in vitro reconstitution studies, and Fourier-transform mass spectrometry-monitored competitive enzyme assays that together support the proposed selective hydrolase activity of EncL toward misprimed acetyl-ACP over benzoyl-ACP to facilitate benzoyl priming of the enterocin PKS complex. While this system resembles the R1128 PKS that also utilizes an editing thioesterase (ZhuC) to purge acetate molecules from its initiation module ACP in favor of alkylacyl groups, the enterocin system is distinct in its usage of a single ACP for both priming and elongating reactions with different substrates. Copyright © 2011 Elsevier Ltd. All rights reserved.

Policing Starter Unit Selection of the Enterocin Type II Polyketide Synthase by the Type II Thioesterase EncL

PubMed Central

Kalaitzis, John A.; Cheng, Qian; Meluzzi, Dario; Xiang, Longkuan; Izumikawa, Miho; Dorrestein, Pieter C.; Moore, Bradley S.

2011-01-01

Enterocin is an atypical type II polyketide synthase (PKS) product from the marine actinomycete “Streptomyces maritimus”. The enterocin biosynthesis gene cluster (enc) codes for proteins involved in the assembly and attachment of the rare benzoate primer that initiates polyketide assembly with the addition of seven malonate molecules and culminates in a Favorskii-like rearrangement of the linear poly-β-ketone to give its distinctive non-aromatic, caged core structure. Fundamental to enterocin biosynthesis, which utilizes a single acyl carrier protein (ACP), EncC, for both priming with benzoate and elongating with malonate, involves maintaining the correct balance of acyl-EncC substrates for efficient polyketide assembly. Here we report the characterization of EncL as a type II thioesterase that functions to edit starter unit (mis)priming of EncC. We performed a series of in vivo mutational studies, heterologous expression experiments, in vitro reconstitution studies, and Fourier-transform mass spectrometry-monitored competitive enzyme assays that together support the proposed selective hydrolase activity of EncL toward misprimed acetyl-ACP over benzoyl-ACP to facilitate benzoyl priming of the enterocin PKS complex. While this system resembles the R1128 PKS that also utilizes an editing thioesterase (ZhuC) to purge acetate molecules from its initiation module ACP in favor of alkylacyl groups, the enterocin system is distinct in its usage of a single ACP for both priming and elongating reactions with different substrates. PMID:21531566

Substrate specificity and copper loading of the manganese-oxidizing multicopper oxidase Mnx from Bacillus sp. PL-12.

PubMed

Butterfield, Cristina N; Tebo, Bradley M

2017-02-22

Manganese(ii) oxidation in the environment is thought to be driven by bacteria because enzymatic catalysis is many orders of magnitude faster than the abiotic processes. The heterologously purified Mn oxidase (Mnx) from marine Bacillus sp. PL-12 is made up of the multicopper oxidase (MCO) MnxG and two small Cu and heme-binding proteins of unknown function, MnxE and MnxF. Mnx binds Cu and oxidizes both Mn(ii) and Mn(iii), generating Mn(iv) oxide minerals that resemble those found on the Bacillus spore surface. Spectroscopic techniques have illuminated details about the metallo-cofactors of Mnx, but very little is known about their requirement for catalytic activity, and even less is known about the substrate specificity of Mnx. Here we quantify the canonical MCO Cu and persistent peripheral Cu bound to Mnx, and test Mnx oxidizing ability toward different substrates at varying pH. Mn(ii) appears to be the best substrate in terms of k cat , but its oxidation does not follow Michaelis-Menten kinetics, instead showing a sigmoidal cooperative behavior. Mnx also oxidizes Fe(ii) substrate, but in a Michaelis-Menten manner and with a decreased activity, as well as organic substrates. The reduced metals are more rapidly consumed than the larger organic substrates, suggesting the hypothesis that the Mnx substrate site is small and tuned for metal oxidation. Of biological relevance is the result that Mnx has the highest catalytic efficiency for Mn(ii) at the pH of sea water, especially when the protein is loaded with greater than the requisite four MCO copper atoms, suggesting that the protein has evolved specifically for Mn oxidation.

A Selective Surface-Enhanced Raman Scattering Sensor for Mercury(II) Based on a Porous Polymer Material and the Target-Mediated Displacement of a T-Rich Strand

NASA Astrophysics Data System (ADS)

Kang, Y.; Zhang, L.; Zhang, H.; Wu, T.; Du, Y.

2017-05-01

A sensitive and selective surface-enhanced Raman scattering (SERS) sensor for mercury(II) was fabricated based on the target-mediated displacement of a T-rich oligonucleotide strand. A DNA/aptamer duplex was prepared by the hybridization between a tetramethylrhodamine(TMR)-labeled thymine(T)-rich Hg2+-specific aptamer (denoted as TMR-aptamer) and a thiolated adenine-rich capturing DNA. The duplex can be immobilized onto the SERS substrate of the Ag-moiety modified glycidyl methacrylate-ethylene dimethacrylate (denoted as Ag-GMA-EDMA) via self-assembly by the thiol anchor, in which the TMR-aptamer exists in a double-stranded chain. In this case, the label of the TMR moiety approaches the substrate surface and produces a strong SERS signal. Upon the addition of the target, a pair of TMR-aptamers could cooperatively coordinate with Hg2+ to form a stable duplex-like structure mediated by the T-Hg2+-T complex between two adjacent strands, which triggers the release of the TMR-aptamer from the SERS substrate surface, thus drawing the TMR tags away from the substrate with a significant decrease in the SERS signal. This optical sensor shows a sensitive response to Hg2+ in a concentration from 5 nM to 2.0 μM with a detection limit of 2.5 nM. The prepared sensor is negligibly responsive to other metal ions, can be easily regenerated, and shows good performance in real sample analysis.

Generation of a Mn(IV)-Peroxo or Mn(III)-Oxo-Mn(III) Species upon Oxygenation of Mono- and Binuclear Thiolate-Ligated Mn(II) Complexes.

PubMed

Lee, Chien-Ming; Wu, Wun-Yan; Chiang, Ming-Hsi; Bohle, D Scott; Lee, Gene-Hsiang

2017-09-05

A thiolate-bridged binuclear complex [PPN] 2 [(Mn II ( TMS PS3)) 2 ] (1, PPN = bis(triphenylphosphine)iminium and TMS PS3H 3 = (2,2',2″-trimercapto-3,3',3″-tris(trimethylsilyl)triphenylphosphine)), prepared from the reaction of MnCl 2 /[PPN]Cl and Li 3 [ TMS PS3], converts into a mononuclear complex [PPN][Mn II ( TMS PS3)(DABCO)] (2) in the presence of excess amounts of DABCO (DABCO = 1,4-diazabicyclo[2.2.2]octane). Variable temperature studies of solution containing 1 and DABCO by UV-vis spectroscopy indicate that 1 and 2 exist in significant amounts in equilibrium and mononuclear 2 is favored at low temperature. Treatment of 1 or 2 with the monomeric O 2 -side-on-bound [PPN][Mn IV (O 2 )( TMS PS3)] (3) produces the mono-oxo-bridged dimer [PPN] 2 [(Mn III ( TMS PS3)) 2 (μ-O)] (4). The electrochemistry of 1 and 2 reveals anodic peak(s) for a Mn III/ Mn II redox couple at shifted potentials against Fc/Fc + , indicating that both complexes can be oxidized by dioxygen. The O 2 activation mediated by 1 and 2 is investigated in both solution and the solid state. Microcrystals of 2 rapidly react with air or dry O 2 to generate the Mn(IV)-peroxo 3 in high yield, revealing a solid-to-solid transformation and two-electron reduction of O 2 . Oxygenation of 1 or 2 in solution, however, is affected by diffusion and transient concentration of dioxygen in the two different substrates, leading to generation of 3 and 4 in variable ratios.

Mechanistic studies of copper(II)-aminoglycoside mediated DNA damage and magnesium catalyzed nuclease activity of hammerhead ribozyme

NASA Astrophysics Data System (ADS)

Patwardhan, Anjali A.

The antibacterial activity of aminoglycosides stems from their high affinity binding to the 16S rRNA in bacteria resulting in inhibition of protein synthesis. Used to treat acute bacterial infections these antibiotics have limited applications due to their high dosage requirements and the emergence of resistant strains. We have synthesized and characterized Cu(II) derivatives of the aminoglycosides, kanamycin A, tobramycin, neamine, kanamycin B, neomycin B, and paromomycin. The first three exhibit preferential and tight binding to Cu(II) as against neomycin B and kanamycin B and paromomycin. EPR of frozen solutions and UV-visible spectroscopy suggest a change in geometry around the Cu(II) but the stabilities of the complexes in water differ. These copper derivatives efficiently cleave plasmid DNA at micromolar concentrations (hydrolytic) and at nanomolar concentrations in the presence co-reactants like hydrogen peroxide or ascorbic acid. Hydrolysis is multi turnover and exhibits Michelis-Menten kinetics with enzyme-like behavior whereas oxidative cleavage is highly specific with C-4' H abstraction resulting in characteristic base propenal and nucleotide base products. Hydroxyl radicals generated are copper based and are generated in close proximity of the substrate. Hammerhead ribozymes are selectively hydrolyzed in the presence of divalent ions with Mg2+ being the metal ion of choice in vivo . Our studies with complex ions like cobalt hexaammine and fac-triamminetriaquochromium(III) establish outer sphere interactions of Mg2+ with the hammerhead in the catalytic site. There are two sets of sites, one structural and one catalytic. Complex ions in the catalytic site and divalent ions in the structural site result in a slow but active hammerhead ribozyme suggesting that the complex ions are not inhibitory, contrary to what was suggested previously.

Group II chaperonins: new TRiC(k)s and turns of a protein folding machine.

PubMed

Gutsche, I; Essen, L O; Baumeister, W

1999-10-22

In the past decade, the eubacterial group I chaperonin GroEL became the paradigm of a protein folding machine. More recently, electron microscopy and X-ray crystallography offered insights into the structure of the thermosome, the archetype of the group II chaperonins which also comprise the chaperonin from the eukaryotic cytosol TRiC. Some structural differences from GroEL were revealed, namely the existence of a built-in lid provided by the helical protrusions of the apical domains instead of a GroES-like co-chaperonin. These structural studies provide a framework for understanding the differences in the mode of action between the group II and the group I chaperonins. In vitro analyses of the folding of non-native substrates coupled to ATP binding and hydrolysis are progressing towards establishing a functional cycle for group II chaperonins. A protein complex called GimC/prefoldin has recently been found to cooperate with TRiC in vivo, and its characterization is under way. Copyright 1999 Academic Press.

Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria.

PubMed

Bernheim, Aude; Calvo-Villamañán, Alicia; Basier, Clovis; Cui, Lun; Rocha, Eduardo P C; Touchon, Marie; Bikard, David

2017-12-12

Type II CRISPR-Cas systems introduce double-strand breaks into DNA of invading genetic material and use DNA fragments to acquire novel spacers during adaptation. These breaks can be the substrate of several DNA repair pathways, paving the way for interactions. We report that non-homologous end-joining (NHEJ) and type II-A CRISPR-Cas systems only co-occur once among 5563 fully sequenced prokaryotic genomes. We investigated experimentally the possible molecular interactions using the NHEJ pathway from Bacillus subtilis and the type II-A CRISPR-Cas systems from Streptococcus thermophilus and Streptococcus pyogenes. Our results suggest that the NHEJ system has no effect on CRISPR immunity. On the other hand, we provide evidence for the inhibition of NHEJ repair by the Csn2 protein. Our findings give insights on the complex interactions between CRISPR-Cas systems and repair mechanisms in bacteria, contributing to explain the scattered distribution of CRISPR-Cas systems in bacterial genome.

Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu,B.; Edstrom, W.; Benach, J.

2006-01-01

Nucleic acid damage by environmental and endogenous alkylation reagents creates lesions that are both mutagenic and cytotoxic, with the latter effect accounting for their widespread use in clinical cancer chemotherapy. Escherichia coliAlkB and the homologous human proteins ABH2 and ABH3 (refs 5, 7) promiscuously repair DNA and RNA bases damaged by SN2 alkylation reagents, which attach hydrocarbons to endocyclic ring nitrogen atoms (N1 of adenine and guanine and N3 of thymine and cytosine). Although the role of AlkB in DNA repair has long been established based on phenotypic studies, its exact biochemical activity was only elucidated recently after sequence profilemore » analysis revealed it to be a member of the Fe-oxoglutarate-dependent dioxygenase superfamily. These enzymes use an Fe(ii) cofactor and 2-oxoglutarate co-substrate to oxidize organic substrates. AlkB hydroxylates an alkylated nucleotide base to produce an unstable product that releases an aldehyde to regenerate the unmodified base. Here we have determined crystal structures of substrate and product complexes of E. coli AlkB at resolutions from 1.8 to 2.3 Angstroms. Whereas the Fe-2-oxoglutarate dioxygenase core matches that in other superfamily members, a unique subdomain holds a methylated trinucleotide substrate into the active site through contacts to the polynucleotide backbone. Amide hydrogen exchange studies and crystallographic analyses suggest that this substrate-binding 'lid' is conformationally flexible, which may enable docking of diverse alkylated nucleotide substrates in optimal catalytic geometry. Different crystal structures show open and closed states of a tunnel putatively gating O2 diffusion into the active site. Exposing crystals of the anaerobic Michaelis complex to air yields slow but substantial oxidation of 2-oxoglutarate that is inefficiently coupled to nucleotide oxidation. These observations suggest that protein dynamics modulate redox chemistry and that a hypothesized migration of the reactive oxy-ferryl ligand on the catalytic Fe ion may be impeded when the protein is constrained in the crystal lattice.« less

Biodegradable Polymeric Materials in Degradable Electronic Devices

PubMed Central

2018-01-01

Biodegradable electronics have great potential to reduce the environmental footprint of devices and enable advanced health monitoring and therapeutic technologies. Complex biodegradable electronics require biodegradable substrates, insulators, conductors, and semiconductors, all of which comprise the fundamental building blocks of devices. This review will survey recent trends in the strategies used to fabricate biodegradable forms of each of these components. Polymers that can disintegrate without full chemical breakdown (type I), as well as those that can be recycled into monomeric and oligomeric building blocks (type II), will be discussed. Type I degradation is typically achieved with engineering and material science based strategies, whereas type II degradation often requires deliberate synthetic approaches. Notably, unconventional degradable linkages capable of maintaining long-range conjugation have been relatively unexplored, yet may enable fully biodegradable conductors and semiconductors with uncompromised electrical properties. While substantial progress has been made in developing degradable device components, the electrical and mechanical properties of these materials must be improved before fully degradable complex electronics can be realized. PMID:29632879

Assessing Mitochondrial Bioenergetics in Isolated Mitochondria from Various Mouse Tissues Using Seahorse XF96 Analyzer.

PubMed

Iuso, Arcangela; Repp, Birgit; Biagosch, Caroline; Terrile, Caterina; Prokisch, Holger

2017-01-01

Working with isolated mitochondria is the gold standard approach to investigate the function of the electron transport chain in tissues, free from the influence of other cellular factors. In this chapter, we outline a detailed protocol to measure the rate of oxygen consumption (OCR) with the high-throughput analyzer Seahorse XF96. More importantly, this protocol wants to provide practical tips for handling many different samples at once, and take a real advantage of using a high-throughput system. As a proof of concept, we have isolated mitochondria from brain, heart, liver, muscle, kidney, and lung of a wild-type mouse, and measured basal respiration (State II), ADP-stimulated respiration (State III), non-ADP-stimulated respiration (State IV o ), and FCCP-stimulated respiration (State III u ) using respiratory substrates specific to the respiratory chain complex I (RCCI) and complex II (RCCII). Mitochondrial purification and Seahorse runs were performed in less than eight working hours.

THE EFFECTS OF TYPE II BINDING ON METABOLIC STABILITY AND BINDING AFFINITY IN CYTOCHROME P450 CYP3A4

PubMed Central

Peng, Chi-Chi; Pearson, Josh T.; Rock, Dan A.; Joswig-Jones, Carolyn A.; Jones, Jeffrey P.

2010-01-01

One goal in drug design is to decrease clearance due to metabolism. It has been suggested that a compound’s metabolic stability can be increased by incorporation of a sp2 nitrogen into an aromatic ring. Nitrogen incorporation is hypothesized to increase metabolic stability by coordination of nitrogen to the heme iron (termed type II binding). However, questions regarding binding affinity, metabolic stability, and how metabolism of type II binders occurs remain unanswered. Herein, we use pyridinyl quinoline-4-carboxamide analogs to answer these questions. We show that type II binding can have a profound influence on binding affinity for CYP3A4, and the difference in binding affinity can be as high as 1,200 fold. We also find that type II binding compounds can be extensively metabolized, which is not consistent with the dead-end complex kinetic model assumed for type II binders. Two alternate kinetic mechanisms are presented to explain the results. The first involves a rapid equilibrium between the type II bound substrate and a metabolically oriented binding mode. The second involves direct reduction of the nitrogen-coordinated heme followed by oxygen binding. PMID:20346909

Pb, Cu, and Zn distributions at humic acid-coated metal-oxide surfaces

NASA Astrophysics Data System (ADS)

Wang, Yingge; Michel, F. Marc; Choi, Yongseong; Eng, Peter J.; Levard, Clement; Siebner, Hagar; Gu, Baohua; Bargar, John R.; Brown, Gordon E.

2016-09-01

Mineral surfaces are often coated by natural organic matter (NOM), which has a major influence on metal-ion sorption and sequestration because of the abundance of binding sites in such coatings and the changes they cause in local nanoscale environments. The effects of NOM coatings on mineral surfaces are, however, still poorly understood at the molecular level due to the complexity of these systems. In this study, we have applied long-period X-ray standing wave-fluorescence yield (LP-XSW-FY) spectroscopy to measure the partitioning of naturally present Cu(II) (0.0226%), Zn(II) (0.009%), and Pb(II) (∼0.0004%) between Elliott Soil Humic Acid (ESHA) coatings and three model single-crystal metal-oxide substrates: α-Al2O3 (0 0 0 1), α-Al2O3 (1 -1 0 2), and α-Fe2O3 (0 0 0 1). The competitive sorption effects among these metal ions for binding sites in the ESHA coatings and on the metal-oxide surfaces were investigated as a function of reaction time, calcium content, and solution pH. Pb(II) ions present in the ESHA coatings were found to redistribute to reactive α-Al2O3 (1 -1 0 2) and α-Fe2O3 (0 0 0 1) surfaces after 3 h of reaction (pH = 6.0, [Ca(II)] = 2 mM). Pb(II) partitioning onto these reactive metal-oxide surfaces increased with increasing reaction time (up to 7 d). In addition, the partitioning of Cu(II) and Zn(II) from the ESHA coating to the α-Fe2O3 (0 0 0 1) substrate increased slightly with reaction time (2.4% and 3.7% for Cu(II) and Zn(II), respectively, after 3 h and 6.4% and 7.7% for Cu(II) and Zn(II), respectively, after 72 h of reaction time). However, no changes in the partitioning of Cu(II) and Zn(II) onto the α-Al2O3 (1 -1 0 2) surface were observed with increasing reaction time, suggesting that these ions strongly complex with functional groups in the ESHA coatings. Similar results were obtained for Cu(II) and Zn(II) on the ESHA-coated α-Al2O3 (1 -1 0 2) surfaces in samples without the addition of calcium. However, the amounts of Pb(II) mobilized from the ESHA coatings onto the α-Al2O3 (1 -1 0 2) surfaces increased from 40% (no added Ca) to 58% (with 2 mM Ca) after 72 h of reaction time, possibly due to displacement of Pb(II) by Ca(II) from binding sites in the ESHA coatings. In contrast, Pb(II), Cu(II), and Zn(II) present in the ESHA coatings were found to be unreactive with the α-Al2O3 (0 0 0 1) surface. The observed reactivities of the three ESHA-coated metal-oxide surfaces with respect to metal-ion sorption are consistent with the trend observed for the uncoated metal-oxide surfaces: α-Fe2O3 (0 0 0 1) > α-Al2O3 (1 -1 0 2) > α-Al2O3 (0 0 0 1). In addition, Pb(II) partitioning onto α-Al2O3 (1 -1 0 2) surfaces increased with increasing pH from 4.0 to 9.0 as a result of the increasingly negative surface charge. These results show that intrinsic properties (nature of binding sites, binding affinities, and surface charge) of the ESHA coatings and metal-oxide surfaces, as well as external parameters such as pH and competing ions, are key factors governing the distribution and speciation of metal ions at complex NOM/mineral interfaces.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schellenberg, Matthew J; Appel, C Denise; Adhikari, Sanjay

The topoisomerase II (topo II) DNA incision-and-ligation cycle can be poisoned (for example following treatment with cancer chemotherapeutics) to generate cytotoxic DNA double-strand breaks (DSBs) with topo II covalently conjugated to DNA. Tyrosyl-DNA phosphodiesterase 2 (Tdp2) protects genomic integrity by reversing 5'-phosphotyrosyl–linked topo II–DNA adducts. Here, X-ray structures of mouse Tdp2–DNA complexes reveal that Tdp2 β–2-helix–β DNA damage–binding 'grasp', helical 'cap' and DNA lesion–binding elements fuse to form an elongated protein-DNA conjugate substrate-interaction groove. The Tdp2 DNA-binding surface is highly tailored for engagement of 5'-adducted single-stranded DNA ends and restricts nonspecific endonucleolytic or exonucleolytic processing. Structural, mutational and functional analysesmore » support a single–metal ion catalytic mechanism for the exonuclease-endonuclease-phosphatase (EEP) nuclease superfamily and establish a molecular framework for targeted small-molecule blockade of Tdp2-mediated resistance to anticancer topoisomerase drugs.« less

Structural Basis for Recognition of L-lysine, L-ornithine, and L-2,4-diamino Butyric Acid by Lysine Cyclodeaminase.

PubMed

Min, Kyungjin; Yoon, Hye-Jin; Matsuura, Atsushi; Kim, Yong Hwan; Lee, Hyung Ho

2018-04-30

L-pipecolic acid is a non-protein amino acid commonly found in plants, animals, and microorganisms. It is a well-known precursor to numerous microbial secondary metabolites and pharmaceuticals, including anticancer agents, immunosuppressants, and several antibiotics. Lysine cyclodeaminase (LCD) catalyzes β-deamination of L-lysine into L-pipecolic acid using β-nicotinamide adenine dinucleotide as a cofactor. Expression of a human homolog of LCD, μ-crystallin, is elevated in prostate cancer patients. To understand the structural features and catalytic mechanisms of LCD, we determined the crystal structures of Streptomyces pristinaespiralis LCD (SpLCD) in (i) a binary complex with NAD + , (ii) a ternary complex with NAD + and L-pipecolic acid, (iii) a ternary complex with NAD + and L-proline, and (iv) a ternary complex with NAD + and L-2,4-diamino butyric acid. The overall structure of SpLCD was similar to that of ornithine cyclodeaminase from Pseudomonas putida . In addition, SpLCD recognized L-lysine, L-ornithine, and L-2,4-diamino butyric acid despite differences in the active site, including differences in hydrogen bonding by Asp236, which corresponds with Asp228 from Pseudomonas putida ornithine cyclodeaminase. The substrate binding pocket of SpLCD allowed substrates smaller than lysine to bind, thus enabling binding to ornithine and L-2,4-diamino butyric acid. Our structural and biochemical data facilitate a detailed understanding of substrate and product recognition, thus providing evidence for a reaction mechanism for SpLCD. The proposed mechanism is unusual in that NAD + is initially converted into NADH and then reverted back into NAD + at a late stage of the reaction.

Role of Disproportionation in the Dissolution of Mn from Lithium Manganate Spinel

DOE PAGES

Benedek, Roy

2017-09-18

Dissolution of Mn from lithium-manganese spinel has hindered its commercialization as a cathode material in Li-ion batteries. Disproportionation of near-surface Mn(III), in the presence of acid, has been widely thought to result in dissolved divalent Mn. To what extent stray acidic water in the cell (as opposed to the organic electrolyte) acts as the solvent for Mn ions has not been established. Simulations by Leung show that a small displacement of trivalent Mn from its equilibrium site at an LiMn 2O 4 (001)/ ethylene carbonate interface leads to its reduction to Mn(II). In the present work, Thermodynamic Integration is performed,more » based on first-principles molecular dynamics simulations within the Blue-Moon ensemble, for the detachment of Mn(III) ions at the LiMn 2O 4 (001)/water interface. The results show that reduction of Mn(III) to Mn(II) occurs also in the case of an aqueous interface. The simulations were performed for both neutral and acidic water (in the presence of HF), with the coordination number of the dissolving Mn ion with substrate oxygen ions taken as the reaction coordinate. The simulations indicate that an F - ion strongly binds to a surface Mn(III) ion, and weakens its adhesion to the substrate. Owing to this weakening, a surface Mn-F complex traverses regions of phase space at room temperature where disproportionation becomes energetically favorable. Although this disproportionation occurs close to the substrate, where the Mn coordination number is only slightly lowered from its equilibrium value, we argue that the likelihood of reattachment after disproportionation is small (Leung arrived at a similar interpretation in the case of the LiMn 2O 4 (001)/ EC interface). We suggest that the critical role of F - in promoting dissolution is to weaken the Mn binding to the substrate so as to enable disproportionation. The partially detached MnF complex may then undergo additional interaction with the solvent to form, e.g., MnF 2, which would enable transport away from the substrate. In conclusion, the EPR measurements by Shilina et al. which appear to show Mn(III) as the predominant solvated species are discussed.« less

Identification of amino acids important for substrate specificity in sucrose transporters using gene shuffling.

PubMed

Reinders, Anke; Sun, Ye; Karvonen, Kayla L; Ward, John M

2012-08-31

Plant sucrose transporters (SUTs) are H(+)-coupled uptake transporters. Type I and II (SUTs) are phylogenetically related but have different substrate specificities. Type I SUTs transport sucrose, maltose, and a wide range of natural and synthetic α- and β-glucosides. Type II SUTs are more selective for sucrose and maltose. Here, we investigated the structural basis for this difference in substrate specificity. We used a novel gene shuffling method called synthetic template shuffling to introduce 62 differentially conserved amino acid residues from type I SUTs into OsSUT1, a type II SUT from rice. The OsSUT1 variants were tested for their ability to transport the fluorescent coumarin β-glucoside esculin when expressed in yeast. Fluorescent yeast cells were selected using fluorescence-activated cell sorting (FACS). Substitution of five amino acids present in type I SUTs in OsSUT1 was found to be sufficient to confer esculin uptake activity. The changes clustered in two areas of the OsSUT1 protein: in the first loop and the top of TMS2 (T80L and A86K) and in TMS5 (S220A, S221A, and T224Y). The substrate specificity of this OsSUT1 variant was almost identical to that of type I SUTs. Corresponding changes in the sugarcane type II transporter ShSUT1 also changed substrate specificity, indicating that these residues contribute to substrate specificity in type II SUTs in general.

Identification of Amino Acids Important for Substrate Specificity in Sucrose Transporters Using Gene Shuffling*

PubMed Central

Reinders, Anke; Sun, Ye; Karvonen, Kayla L.; Ward, John M.

2012-01-01

Plant sucrose transporters (SUTs) are H+-coupled uptake transporters. Type I and II (SUTs) are phylogenetically related but have different substrate specificities. Type I SUTs transport sucrose, maltose, and a wide range of natural and synthetic α- and β-glucosides. Type II SUTs are more selective for sucrose and maltose. Here, we investigated the structural basis for this difference in substrate specificity. We used a novel gene shuffling method called synthetic template shuffling to introduce 62 differentially conserved amino acid residues from type I SUTs into OsSUT1, a type II SUT from rice. The OsSUT1 variants were tested for their ability to transport the fluorescent coumarin β-glucoside esculin when expressed in yeast. Fluorescent yeast cells were selected using fluorescence-activated cell sorting (FACS). Substitution of five amino acids present in type I SUTs in OsSUT1 was found to be sufficient to confer esculin uptake activity. The changes clustered in two areas of the OsSUT1 protein: in the first loop and the top of TMS2 (T80L and A86K) and in TMS5 (S220A, S221A, and T224Y). The substrate specificity of this OsSUT1 variant was almost identical to that of type I SUTs. Corresponding changes in the sugarcane type II transporter ShSUT1 also changed substrate specificity, indicating that these residues contribute to substrate specificity in type II SUTs in general. PMID:22807445

Iron(IV)hydroxide pK(a) and the role of thiolate ligation in C-H bond activation by cytochrome P450.

PubMed

Yosca, Timothy H; Rittle, Jonathan; Krest, Courtney M; Onderko, Elizabeth L; Silakov, Alexey; Calixto, Julio C; Behan, Rachel K; Green, Michael T

2013-11-15

Cytochrome P450 enzymes activate oxygen at heme iron centers to oxidize relatively inert substrate carbon-hydrogen bonds. Cysteine thiolate coordination to iron is posited to increase the pK(a) (where K(a) is the acid dissociation constant) of compound II, an iron(IV)hydroxide complex, correspondingly lowering the one-electron reduction potential of compound I, the active catalytic intermediate, and decreasing the driving force for deleterious auto-oxidation of tyrosine and tryptophan residues in the enzyme's framework. Here, we report on the preparation of an iron(IV)hydroxide complex in a P450 enzyme (CYP158) in ≥90% yield. Using rapid mixing technologies in conjunction with Mössbauer, ultraviolet/visible, and x-ray absorption spectroscopies, we determine a pK(a) value for this compound of 11.9. Marcus theory analysis indicates that this elevated pK(a) results in a >10,000-fold reduction in the rate constant for oxidations of the protein framework, making these processes noncompetitive with substrate oxidation.

Differential effects of buffer pH on Ca2+-induced ROS emission with inhibited mitochondrial complexes I and III

PubMed Central

Lindsay, Daniel P.; Camara, Amadou K. S.; Stowe, David F.; Lubbe, Ryan; Aldakkak, Mohammed

2015-01-01

Excessive mitochondrial reactive oxygen species (ROS) emission is a critical component in the etiology of ischemic injury. Complex I and complex III of the electron transport chain are considered the primary sources of ROS emission during cardiac ischemia and reperfusion (IR) injury. Several factors modulate ischemic ROS emission, such as an increase in extra-matrix Ca2+, a decrease in extra-matrix pH, and a change in substrate utilization. Here we examined the combined effects of these factors on ROS emission from respiratory complexes I and III under conditions of simulated IR injury. Guinea pig heart mitochondria were suspended in experimental buffer at a given pH and incubated with or without CaCl2. Mitochondria were then treated with either pyruvate, a complex I substrate, followed by rotenone, a complex I inhibitor, or succinate, a complex II substrate, followed by antimycin A, a complex III inhibitor. H2O2 release rate and matrix volume were compared with and without adding CaCl2 and at pH 7.15, 6.9, or 6.5 with pyruvate + rotenone or succinate + antimycin A to simulate conditions that may occur during in vivo cardiac IR injury. We found a large increase in H2O2 release with high [CaCl2] and pyruvate + rotenone at pH 6.9, but not at pHs 7.15 or 6.5. Large increases in H2O2 release rate also occurred at each pH with high [CaCl2] and succinate + antimycin A, with the highest levels observed at pH 7.15. The increases in H2O2 release were associated with significant mitochondrial swelling, and both H2O2 release and swelling were abolished by cyclosporine A, a desensitizer of the mitochondrial permeability transition pore (mPTP). These results indicate that ROS production by complex I and by complex III is differently affected by buffer pH and Ca2+ loading with mPTP opening. The study suggests that changes in the levels of cytosolic Ca2+ and pH during IR alter the relative amounts of ROS produced at mitochondrial respiratory complex I and complex III. PMID:25805998

Probing the hammerhead ribozyme structure with ribonucleases.

PubMed Central

Hodgson, R A; Shirley, N J; Symons, R H

1994-01-01

Susceptibility to RNase digestion has been used to probe the conformation of the hammerhead ribozyme structure prepared from chemically synthesised RNAs. Less than about 1.5% of the total sample was digested to obtain a profile of RNase digestion sites. The observed digestion profiles confirmed the predicted base-paired secondary structure for the hammerhead. Digestion profiles of both cis and trans hammerhead structures were nearly identical which indicated that the structural interactions leading to self-cleavage were similar for both systems. Furthermore, the presence or absence of Mg2+ did not affect the RNase digestion profiles, thus indicating that Mg2+ did not modify the hammerhead structure significantly to induce self-cleavage. The base-paired stems I and II in the hammerhead structure were stable whereas stem III, which was susceptible to digestion, appeared to be an unstable region. The single strand domains separating the stems were susceptible to digestion with the exception of sites adjacent to guanosines; GL2.1 in the stem II loop and G12 in the conserved GAAAC sequence, which separates stems II and III. The absence of digestion at GL2.1 in the stem II hairpin loop of the hammerhead complex was maintained in uncomplexed ribozyme and in short oligonucleotides containing only the stem II hairpin region. In contrast, the G12 site became susceptible when the ribozyme was not complexed with its substrate. Overall the results are consistent with the role of Mg2+ in the hammerhead self-cleavage reaction being catalytic and not structural. Images PMID:8202361

Determination of Key Residues for Catalysis and RNA Cleavage Specificity

PubMed Central

Barbas, Ana; Matos, Rute G.; Amblar, Mónica; López-Viñas, Eduardo; Gomez-Puertas, Paulino; Arraiano, Cecília M.

2009-01-01

RNase II is the prototype of a ubiquitous family of enzymes that are crucial for RNA metabolism. In Escherichia coli this protein is a single-stranded-specific 3′-exoribonuclease with a modular organization of four functional domains. In eukaryotes, the RNase II homologue Rrp44 (also known as Dis3) is the catalytic subunit of the exosome, an exoribonuclease complex essential for RNA processing and decay. In this work we have performed a functional characterization of several highly conserved residues located in the RNase II catalytic domain to address their precise role in the RNase II activity. We have constructed a number of RNase II mutants and compared their activity and RNA binding to the wild type using different single- or double-stranded substrates. The results presented in this study substantially improve the RNase II model for RNA degradation. We have identified the residues that are responsible for the discrimination of cleavage of RNA versus DNA. We also show that the Arg-500 residue present in the RNase II active site is crucial for activity but not for RNA binding. The most prominent finding presented is the extraordinary catalysis observed in the E542A mutant that turns RNase II into a “super-enzyme.” PMID:19458082

Obtaining Thickness-Limited Electrospray Deposition for 3D Coating.

PubMed

Lei, Lin; Kovacevich, Dylan A; Nitzsche, Michael P; Ryu, Jihyun; Al-Marzoki, Kutaiba; Rodriguez, Gabriela; Klein, Lisa C; Jitianu, Andrei; Singer, Jonathan P

2018-04-04

Electrospray processing utilizes the balance of electrostatic forces and surface tension within a charged spray to produce charged microdroplets with a narrow dispersion in size. In electrospray deposition, each droplet carries a small quantity of suspended material to a target substrate. Past electrospray deposition results fall into two major categories: (1) continuous spray of films onto conducting substrates and (2) spray of isolated droplets onto insulating substrates. A crossover regime, or a self-limited spray, has only been limitedly observed in the spray of insulating materials onto conductive substrates. In such sprays, a limiting thickness emerges, where the accumulation of charge repels further spray. In this study, we examined the parametric spray of several glassy polymers to both categorize past electrospray deposition results and uncover the critical parameters for thickness-limited sprays. The key parameters for determining the limiting thickness were (1) field strength and (2) spray temperature, related to (i) the necessary repulsive field and (ii) the ability for the deposited materials to swell in the carrier solvent vapor and redistribute charge. These control mechanisms can be applied to the uniform or controllably-varied microscale coating of complex three-dimensional objects.

Model-based confirmation of alternative substrates of mitochondrial electron transport chain.

PubMed

Kleessen, Sabrina; Araújo, Wagner L; Fernie, Alisdair R; Nikoloski, Zoran

2012-03-30

Discrimination of metabolic models based on high throughput metabolomics data, reflecting various internal and external perturbations, is essential for identifying the components that contribute to the emerging behavior of metabolic processes. Here, we investigate 12 different models of the mitochondrial electron transport chain (ETC) in Arabidopsis thaliana during dark-induced senescence in order to elucidate the alternative substrates to this metabolic pathway. Our findings demonstrate that the coupling of the proposed computational approach, based on dynamic flux balance analysis, with time-resolved metabolomics data results in model-based confirmations of the hypotheses that, during dark-induced senescence in Arabidopsis, (i) under conditions where the main substrate for the ETC are not fully available, isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase are able to donate electrons to the ETC, (ii) phytanoyl-CoA does not act even as an indirect substrate of the electron transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase complex, and (iii) the mitochondrial γ-aminobutyric acid transporter has functional significance in maintaining mitochondrial metabolism. Our study provides a basic framework for future in silico studies of alternative pathways in mitochondrial metabolism under extended darkness whereby the role of its components can be computationally discriminated based on available molecular profile data.

Substrate specificity of human metallocarboxypeptidase D: Comparison of the two active carboxypeptidase domains

PubMed Central

Tanco, Sebastian; Díaz, Lucía; Dasgupta, Sayani; Fernandez-Recio, Juan; Lorenzo, Julia; Aviles, Francesc X.; Fricker, Lloyd D.

2017-01-01

Metallocarboxypeptidase D (CPD) is a membrane-bound component of the trans-Golgi network that cycles to the cell surface through exocytic and endocytic pathways. Unlike other members of the metallocarboxypeptidase family, CPD is a multicatalytic enzyme with three carboxypeptidase-like domains, although only the first two domains are predicted to be enzymatically active. To investigate the enzymatic properties of each domain in human CPD, a critical active site Glu in domain I and/or II was mutated to Gln and the protein expressed, purified, and assayed with a wide variety of peptide substrates. CPD with all three domains intact displays >50% activity from pH 5.0 to 7.5 with a maximum at pH 6.5, as does CPD with mutation of domain I. In contrast, the domain II mutant displayed >50% activity from pH 6.5–7.5. CPD with mutations in both domains I and II was completely inactive towards all substrates and at all pH values. A quantitative peptidomics approach was used to compare the activities of CPD domains I and II towards a large number of peptides. CPD cleaved C-terminal Lys or Arg from a subset of the peptides. Most of the identified substrates of domain I contained C-terminal Arg, whereas comparable numbers of Lys- and Arg-containing peptides were substrates of domain II. We also report that some peptides with C-terminal basic residues were not cleaved by either domain I or II, showing the importance of the P1 position for CPD activity. Finally, the preference of domain I for C-terminal Arg was validated through molecular docking experiments. Together with the differences in pH optima, the different substrate specificities of CPD domains I and II allow the enzyme to perform distinct functions in the various locations within the cell. PMID:29131831

Soliton Analysis in Complex Molecular Systems: A Zig-Zag Chain

NASA Astrophysics Data System (ADS)

Christiansen, P. L.; Savin, A. V.; Zolotaryuk, A. V.

1997-06-01

A simple numerical method for seeking solitary wavesolutions of a permanent profile in molecular systems of big complexity is presented. The method is essentially based on the minimization of a finite-dimensional function which is chosen under an appropriate discretization of time derivatives in equations of motion. In the present paper, it is applied to a zig-zag chain backbone of coupled particles, each of which has twodegrees of freedom (longitudinal and transverse). Both topological and nontopological soliton solutions are treated for this chain when it is (i) subjected to a two-dimensional periodic substrate potential or (ii) considered as an isolated object, respectively. In the first case, which may be considered as a zig-zag generalization of the Frenkel-Kontorova chain model, two types of kink solutions with different topological charges, describing vacancies of one or two atoms (I- or II-kinks) and defects with excess one or two atoms in the chain (I- or II-antikinks), have been found. The second case (isolated chain) is a generalization of the well-known Fermi-Pasta-Ulam chain model, which takes into account transverse degrees of freedom of the chain molecules. Two types of stable nontopological soliton solutions which describe either (i) a supersonic solitary wave of longitudinal stretching accompanied by transverse slendering or (ii) supersonic pulses of longitudinal compression propagating together with localized transverse thickening (bulge) have been obtained.

Active Site Metal Identity Alters Histone Deacetylase 8 Substrate Selectivity: A Potential Novel Regulatory Mechanism.

PubMed

Castaneda, Carol Ann; Lopez, Jeffrey E; Joseph, Caleb G; Scholle, Michael D; Mrksich, Milan; Fierke, Carol A

2017-10-24

Histone deacetylase 8 (HDAC8) is a well-characterized member of the class I acetyl-lysine deacetylase (HDAC) family. Previous work has shown that the efficiency of HDAC8-catalyzed deacetylation of a methylcoumarin peptide varies depending on the identity of the divalent metal ion in the HDAC8 active site. Here we demonstrate that both HDAC8 activity and substrate selectivity for a diverse range of peptide substrates depend on the identity of the active site metal ion. Varied deacetylase activities of Fe(II)- and Zn(II)-HDAC8 toward an array of peptide substrates were identified using self-assembled monolayers for matrix-assisted laser desorption ionization (SAMDI) mass spectrometry. Subsequently, the metal dependence of deacetylation of peptides of biological interest was measured using an in vitro peptide assay. While Fe(II)-HDAC8 is generally more active than Zn(II)-HDAC8, the Fe(II)/Zn(II) HDAC8 activity ratio varies widely (from 2 to 150) among the peptides tested. These data provide support for the hypothesis that HDAC8 may undergo metal switching in vivo that, in turn, may regulate its activity. However, future studies are needed to explore the identity of the metal ion bound to HDAC8 in cells under varied conditions.

Analysis of RNA Processing Reactions Using Cell Free Systems: 3' End Cleavage of Pre-mRNA Substrates in vitro

PubMed Central

Jablonski, Joseph; Clementz, Mark; Ryan, Kevin; Valente, Susana T.

2014-01-01

The 3’ end of mammalian mRNAs is not formed by abrupt termination of transcription by RNA polymerase II (RNPII). Instead, RNPII synthesizes precursor mRNA beyond the end of mature RNAs, and an active process of endonuclease activity is required at a specific site. Cleavage of the precursor RNA normally occurs 10-30 nt downstream from the consensus polyA site (AAUAAA) after the CA dinucleotides. Proteins from the cleavage complex, a multifactorial protein complex of approximately 800 kDa, accomplish this specific nuclease activity. Specific RNA sequences upstream and downstream of the polyA site control the recruitment of the cleavage complex. Immediately after cleavage, pre-mRNAs are polyadenylated by the polyA polymerase (PAP) to produce mature stable RNA messages. Processing of the 3’ end of an RNA transcript may be studied using cellular nuclear extracts with specific radiolabeled RNA substrates. In sum, a long 32P-labeled uncleaved precursor RNA is incubated with nuclear extracts in vitro, and cleavage is assessed by gel electrophoresis and autoradiography. When proper cleavage occurs, a shorter 5’ cleaved product is detected and quantified. Here, we describe the cleavage assay in detail using, as an example, the 3’ end processing of HIV-1 mRNAs. PMID:24835792

Roles of type II thioesterases and their application for secondary metabolite yield improvement.

PubMed

Kotowska, Magdalena; Pawlik, Krzysztof

2014-09-01

A large number of antibiotics and other industrially important microbial secondary metabolites are synthesized by polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). These multienzymatic complexes provide an enormous flexibility in formation of diverse chemical structures from simple substrates, such as carboxylic acids and amino acids. Modular PKSs and NRPSs, often referred to as megasynthases, have brought about a special interest due to the colinearity between enzymatic domains in the proteins working as an "assembly line" and the chain elongation and modification steps. Extensive efforts toward modified compound biosynthesis by changing organization of PKS and NRPS domains in a combinatorial manner laid good grounds for rational design of new structures and their controllable biosynthesis as proposed by the synthetic biology approach. Despite undeniable progress made in this field, the yield of such "unnatural" natural products is often not satisfactory. Here, we focus on type II thioesterases (TEIIs)--discrete hydrolytic enzymes often encoded within PKS and NRPS gene clusters which can be used to enhance product yield. We review diverse roles of TEIIs (removal of aberrant residues blocking the megasynthase, participation in substrate selection, intermediate, and product release) and discuss their application in new biosynthetic systems utilizing PKS and NRPS parts.

In Vitro Biosynthesis of Unnatural Enterocin and Wailupemycin Polyketides¥

PubMed Central

Kalaitzis, John A.; Cheng, Qian; Thomas, Paul M.; Kelleher, Neil L.; Moore, Bradley S.

2009-01-01

Nature has evolved finely tuned strategies to synthesize rare and complex natural products such as the enterocin family of polyketides from the marine bacterium Streptomyces maritimus. Herein we report the directed ex vivo multienzyme syntheses of 24 unnatural 5-deoxyenterocin and wailupemycin F and G analogues, 18 of which are new. We have generated molecular diversity by priming the enterocin biosynthesis enzymes with unnatural substrates and have illustrated further the uniqueness of this type II polyketide synthase by way of exploiting its unusual starter unit biosynthesis pathways. PMID:19215142

In vitro biosynthesis of unnatural enterocin and wailupemycin polyketides.

PubMed

Kalaitzis, John A; Cheng, Qian; Thomas, Paul M; Kelleher, Neil L; Moore, Bradley S

2009-03-27

Nature has evolved finely tuned strategies to synthesize rare and complex natural products such as the enterocin family of polyketides from the marine bacterium Streptomyces maritimus. Herein we report the directed ex vivo multienzyme syntheses of 24 unnatural 5-deoxyenterocin and wailupemycin F and G analogues, 18 of which are new. We have generated molecular diversity by priming the enterocin biosynthesis enzymes with unnatural substrates and have illustrated further the uniqueness of this type II polyketide synthase by way of exploiting its unusual starter unit biosynthesis pathways.

Enantioselective addition of nitromethane to 2-acylpyridine N-oxides. Expanding the generation of quaternary stereocenters with the Henry reaction.

PubMed

Holmquist, Melireth; Blay, Gonzalo; Muñoz, M Carmen; Pedro, José R

2014-02-21

The direct asymmetric Henry reaction with prochiral ketones, leading to tertiary nitroaldols, is an elusive reaction so far limited to a reduced number of reactive substrates such as trifluoromethyl ketones or α-keto carbonyl compounds. Expanding the scope of this important reaction, the direct asymmetric addition of nitromethane to 2-acylpyridine N-oxides catalyzed by a BOX-Cu(II) complex to give the corresponding pyridine-derived tertiary nitroaldols having a quaternary stereogenic center with variable yields and good enantioselectivity, is described.

T cell activation is determined by the number of presented antigens.

PubMed

Deeg, Janosch; Axmann, Markus; Matic, Jovana; Liapis, Anastasia; Depoil, David; Afrose, Jehan; Curado, Silvia; Dustin, Michael L; Spatz, Joachim P

2013-01-01

Antigen recognition is a key event during T cell activation. Here, we introduce nanopatterned antigen arrays that mimic the antigen presenting cell surface during T cell activation. The assessment of activation related events revealed the requirement of a minimal density of 90-140 stimulating major histocompatibility complex class II proteins (pMHC) molecules per μm(2). We demonstrate that these substrates induce T cell responses in a pMHC dose-dependent manner and that the number of presented pMHCs dominates over local pMHC density.

T Cell Activation is Determined by the Number of Presented Antigens

PubMed Central

2013-01-01

Antigen recognition is a key event during T cell activation. Here, we introduce nanopatterned antigen arrays that mimic the antigen presenting cell surface during T cell activation. The assessment of activation related events revealed the requirement of a minimal density of 90–140 stimulating major histocompatibility complex class II proteins (pMHC) molecules per μm2. We demonstrate that these substrates induce T cell responses in a pMHC dose-dependent manner and that the number of presented pMHCs dominates over local pMHC density. PMID:24117051

Differential affinity of BsSCO for Cu(II) and Cu(I) suggests a redox role in copper transfer to the Cu(A) center of cytochrome c oxidase.

PubMed

Hill, Bruce C; Andrews, Diann

2012-06-01

SCO (synthesis of cytochrome c oxidase) proteins are involved in the assembly of the respiratory chain enzyme cytochrome c oxidase acting to assist in the assembly of the Cu(A) center contained within subunit II of the oxidase complex. The Cu(A) center receives electrons from the reductive substrate ferrocytochrome c, and passes them on to the cytochrome a center. Cytochrome a feeds electrons to the oxygen reaction site composed of cytochrome a(3) and Cu(B). Cu(A) consists of two copper ions positioned within bonding distance and ligated by two histidine side chains, one methionine, a backbone carbonyl and two bridging cysteine residues. The complex structure and redox capacity of Cu(A) present a potential assembly challenge. SCO proteins are members of the thioredoxin family which led to the early suggestion of a disulfide exchange function for SCO in Cu(A) assembly, whereas the copper binding capacity of the Bacillus subtilis version of SCO (i.e., BsSCO) suggests a direct role for SCO proteins in copper transfer. We have characterized redox and copper exchange properties of apo- and metalated-BsSCO. The release of copper (II) from its complex with BsSCO is best achieved by reducing it to Cu(I). We propose a mechanism involving both disulfide and copper exchange between BsSCO and the apo-Cu(A) site. This article is part of a Special Issue entitled: Biogenesis/Assembly of Respiratory Enzyme Complexes. Copyright © 2011 Elsevier B.V. All rights reserved.

Multiple Metal Binding Domains Enhance the Zn(II) Selectivity of the Divalent Metal Ion Transporter AztA†

PubMed Central

Liu, Tong; Reyes-Caballero, Hermes; Li, Chenxi; Scott, Robert A.; Giedroc, David P.

2013-01-01

Transition metal-transporting P1B-type CPx ATPases play crucial roles in mediating metal homeostasis and resistance in all cells. The degree to which N-terminal metal binding domains (MBDs) confer metal specificity to the transporter is unclear. We show that the two MBDs of the Zn/Cd/Pb effluxing pump Anabaena AztA are functionally nonequivalent, but only with respect to zinc resistance. Inactivation of the a-MBD largely abrogates resistance to high intracellular Zn(II) levels, whereas inactivation of the b-MBD is not as deleterious. In contrast, inactivation of either the a- or b-MBD has little measurable impact on Cd(II) and Pb(II) resistance. The membrane proximal b-MBD binds Zn(II) with a higher affinity than the distal N-terminal a-MBD. Facile Zn(II)-specific intermolecular transfer from the a-MBD to the higher-affinity b-MBD is readily observed by 1H–15N HSQC spectroscopy. Unlike Zn(II), Cd(II) and Pb(II) form saturated 1:1 S4 or S3(O/N) complexes with AztAaHbH, where a single metal ion bridges the two MBDs. We propose that the tandem MBDs enhance Zn(II)-specific transport, while stabilizing a non-native inter-MBD Cd/Pb cross-linked structure that is a poor substrate and/or regulator for the transporter. PMID:17824670

A Price To Pay for Relaxed Substrate Specificity: A Comparative Kinetic Analysis of the Class II Lanthipeptide Synthetases ProcM and HalM2

PubMed Central

2015-01-01

Lanthipeptides are a class of ribosomally synthesized and posttranslationally modified peptide natural products (RiPPs) that typically harbor multiple intramolecular thioether linkages. For class II lanthipeptides, these cross-links are installed in a multistep reaction pathway by a single enzyme (LanM). The multifunctional nature of LanMs and the manipulability of their genetically encoded peptide substrates (LanAs) make LanM/LanA systems promising targets for the engineering of new antibacterial compounds. Here, we report the development of a semiquantitative mass spectrometry-based assay for kinetic characterization of LanM-catalyzed reactions. The assay was used to conduct a comparative kinetic analysis of two LanM enzymes (HalM2 and ProcM) that exhibit drastically different substrate selectivity. Numerical simulation of the kinetic data was used to develop models for the multistep HalM2- and ProcM-catalyzed reactions. These models illustrate that HalM2 and ProcM have markedly different catalytic efficiencies for the various reactions they catalyze. HalM2, which is responsible for the biosynthesis of a single compound (the Halβ subunit of the lantibiotic haloduracin), catalyzes reactions with higher catalytic efficiency than ProcM, which modifies 29 different ProcA precursor peptides during prochlorosin biosynthesis. In particular, the rates of thioether ring formation are drastically reduced in ProcM, likely because this enzyme is charged with installing a variety of lanthipeptide ring architectures in its prochlorosin products. Thus, ProcM appears to pay a kinetic price for its relaxed substrate specificity. In addition, our kinetic models suggest that conformational sampling of the LanM/LanA Michaelis complex could play an important role in the kinetics of LanA maturation. PMID:25409537

Rat liver mitochondrial dysfunction by addition of copper(II) or iron(III) ions.

PubMed

Saporito-Magriñá, Christian; Musacco-Sebio, Rosario; Acosta, Juan M; Bajicoff, Sofía; Paredes-Fleitas, Paola; Boveris, Alberto; Repetto, Marisa G

2017-01-01

Increased copper (Cu) and iron (Fe) levels in liver and brain are associated to oxidative stress and damage with increased phospholipid oxidation process. The aim of this work was to assess the toxic effects of Cu 2+ and Fe 3+ addition to rat liver mitochondria by determining mitochondrial respiration in states 3 (active respiration) and 4 (resting respiration), and phospholipid peroxidation. Both, Cu 2+ and Fe 3+ produced decreases in O 2 consumption in a concentration-dependent manner in active state 3: both ions by 42% with malate-glutamate as complex I substrate (concentration for half maximal response (C 50 ) 60μM Cu 2+ and 1.25mM Fe 3+ ), and with succinate as complex II substrate: 64-69% with C 50 of 50μM Cu 2+ and with C 50 of 1.25mM of Fe 3+ . Respiratory control decreased with Cu 2+ (C 50 50μM) and Fe 3+ (C 50 1.25-1-75mM) with both substrates. Cu 2+ produced a 2-fold increase and Fe 3+ a 5-fold increase of thiobarbituric acid-reactive substances (TBARS) content from 25μM Cu 2+ (C 50 40μM) and from 100μM Fe 3+ (C 50 1.75mM). Supplementations with Cu 2+ and Fe 3+ ions induce mitochondrial dysfunction with phospholipid peroxidation in rat liver mitochondria. Although is proved that a Fenton/Haber Weiss mechanism of oxidative damage occurs in metal-ion induced mitochondrial toxicity, slightly different responses to the metal ions suggest some differences in the mechanism of intracellular toxicity. The decreased rates of mitochondrial respiration and the alteration of mitochondrial function by phospholipid and protein oxidations lead to mitochondrial dysfunction, cellular dyshomeostasis and cell death. Copyright © 2016 Elsevier Inc. All rights reserved.

Effect of ultrasonic waves on the water turbidity during the oxidation of phenol. Formation of (hydro)peroxo complexes.

PubMed

Villota, Natalia; Lomas, Jose M; Camarero, Luis M

2017-11-01

Analysis of the kinetics of aqueous phenol oxidation by a sono-Fenton process reveals that the via involving ortho-substituted intermediates prevails: catechol (25.0%), hydroquinone (7.7%) and resorcinol (0.6%). During the oxidation, water rapidly acquires color that reaches its maximum intensity at the maximum concentration of p-benzoquinone. Turbidity formation occurs at a slower rate. Oxidant dosage determines the nature of the intermediates, being trihydroxylated benzenes (pyrogallol, hydroxyhydroquinone) and muconic acid the main precursors causing turbidity. It is found that the concentration of iron species and ultrasonic waves affects the intensity of the turbidity. The pathway of (hydro)peroxo-iron(II) complexes formation is proposed. Operating with 20.0-27.8mgFe 2+ /kW rates leads to formation of (hydro)peroxo-iron(II) complexes, which induce high turbidity levels. These species would dissociate into ZZ-muconic acid and ferrous ions. Applying relationships around 13.9mgFe 2+ /kW, the formation of (hydro)peroxo-iron(III) complexes would occur, which could react with carboxylic acids (2,5-dioxo-3-hexenedioic acid). That reaction induces turbidity slower. This is due to the organic substrate reacting with two molecules of the (hydro)peroxo complex. Therefore, it is necessary to accelerate the iron regeneration, intensifying the ultrasonic irradiation. Afterwards, this complex would dissociate into maleic acid and ferric ions. Copyright © 2017 Elsevier B.V. All rights reserved.

Contribution of the C-Terminal Region of a Group II Chaperonin to its Interaction with Prefoldin and Substrate Transfer.

PubMed

Zako, Tamotsu; Sahlan, Muhamad; Fujii, Sayaka; Yamamoto, Yohei Y; Tai, Phan The; Sakai, Kotaro; Maeda, Mizuo; Yohda, Masafumi

2016-06-05

Prefoldin is a molecular chaperone that captures an unfolded protein substrate and transfers it to a group II chaperonin. Previous studies have shown that the interaction sites for prefoldin are located in the helical protrusions of group II chaperonins. However, it does not exclude the possibility of the existence of other interaction sites. In this study, we constructed C-terminal truncation mutants of a group II chaperonin and examined the effects of these mutations on the chaperone's function and interaction with prefoldin. Whereas the mutants with up to 6 aa truncation from the C-terminus retained more than 90% chaperone activities for protecting citrate synthase from thermal aggregation and refolding of green fluorescent protein and isopropylmalate dehydrogenase, the truncation mutants showed decreased affinities for prefoldin. Consequently, the truncation mutants showed reduced transfer efficiency of the denatured substrate protein from prefoldin and subsequent chaperonin-dependent refolding. The results clearly show that the C-terminal region of group II chaperonins contributes to their interactions with prefoldin, the transfer of the substrate protein from prefoldin and its refolding. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Catalytic Domain of Topological Knot tRNA Methyltransferase (TrmH) Discriminates between Substrate tRNA and Nonsubstrate tRNA via an Induced-fit Process*

PubMed Central

Ochi, Anna; Makabe, Koki; Yamagami, Ryota; Hirata, Akira; Sakaguchi, Reiko; Hou, Ya-Ming; Watanabe, Kazunori; Nureki, Osamu; Kuwajima, Kunihiro; Hori, Hiroyuki

2013-01-01

A conserved guanosine at position 18 (G18) in the D-loop of tRNAs is often modified to 2′-O-methylguanosine (Gm). Formation of Gm18 in eubacterial tRNA is catalyzed by tRNA (Gm18) methyltransferase (TrmH). TrmH enzymes can be divided into two types based on their substrate tRNA specificity. Type I TrmH, including Thermus thermophilus TrmH, can modify all tRNA species, whereas type II TrmH, for example Escherichia coli TrmH, modifies only a subset of tRNA species. Our previous crystal study showed that T. thermophilus TrmH is a class IV S-adenosyl-l-methionine-dependent methyltransferase, which maintains a topological knot structure in the catalytic domain. Because TrmH enzymes have short stretches at the N and C termini instead of a clear RNA binding domain, these stretches are believed to be involved in tRNA recognition. In this study, we demonstrate by site-directed mutagenesis that both N- and C-terminal regions function in tRNA binding. However, in vitro and in vivo chimera protein studies, in which four chimeric proteins of type I and II TrmHs were used, demonstrated that the catalytic domain discriminates substrate tRNAs from nonsubstrate tRNAs. Thus, the N- and C-terminal regions do not function in the substrate tRNA discrimination process. Pre-steady state analysis of complex formation between mutant TrmH proteins and tRNA by stopped-flow fluorescence measurement revealed that the C-terminal region works in the initial binding process, in which nonsubstrate tRNA is not excluded, and that structural movement of the motif 2 region of the catalytic domain in an induced-fit process is involved in substrate tRNA discrimination. PMID:23867454

A Collapsin Response Mediator Protein 2 Isoform Controls Myosin II-Mediated Cell Migration and Matrix Assembly by Trapping ROCK II

PubMed Central

Morgan-Fisher, Marie; Wait, Robin; Couchman, John R.; Wewer, Ulla M.

2012-01-01

Collapsin response mediator protein 2 (CRMP-2) is known as a regulator of neuronal polarity and differentiation through microtubule assembly and trafficking. Here, we show that CRMP-2 is ubiquitously expressed and a splice variant (CRMP-2L), which is expressed mainly in epithelial cells among nonneuronal cells, regulates myosin II-mediated cellular functions, including cell migration. While the CRMP-2 short form (CRMP-2S) is recognized as a substrate of the Rho-GTP downstream kinase ROCK in neuronal cells, a CRMP-2 complex containing 2L not only bound the catalytic domain of ROCK II through two binding domains but also trapped and inhibited the kinase. CRMP-2L protein levels profoundly affected haptotactic migration and the actin-myosin cytoskeleton of carcinoma cells as well as nontransformed epithelial cell migration in a ROCK activity-dependent manner. Moreover, the ectopic expression of CRMP-2L but not -2S inhibited fibronectin matrix assembly in fibroblasts. Underlying these responses, CRMP-2L regulated the kinase activity of ROCK II but not ROCK I, independent of GTP-RhoA levels. This study provides a new insight into CRMP-2 as a controller of myosin II-mediated cellular functions through the inhibition of ROCK II in nonneuronal cells. PMID:22431514

Computational Insight into the Mechanism of Alkane Hydroxylation by Non-heme Fe(PyTACN) Iron Complexes. Effects of the Substrate and Solvent.

PubMed

Postils, Verònica; Company, Anna; Solà, Miquel; Costas, Miquel; Luis, Josep M

2015-09-08

The reaction mechanisms for alkane hydroxylation catalyzed by non-heme Fe(V)O complexes presented in the literature vary from rebound stepwise to concerted highly asynchronous processes. The origin of these important differences is still not completely understood. Herein, in order to clarify this apparent inconsistency, the hydroxylation of a series of alkanes (methane and substrates bearing primary, secondary, and tertiary C-H bonds) through a Fe(V)O species, [Fe(V)(O)(OH)(PyTACN)](2+) (PyTACN = 1-(2'-pyridylmethyl)-4,7-dimethyl-1,4,7-triazacyclononane), has been computationally examined at the gas phase and in acetonitrile solution. The initial breaking of the C-H bond can occur via hydrogen atom transfer (HAT), leading to an intermediate where there is an interaction between the radical substrate and [Fe(IV)(OH)2(PyTACN)](2+), or through hydride transfer to form a cationic substrate interacting with the [Fe(III)(OH)2(PyTACN)](+) species. Our calculations show the following: (i) except for methane in the rest of the alkanes studied, the intermediate formed by R(+) and [Fe(III)(OH)2(PyTACN)](+) is more stable than that involving the alkyl radical and the [Fe(IV)(OH)2(PyTACN)](2+) complex; (ii) in spite of (i), the first step of the reaction mechanism for all substrates is a HAT instead of hydride abstraction; (iii) the HAT is the rate-determining step for all analyzed cases; and (iv) the barrier for the HAT decreases along methane → primary → secondary → tertiary carbon. The second part of the reaction mechanism corresponds to the rebound process. Therefore, the stereospecific hydroxylation of alkane C-H bonds by non-heme Fe(V)(O) species occurs through a rebound stepwise mechanism that resembles that taking place at heme analogues. Finally, our study also shows that, to properly describe alkane hydroxylation processes mediated by Fe(V)O species, it is essential to consider the solvent effects during geometry optimizations. The use of gas-phase geometries explains the variety of mechanisms for the hydroxylation of alkanes reported in the literature.

Multiple binding modes of substrate to the catalytic RNA subunit of RNase P from Escherichia coli.

PubMed Central

Pomeranz Krummel, D A; Altman, S

1999-01-01

M1 RNA that contained 4'-thiouridine was photochemically cross-linked to different substrates and to a product of the reaction it governs. The locations of the cross-links in these photochemically induced complexes were identified. The cross-links indicated that different substrates share some contacts but have distinct binding modes to M1 RNA. The binding of some substrates also results in a substrate-dependent conformational change in the enzymatic RNA, as evidenced by the appearance of an M1 RNA intramolecular cross-link. The identification of the cross-links between M1 RNA and product indicate that they are shared with only one of the three cross-linked E-S complexes that were identified, an indication of noncompetitive inhibition by the product. We also examined whether the cross-linked complexes between M1 RNA and substrate(s) or product are altered in the presence of the enzyme's protein cofactor (C5 protein) and in the presence of different concentrations of divalent metal ions. C5 protein enhanced the yield of certain M1 RNA-substrate cross-linked complexes for both wild-type M1 RNA and a deletion mutant of M1 RNA (delta[273-281]), but not for the M1 RNA-product complex. High concentrations of Mg2+ increased the yield of all M1 RNA-substrate complexes but not the M1 RNA-product complex. PMID:10445877

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shen, Yan; Chen, Wang; Zhao, Baobing

Highlights: • CS1 is a novel nonintercalating topoisomerase IIα poison. • CS1 shows potent in vitro and in vivo antitumor activity. • CS1 shows 6–10-fold less toxicity to normal cells compared with etoposide. • CS1 is not a substrate of P-glycoprotein and multidrug resistance irrelevant. - Abstract: DNA topoisomerase II (Topo II) is an essential nuclear enzyme and a validated target for anticancer agent screening. CS1, a novel 2-phenylnaphthalene, had potent cytotoxicity against nine tested tumor cell lines and showed 6–10-fold less toxicity against normal cell lines compared with etoposide. In addition, CS1 showed potential anti-multidrug resistance capabilities. kDNA decatenation,more » DNA relaxation and cleavage complex assays indicated that CS1 acted as a nonintercalating topoisomerase IIα (Topo IIα) inhibitor by stabilizing the DNA-Topo IIα cleavage complex. CS1 also induced DNA breaks in MDA-MB-231 cells evidenced by comet tails and the accumulation of γH2AX foci. The ability of CS1 in inducing DNA breaks mediated by Topo II resulted in G2/M phase arrest and apoptosis. Moreover, CS1 exhibited dramatic in vivo antitumor activity and lower toxicity compared with etoposide. This work supports the development of CS1 as a promising candidate for the treatment of cancer by targeting Topo IIα.« less

Type II Fatty Acid Synthesis Is Essential for the Replication of Chlamydia trachomatis*

PubMed Central

Yao, Jiangwei; Abdelrahman, Yasser M.; Robertson, Rosanna M.; Cox, John V.; Belland, Robert J.; White, Stephen W.; Rock, Charles O.

2014-01-01

The major phospholipid classes of the obligate intracellular bacterial parasite Chlamydia trachomatis are the same as its eukaryotic host except that they also contain chlamydia-made branched-chain fatty acids in the 2-position. Genomic analysis predicts that C. trachomatis is capable of type II fatty acid synthesis (FASII). AFN-1252 was deployed as a chemical tool to specifically inhibit the enoyl-acyl carrier protein reductase (FabI) of C. trachomatis to determine whether chlamydial FASII is essential for replication within the host. The C. trachomatis FabI (CtFabI) is a homotetramer and exhibited typical FabI kinetics, and its expression complemented an Escherichia coli fabI(Ts) strain. AFN-1252 inhibited CtFabI by binding to the FabI·NADH complex with an IC50 of 0.9 μm at saturating substrate concentration. The x-ray crystal structure of the CtFabI·NADH·AFN-1252 ternary complex revealed the specific interactions between the drug, protein, and cofactor within the substrate binding site. AFN-1252 treatment of C. trachomatis-infected HeLa cells at any point in the infectious cycle caused a decrease in infectious titers that correlated with a decrease in branched-chain fatty acid biosynthesis. AFN-1252 treatment at the time of infection prevented the first cell division of C. trachomatis, although the cell morphology suggested differentiation into a metabolically active reticulate body. These results demonstrate that FASII activity is essential for C. trachomatis proliferation within its eukaryotic host and validate CtFabI as a therapeutic target against C. trachomatis. PMID:24958721

Spontaneous wrinkling in azlactone-based functional polymer thin films in 2D and 3D geometries for guided nanopatterning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramanathan, Muruganathan; Lokitz, Bradley S.; Messman, Jamie M.

We report a simple, one step process for developing wrinkling patterns in azlactone-based polymer thin films and brushes in 2D and 3D surfaces. The polymer used in this work wrinkles spontaneously upon deposition and solidification on a substrate without applying any external strain to the substrate, with the mode of deposition defining the direction of the wrinkles. Wrinkle formation is shown to occur on a variety of substrates over large areas. We also find that a very thin brush-like layer of an azlactone-containing block copolymer also exhibits wrinkled topology. Given the spontaneity and versatility of wrinkle formation, we further demonstratemore » two proofs-of-concept, i) that these periodic wrinkled structures are not limited to planar surfaces, but are also developed in complex geometries including tubes, cones and other 3D structures; and ii) that this one-step wrinkling process can be used to guide the deposition of metal nanoparticles and quantum dots, creating a periodic, nanopatterned film.« less

First-principles simulations of doping-dependent mesoscale screening of adatoms in graphene

NASA Astrophysics Data System (ADS)

Mostofi, Arash; Corsetti, Fabiano; Wong, Dillon; Crommie, Michael; Lischner, Johannes

Adsorbed atoms and molecules play an important role in controlling and tuning the functional properties of 2D materials. Understanding and predicting this phenomenon from theory is challenging because of the need to capture both the local chemistry of the adsorbate-substrate interaction and its complex interplay with the long-range screening response of the substrate. To address this challenge, we have developed a first-principles multi-scale approach that combines linear-scaling density-functional theory, continuum screening theory and large-scale tight-binding simulations. Focussing on the case of a calcium adatom on graphene, we draw comparison between the effect of (i) non-linearity, (ii) intraband and interband transitions, and (iii) the exchange-correlation potential, thus providing insight into the relative importance of these different factors on the screening response. We also determine the charge transfer from the adatom to the graphene substrate (the key parameter used in continuum screening models), showing it to be significantly larger than previous estimates. AM and FC acknowledge support of the EPSRC under Grant EP/J015059/1, and JL under Grant EP/N005244/1.

New Rh 2 (II,II) Architecture for the Catalytic Reduction of H +

DOE PAGES

White, Travis A.; Witt, Suzanne E.; Li, Zhanyong; ...

2015-09-25

Formamidinate-bridged Rh 2 II,II complexes containing diimine ligands of the formula cis-[Rh 2 II,II(μ-DTolF) 2(NN) 2] 2+ (Rh 2-NN 2), where DTolF = p-ditolylformamidinate and NN = dppn (benzo[i]dipyrido[3,2-a:2',3'-h]quinoxaline), dppz (dipyrido[3,2-a:2',3'-c]phenazine), and phen (1,10-phenanthroline), electrocatalytically reduce H + to H 2 in DMF solutions containing CH 3COOH at a glassy carbon electrode. Cathodic scans in the absence of acid display a Rh III,II/II,II reduction at -0.90 V vs Fc +/Fc followed by NN 0/– reduction at -1.13, -1.36, and -1.65 V for Rh 2-dppn 2, Rh 2-dppz 2, and Rh 2-phen 2, respectively. Upon the addition of acid, Rh 2-dppnmore » 2 and Rh 2-dppz 2 undergo reduction–protonation–reduction at each pyrazine-containing NN ligand prior to the Rh 2 II,II/II,I reduction. The Rh 2 II,I species is thus protonated at one of the metal centers, resulting in the formation of the corresponding Rh 2 II,III-hydride. In the case of Rh 2-phen 2, the reduction of the phen ligand is followed by intramolecular electron transfer to the Rh 2 II,II core in the presence of protons to form a Rh 2 II,III-hydride species. Further reduction and protonation at the Rh 2 core for all three complexes rapidly catalyzes H 2 formation with varied calculated turnover frequencies (TOF) and overpotential values (η): 2.6 × 10 4 s –1 and 0.56 V for Rh 2-dppn, 2.8 × 10 4 s –1 and 0.50 V for Rh 2-dppz 2, and 5.9 × 10 4 s –1 and 0.64 V for Rh 2-phen 2. Bulk electrolysis confirmed H 2 formation, and further CH 3COOH addition regenerates H 2 production, attesting to the robust nature of the architecture. The cis-[Rh 2 II,II(μ-DTolF) 2(NN) 2] 2+ architecture benefits by combining electron-rich formamidinate bridges, a redox-active Rh 2 II,II core, and electron-accepting NN diimine ligands to allow for the electrocatalysis of H + substrate to H 2 fuel.« less

A Ni(iii) complex stabilized by silica nanoparticles as an efficient nanoheterogeneous catalyst for oxidative C-H fluoroalkylation.

PubMed

Khrizanforov, Mikhail N; Fedorenko, Svetlana V; Strekalova, Sofia O; Kholin, Kirill V; Mustafina, Asiya R; Zhilkin, Mikhail Ye; Khrizanforova, Vera V; Osin, Yuri N; Salnikov, Vadim V; Gryaznova, Tatyana V; Budnikova, Yulia H

2016-07-26

We have developed Ni(III)-doped silica nanoparticles ([(bpy)xNi(III)]@SiO2) as a recyclable, low-leaching, and efficient oxidative functionalization nanocatalyst for aromatic C-H bonds. The catalyst is obtained by doping the complex [(bpy)3Ni(II)] on silica nanoparticles along with its subsequent electrooxidation to [(bpy)xNi(III)] without an additional oxidant. The coupling reaction of arenes with perfluoroheptanoic acid occurs with 100% conversion of reactants in a single step at room temperature under nanoheterogeneous conditions. The catalyst content is only 1% with respect to the substrates under electrochemical regeneration conditions. The catalyst can be easily separated from the reaction mixture and reused a minimum of five times. The results emphasize immobilization on the silica support and the electrochemical regeneration of Ni(III) complexes as a facile route for developing an efficient nanocatalyst for oxidative functionalization.

Custom fabrication of biomass containment devices using 3-D printing enables bacterial growth analyses with complex insoluble substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Cassandra E.; Beri, Nina R.; Gardner, Jeffrey G.

Physiological studies of recalcitrant polysaccharide degradation are challenging for several reasons, one of which is the difficulty in obtaining a reproducibly accurate real-time measurement of bacterial growth using insoluble substrates. Current methods suffer from several problems including (i) high background noise due to the insoluble material interspersed with cells, (ii) high consumable and reagent cost and (iii) significant time delay between sampling and data acquisition. A customizable substrate and cell separation device would provide an option to study bacterial growth using optical density measurements. To test this hypothesis we used 3-D printing to create biomass containment devices that allow interactionmore » between insoluble substrates and microbial cells but do not interfere with spectrophotometer measurements. Evaluation of materials available for 3-D printing indicated that UV-cured acrylic plastic was the best material, being superior to nylon or stainless steel when examined for heat tolerance, reactivity, and ability to be sterilized. Cost analysis of the 3-D printed devices indicated they are a competitive way to quantitate bacterial growth compared to viable cell counting or protein measurements, and experimental conditions were scalable over a 100-fold range. The presence of the devices did not alter growth phenotypes when using either soluble substrates or insoluble substrates. Furthermore, we applied biomass containment to characterize growth of Cellvibrio japonicus on authentic lignocellulose (non-pretreated corn stover), and found physiological evidence that xylan is a significant nutritional source despite an abundance of cellulose present.« less

Custom fabrication of biomass containment devices using 3-D printing enables bacterial growth analyses with complex insoluble substrates

DOE PAGES

Nelson, Cassandra E.; Beri, Nina R.; Gardner, Jeffrey G.

2016-09-21

Physiological studies of recalcitrant polysaccharide degradation are challenging for several reasons, one of which is the difficulty in obtaining a reproducibly accurate real-time measurement of bacterial growth using insoluble substrates. Current methods suffer from several problems including (i) high background noise due to the insoluble material interspersed with cells, (ii) high consumable and reagent cost and (iii) significant time delay between sampling and data acquisition. A customizable substrate and cell separation device would provide an option to study bacterial growth using optical density measurements. To test this hypothesis we used 3-D printing to create biomass containment devices that allow interactionmore » between insoluble substrates and microbial cells but do not interfere with spectrophotometer measurements. Evaluation of materials available for 3-D printing indicated that UV-cured acrylic plastic was the best material, being superior to nylon or stainless steel when examined for heat tolerance, reactivity, and ability to be sterilized. Cost analysis of the 3-D printed devices indicated they are a competitive way to quantitate bacterial growth compared to viable cell counting or protein measurements, and experimental conditions were scalable over a 100-fold range. The presence of the devices did not alter growth phenotypes when using either soluble substrates or insoluble substrates. Furthermore, we applied biomass containment to characterize growth of Cellvibrio japonicus on authentic lignocellulose (non-pretreated corn stover), and found physiological evidence that xylan is a significant nutritional source despite an abundance of cellulose present.« less

Syntheses and molecular structures of novel Ru(II) complexes with bidentate benzimidazole based ligands and their catalytic efficiency for oxidation of benzyl alcohol

NASA Astrophysics Data System (ADS)

Dayan, Osman; Tercan, Melek; Özdemir, Namık

2016-11-01

Five bidentate ligands derived from quinoline-2-carboxylic acid, i.e. 2-(1H-benzimidazol-2-yl)quinoline (L1), 2-(1-benzyl-1H-benzimidazol-2-yl)quinoline (L2), 2-[1-(2,3,5,6-tetramethylbenzyl)-1H-benzimidazol-2-yl]quinoline (L3), 2-[1-(4-chlorobenzyl)-1H-benzimidazol-2-yl]quinoline (L4), and 2-[1-(4-methylbenzyl)-1H-benzimidazol-2-yl]quinoline (L5) were synthesized. Treatment of L1-5 with [RuCl2(p-cymene)]2 and KPF6 afforded six-coordinate piano-stool Ru(II) complexes, namely, [RuCl(L1)(p-cymene)]PF6 (C1), [RuCl(L2)(p-cymene)]PF6 (C2), [RuCl(L3)(p-cymene)]PF6 (C3), [RuCl(L4)(p-cymene)]PF6 (C4), and [RuCl(L5)(p-cymene)]PF6 (C5). Synthesized compounds were characterized with different techniques such as 1H and 13C NMR, FT-IR, and UV-vis spectroscopy. The solid state structure of L1 and C3 was confirmed by single-crystal X-ray diffraction analysis. The single crystal structure of C3 verified coordination of L3 to the Ru(II) center. The Ru(II) center has a pseudo-octahedral three legged piano stool geometry. The complexes C1-5 were tested as catalysts for the catalytic oxidation of benzyl alcohol to benzaldehyde in the presence of periodic acid (H5IO6) (Substrate/Catalyst/Oxidant = 1/0.01/0.5). The best result was obtained with C2 (3 h→90%).

Effect of substrate RNA sequence on the cleavage reaction by a short ribozyme.

PubMed Central

Ohmichi, T; Okumoto, Y; Sugimoto, N

1998-01-01

Leadzyme is a ribozyme that requires Pb2+. The catalytic sequence, CUGGGAGUCC, binds to an RNA substrate, GGACC downward arrowGAGCCAG, cleaving the RNA substrate at one site. We have investigated the effect of the substrate sequence on the cleavage activity of leadzyme using mutant substrates in order to structurally understand the RNA catalysis. The results showed that leadzyme acted as a catalyst for single site cleavage of a C5 deletion mutant substrate, GGAC downward arrowGAGCCAG, as well as the wild-type substrate. However, a mutant substrate GGACCGACCAG, which had G8 deleted from the wild-type substrate, was not cleaved. Kinetic studies by surface plasmon resonance indicated that the difference between active and inactive structures reflected the slow association and dissociation rate constants of complex formation induced by Pb2+rather than differences in complex stability. CD spectra showed that the active form of the substrate-leadzyme complex was rearranged by Pb2+binding. The G8 of the wild-type substrate, which was absent in the inactive complex, is not near the cleavage site. Thus, these results show that the active substrate-leadzyme complex has a Pb2+binding site at the junction between the unpaired region (asymmetric internal loop) and the stem region, which is distal to the cleavage site. Pb2+may play a role in rearranging the bases in the asymmetric internal loop to the correct position for catalysis. PMID:9837996

Laser direct-write and crystallization of FeSi II micro-dot array for NIR light-emitting device application

NASA Astrophysics Data System (ADS)

Narazaki, Aiko; Kurosaki, Ryozo; Sato, Tadatake; Kawaguchi, Yoshizo; Niino, Hiroyuki

2007-02-01

We printed FeSi II micro-dot array on various kinds of substrates utilizing laser-induced forward transfer (LIFT). An amorphous FeSi II was deposited by sputtering on a transparent plate as a source film. A single KrF excimer laser pulse through a mask-projection system was imaged with a small micrometer-sized grid pattern onto a film/plate interface, resulting in the deposition of FeSi II micro-dot array on a facing substrate with a high number density of 10 4 mm -2. FeSi II in the β crystalline phase is a promising eco-friendly semiconductor because of NIR electroluminescence used for optical networking as well as abundant components reserve on the earth and non-toxicity. However, the β-FeSi II film fabrication generally required high-temperature multi-processes which hamper its integration and performance reproducibility. Using the LIFT of micro-dot array, we succeeded in room-temperature preparation of β-FeSi II. Micro-Raman spectroscopy confirmed the β crystalline phase in the micro-dots deposited on an unheated silica glass substrate. Thus, the LIFT is useful for integrating functional micro-dot array accompanied by the crystallization at lower temperatures.

Impact of aldosterone antagonists on the substrate for atrial fibrillation: Aldosterone promotes oxidative stress and atrial structural/electrical remodeling

PubMed Central

Mayyas, Fadia; Alzoubi, Karem H.; Van Wagoner, David R.

2014-01-01

Atrial fibrillation (AF), the most common cardiac arrhythmia, is an electrocardiographic description of a condition with multiple and complex underlying mechanisms. Oxidative stress is an important driver of structural remodeling that creates a substrate for AF. Oxidant radicals may promote increase of atrial oxidative damage, electrical and structural remodeling, and atrial inflammation. AF and other cardiovascular morbidities activate angiotensin (Ang-II)-dependent and independent cascades. A key component of the renin–angiotensin-aldosterone system (RAAS) is the mineralocorticoid aldosterone. Recent studies provide evidence of myocardial aldosterone synthesis. Aldosterone promotes cardiac oxidative stress, inflammation and structural/electrical remodeling via multiple mechanisms. In HF patients, aldosterone production is enhanced. In patients and in experimental HF and AF models, aldosterone receptor antagonists have favorable influences on cardiac remodeling and oxidative stress. Therapeutic approaches that seek to reduce AF burden by modulating the aldosterone system are likely beneficial but underutilized. PMID:23993726

Efficient Destruction of Pollutants in Water by a Dual-Reaction-Center Fenton-like Process over Carbon Nitride Compounds-Complexed Cu(II)-CuAlO2.

PubMed

Lyu, Lai; Yan, Dengbiao; Yu, Guangfei; Cao, Wenrui; Hu, Chun

2018-04-03

Carbon nitride compounds (CN) complexed with the in-situ-produced Cu(II) on the surface of CuAlO 2 substrate (CN-Cu(II)-CuAlO 2 ) is prepared via a surface growth process for the first time and exhibits exceptionally high activity and efficiency for the degradation of the refractory pollutants in water through a Fenton-like process in a wide pH range. The reaction rate for bisphenol A removal is ∼25 times higher than that of the CuAlO 2 . According to the characterization, Cu(II) generation on the surface of CuAlO 2 during the surface growth process results in the marked decrease of the surface oxygen vacancies and the formation of the C-O-Cu bridges between CN and Cu(II)-CuAlO 2 in the catalyst. The electron paramagnetic resonance (EPR) analysis and density functional theory (DFT) calculations demonstrate that the dual reaction centers are produced around the Cu and C sites due to the cation-π interactions through the C-O-Cu bridges in CN-Cu(II)-CuAlO 2 . During the Fenton-like reactions, the electron-rich center around Cu is responsible for the efficient reduction of H 2 O 2 to • OH, and the electron-poor center around C captures electrons from H 2 O 2 or pollutants and diverts them to the electron-rich area via the C-O-Cu bridge. Thus, the catalyst exhibits excellent catalytic performance for the refractory pollutant degradation. This study can deepen our understanding on the enhanced Fenton reactivity for water purification through functionalizing with organic solid-phase ligands on the catalyst surface.

Rsp5 WW domains interact directly with the carboxyl-terminal domain of RNA polymerase II.

PubMed

Chang, A; Cheang, S; Espanel, X; Sudol, M

2000-07-07

RSP5 is an essential gene in Saccharomyces cerevisiae and was recently shown to form a physical and functional complex with RNA polymerase II (RNA pol II). The amino-terminal half of Rsp5 consists of four domains: a C2 domain, which binds membrane phospholipids; and three WW domains, which are protein interaction modules that bind proline-rich ligands. The carboxyl-terminal half of Rsp5 contains a HECT (homologous to E6-AP carboxyl terminus) domain that catalytically ligates ubiquitin to proteins and functionally classifies Rsp5 as an E3 ubiquitin-protein ligase. The C2 and WW domains are presumed to act as membrane localization and substrate recognition modules, respectively. We report that the second (and possibly third) Rsp5 WW domain mediates binding to the carboxyl-terminal domain (CTD) of the RNA pol II large subunit. The CTD comprises a heptamer (YSPTSPS) repeated 26 times and a PXY core that is critical for interaction with a specific group of WW domains. An analysis of synthetic peptides revealed a minimal CTD sequence that is sufficient to bind to the second Rsp5 WW domain (Rsp5 WW2) in vitro and in yeast two-hybrid assays. Furthermore, we found that specific "imperfect" CTD repeats can form a complex with Rsp5 WW2. In addition, we have shown that phosphorylation of this minimal CTD sequence on serine, threonine and tyrosine residues acts as a negative regulator of the Rsp5 WW2-CTD interaction. In view of the recent data pertaining to phosphorylation-driven interactions between the RNA pol II CTD and the WW domain of Ess1/Pin1, we suggest that CTD dephosphorylation may be a prerequisite for targeted RNA pol II degradation.

Electrostatic measures for a piezoelectric thin film with an embedded crack in the substrate: II. Mode II

NASA Astrophysics Data System (ADS)

Ali, Rizwaan; Mahapatra, D. Roy; Gopalakrishnan, S.

2008-04-01

This paper is a successor to the previous paper by Ali et al (2008 Smart Mater. Struct. 17 025037); it presents the analysis for sensing an embedded mode-II crack in a substrate. The displacement field kinematics for the film-substrate system is extended to the problem of applied surface shear stress. This extension requires modifying the model presented in the previous paper to include the differences due to changes in boundary and excitation conditions. The film response in terms of voltage pattern over the film area—peculiar to the presence of a mode-II crack in the substrate—is illustrated here through the results of numerical simulations. Our analysis shows that the proposed electrostatic measures of the voltage and its gradients are useful in identifying the axial and depth-wise location, as well as the crack-face area of a planar mode-II crack. There is a marked difference in the pattern of results presented in this paper with the results in part I of this work for a mode-I crack. This distinction is of utmost importance, for it singularly suffices to identify the mode of crack in a substrate for a given set of boundary conditions.

CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction endonucleases

PubMed Central

Toliusis, Paulius; Silanskas, Arunas; Szczelkun, Mark D.

2017-01-01

Abstract The restriction endonuclease CglI from Corynebacterium glutamicum recognizes an asymmetric 5′-GCCGC-3′ site and cleaves the DNA 7 and 6/7 nucleotides downstream on the top and bottom DNA strands, respectively, in an NTP-hydrolysis dependent reaction. CglI is composed of two different proteins: an endonuclease (R.CglI) and a DEAD-family helicase-like ATPase (H.CglI). These subunits form a heterotetrameric complex with R2H2 stoichiometry. However, the R2H2·CglI complex has only one nuclease active site sufficient to cut one DNA strand suggesting that two complexes are required to introduce a double strand break. Here, we report studies to evaluate the DNA cleavage mechanism of CglI. Using one- and two-site circular DNA substrates we show that CglI does not require two sites on the same DNA for optimal catalytic activity. However, one-site linear DNA is a poor substrate, supporting a mechanism where CglI complexes must communicate along the one-dimensional DNA contour before cleavage is activated. Based on experimental data, we propose that adenosine triphosphate (ATP) hydrolysis by CglI produces translocation on DNA preferentially in a downstream direction from the target, although upstream translocation is also possible. Our results are consistent with a mechanism of CglI action that is distinct from that of other ATP-dependent restriction-modification enzymes. PMID:28854738

Redox homeostasis and respiratory metabolism in camels (Camelus dromedaries): comparisons with domestic goats and laboratory rats and mice.

PubMed

Al-Otaiba, Amna; John, Annie; Al-Belooshi, Thekra; Raza, Haider

2010-11-01

We have previously reported the occurrence of multiple forms of drug-metabolizing enzymes in camel tissues. Here, we investigate glutathione (GSH)-dependent redox homeostasis, reactive oxygen species (ROS) production and mitochondrial respiratory functions in camel tissues and compare them with imported domestic goats and laboratory rats and mice. Cytochrome P450 2E1 (CYP 2E1) and GSH-metabolizing enzymes were differentially expressed in the liver and kidney of these animals. Camel liver has significantly lower GSH pool than that in goats, rats and mice. Mitochondria isolated from the tissues of these animals showed a comparable ability to metabolize specific substrates for respiratory enzyme complexes I, II/III and IV. These complexes were metabolically more active in the kidney than in the liver of all the species. Furthermore, the activity of complex IV in camel tissues was significantly lower than in other species. On the other hand, complex II/III activity in camel kidney was higher compared to the other species. In addition, as expected, we observed that inhibitors of these enzyme complexes augment the production of mitochondrial ROS in camel and goat tissues. These results help to better understand the metabolic ability and adaptation in desert camels in comparison with domestic goats and laboratory rats and mice since they are exposed to different environmental and dietary conditions. Our study may also have implications in the pharmacology and toxicology of drugs and pollutants in these species.

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Travis A.; Witt, Suzanne E.; Li, Zhanyong

Formamidinate-bridged Rh 2 II,II complexes containing diimine ligands of the formula cis-[Rh 2 II,II(μ-DTolF) 2(NN) 2] 2+ (Rh 2-NN 2), where DTolF = p-ditolylformamidinate and NN = dppn (benzo[i]dipyrido[3,2-a:2',3'-h]quinoxaline), dppz (dipyrido[3,2-a:2',3'-c]phenazine), and phen (1,10-phenanthroline), electrocatalytically reduce H + to H 2 in DMF solutions containing CH 3COOH at a glassy carbon electrode. Cathodic scans in the absence of acid display a Rh III,II/II,II reduction at -0.90 V vs Fc +/Fc followed by NN 0/– reduction at -1.13, -1.36, and -1.65 V for Rh 2-dppn 2, Rh 2-dppz 2, and Rh 2-phen 2, respectively. Upon the addition of acid, Rh 2-dppnmore » 2 and Rh 2-dppz 2 undergo reduction–protonation–reduction at each pyrazine-containing NN ligand prior to the Rh 2 II,II/II,I reduction. The Rh 2 II,I species is thus protonated at one of the metal centers, resulting in the formation of the corresponding Rh 2 II,III-hydride. In the case of Rh 2-phen 2, the reduction of the phen ligand is followed by intramolecular electron transfer to the Rh 2 II,II core in the presence of protons to form a Rh 2 II,III-hydride species. Further reduction and protonation at the Rh 2 core for all three complexes rapidly catalyzes H 2 formation with varied calculated turnover frequencies (TOF) and overpotential values (η): 2.6 × 10 4 s –1 and 0.56 V for Rh 2-dppn, 2.8 × 10 4 s –1 and 0.50 V for Rh 2-dppz 2, and 5.9 × 10 4 s –1 and 0.64 V for Rh 2-phen 2. Bulk electrolysis confirmed H 2 formation, and further CH 3COOH addition regenerates H 2 production, attesting to the robust nature of the architecture. The cis-[Rh 2 II,II(μ-DTolF) 2(NN) 2] 2+ architecture benefits by combining electron-rich formamidinate bridges, a redox-active Rh 2 II,II core, and electron-accepting NN diimine ligands to allow for the electrocatalysis of H + substrate to H 2 fuel.« less

Effect of Trichoderma on horticultural seedlings' growth promotion depending on inoculum and substrate type.

PubMed

Marín-Guirao, J I; Rodríguez-Romera, P; Lupión-Rodríguez, B; Camacho-Ferre, F; Tello-Marquina, J C

2016-10-01

The biostimulant effect of Trichoderma spp. on horticultural crops are highly variable. Thus, practical use of Trichoderma sp. requires feasible formulated products and suitable substrates. This study evaluates the survival and the growth-promotion effect of a Trichoderma saturnisporum rice formulation compared with a nonformulated conidia suspension (seven treatments in total), on tomato, pepper and cucumber seedlings grown in two substrates: (i) rich in organic matter (OM) and (ii) mineral substrate without OM. The results showed beneficial effects on seedling growth in the OM-rich substrate when T. saturnisporum rice formulation (mainly at maximum concentration) was applied, but the effects were opposite when the mineral substrate without OM was used. The effects were closely linked to the level of inoculum in the substrate, which was greater upon application of the formulated inoculum as opposed to the nonformulated one. The use of rice to prepare the inoculum of T. saturnisporum seems to be promising for seedling growth in the nursery when it is applied in a substrate that is rich in organic matter, but it must be considered that under certain conditions of food shortage, Trichoderma sp. could show pathogenicity to seedlings. This study provides evidence of the complexity inherent in the use of micro-organisms in agriculture, while also confirming that the activity of the biofertilizers based on Trichoderma depends on the type of inoculum and its concentration, as well as the properties of the medium in which the fungi develop. Further studies assessing the effectiveness or possible pathogenicity of Trichoderma in different soils under greenhouse conditions must be addressed. © 2016 The Society for Applied Microbiology.

Copper(II) carboxylate promoted intramolecular diamination of terminal alkenes: improved reaction conditions and expanded substrate scope.

PubMed

Zabawa, Thomas P; Chemler, Sherry R

2007-05-10

The copper(II) carboxylate promoted diamination reaction has been improved by the use of the organic soluble copper(II) neodecanoate [Cu(ND)2]. Cu(ND)2 allowed the less-polar solvent dichloroethane (DCE) to be used, and as a consequence, decomposition of less-reactive substrates could be avoided. High diastereoselectivity was observed in the synthesis of 2,5-disubstituted pyrrolidines. Ureas, bis(anilines), and alpha-amido pyrroles derived from 2-allylaniline could also participate in the diamination reaction.

Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA

DOE PAGES

Hashimoto, Hideharu; Pais, June E.; Dai, Nan; ...

2015-08-31

The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and α-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solvedmore » NgTet1–5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH 2-) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH 2 towards the metal-ligand water molecule, where a dioxygen O 2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably due to the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate.« less

Interaction mode between catalytic and regulatory subunits in glucosidase II involved in ER glycoprotein quality control.

PubMed

Satoh, Tadashi; Toshimori, Takayasu; Noda, Masanori; Uchiyama, Susumu; Kato, Koichi

2016-11-01

The glycoside hydrolase family 31 (GH31) α-glucosidases play vital roles in catabolic and regulated degradation, including the α-subunit of glucosidase II (GIIα), which catalyzes trimming of the terminal glucose residues of N-glycan in glycoprotein processing coupled with quality control in the endoplasmic reticulum (ER). Among the known GH31 enzymes, only GIIα functions with its binding partner, regulatory β-subunit (GIIβ), which harbors a lectin domain for substrate recognition. Although the structural data have been reported for GIIα and the GIIβ lectin domain, the interaction mode between GIIα and GIIβ remains unknown. Here, we determined the structure of a complex formed between GIIα and the GIIα-binding domain of GIIβ, thereby providing a structural basis underlying the functional extension of this unique GH31 enzyme. © 2016 The Protein Society.

Shape-engineering substrate-based plasmonic nanomaterials

NASA Astrophysics Data System (ADS)

Gilroy, Kyle D.

The advancement of next generation technologies is reliant on our ability to engineer matter at the nanoscale. Since the morphological features of nanomaterials dictate their chemical and physical properties, a significant effort has been put forth to develop syntheses aimed at fine tuning their size, shape and composition. This massive effort has resulted in a maturing colloidal chemistry containing an extensive collection of morphologies with compositions nearly spanning the entire transition of the periodic table. While colloidal nanoparticles have opened the door to promising applications in fields such as cancer theranostics, drug delivery, catalysis and sensing; the synthetic protocols for the placement of nanomaterials on surfaces, a requisite for chip-based devices, are ill-developed. This dissertation serves to address this limitation by highlighting a series of syntheses related to the design of substrate-based nanoparticles whose size, shape and composition are controllably engineered to a desired endpoint. The experimental methods are based on a template-mediated approach which sees chemical modifications made to prepositioned thermally assembled metal nanostructures which are well bonded to a sapphire substrate. The first series of investigations will highlight synthetic routes utilizing galvanic replacement reactions, where the prepositioned templates are chemically transformed into hollow nanoshells. Detailed studies are provided highlighting discoveries related to (i) hollowing, (ii) defect transfer, (iii) strain induction, (iv) interdiffusion, (v) crystal structure and (vi) the localized surface plasmon resonance (LSPR). The second series of investigations, based on heterogeneous nucleation, have Au templates serve as nucleation sites for metal atoms arriving in either the solution- or vapor phase. The solution-phase heterogeneous nucleation of Ag on Au reveals that chemical kinetics (injection rate & precursor concentration) can be used to control the nature of how Ag atoms grow on the Au template. It was discovered that (i) slow kinetics leads to an anisotropic growth mode (heterodimeric structures), (ii) fast kinetics causes a very uniform deposition (Au-Ag coreshell morphology, or Au Ag) and (iii) medium kinetics produces structures with an intermediate morphology (truncated octahedron). In the second case, where the nucleation event is carried out at high temperatures, the Ag vapor is sourced from a sublimating foil onto adjacent Au templates. This process drives the composition and morphology from a Au Wulff-shape to a homogeneous Au-Ag nanoprism. By tracking over time the (i) morphological features, (ii) LSPR and (iii) composition; insights into the fundamental atomic scale growth mechanisms are elucidated. Overall, substrate-based template-mediated syntheses have proven to be an effective route for directing growth pathways toward a desired endpoint giving rise to an impressive new group of complex substrate-based nanostructures with asymmetric, core-shell and hollowed morphologies. While this dissertation is focused heavily on the development of synthetic procedures aimed at generating substrate-based plasmonic nanomaterials, the last chapter will serve to highlight a series of on-going studies aimed at defining these nanomaterials as highly effective heterogeneous catalysts. Several examples are shown including (i) nanoparticle films synthesize via sputter deposition, (ii) mechanically induced nanotexturing of bulk copper foils, (iii) ultra-small AuPd nanoparticles synthesized via pulse laser, (iv) substrate-based AuCu nanoprisms and (v) the Wulff in a Cage Morphology.

Structural and biochemical analyses reveal insights into covalent flavinylation of the Escherichia coli Complex II homolog quinol:fumarate reductase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starbird, C. A.; Maklashina, Elena; Sharma, Pankaj

The Escherichia coli Complex II homolog quinol:fumarate reductase (QFR, FrdABCD) catalyzes the interconversion of fumarate and succinate at a covalently attached FAD within the FrdA subunit. The SdhE assembly factor enhances covalent flavinylation of Complex II homologs, but the mechanisms underlying the covalent attachment of FAD remain to be fully elucidated. Here, we explored the mechanisms of covalent flavinylation of the E. coli QFR FrdA subunit. Using a ΔsdhE E. coli strain, we show that the requirement for the assembly factor depends on the cellular redox environment. We next identified residues important for the covalent attachment and selected the FrdAE245more » residue, which contributes to proton shuttling during fumarate reduction, for detailed biophysical and structural characterization. We found that QFR complexes containing FrdAE245Q have a structure similar to that of the WT flavoprotein, but lack detectable substrate binding and turnover. In the context of the isolated FrdA subunit, the anticipated assembly intermediate during covalent flavinylation, FrdAE245 variants had stability similar to that of WT FrdA, contained noncovalent FAD, and displayed a reduced capacity to interact with SdhE. However, small-angle X-ray scattering (SAXS) analysis of WT FrdA cross-linked to SdhE suggested that the FrdAE245 residue is unlikely to contribute directly to the FrdA-SdhE protein-protein interface. We also found that no auxiliary factor is absolutely required for flavinylation, indicating that the covalent flavinylation is autocatalytic. We propose that multiple factors, including the SdhE assembly factor and bound dicarboxylates, stimulate covalent flavinylation by preorganizing the active site to stabilize the quinone-methide intermediate.« less

Michael Addition Reactions between Chiral Equivalents of a Nucleophilic Glycine and (S)- or (R)-3-[(E)-Enoyl]-4-phenyl-1,3-oxazolidin-2-ones as a General Method for Efficient Preparation of β-Substituted Pyroglutamic Acids. Case of Topographically Controlled Stereoselectivity

PubMed Central

Soloshonok*, Vadim A.; Cai, Chaozhong; Yamada, Takeshi; Ueki, Hisanori; Ohfune, Yasufumi; Hruby, Victor J.

2006-01-01

This paper describes a systematic study of addition reactions between the chiral Ni(II) complex of the Schiff base of glycine with (S)-o-[N-(N-benzylprolyl)amino]benzophenone and (S)- or (R)-3-[(E)-enoyl]-4-phenyl-1,3-oxazolidin-2-ones as a general and synthetically efficient approach to β-substituted pyroglutamic acids and relevant compounds. These reactions were shown to occur at room temperature in the presence of nonchelating organic bases and, most notably, with very high (>98% diastereomeric excess (de)) stereoselectivity at both newly formed stereogenic centers. The stereochemical outcome of the reactions was found to be overwhelmingly controlled by the stereochemical preferences of the Michael acceptors, and the chirality of the glycine complex influenced only the reaction rate. Thus, in the reactions of both the (S)-configured Ni(II) complex and the Michael acceptors, the reaction rates were exceptionally high, allowing preparation of the corresponding products with virtually quantitative (>98%) chemical and stereochemical yields. In contrast, reactions of the (S)-configured Ni(II) complex and (R)-configured Michael acceptors proceeded at noticeably lower rates, but the addition products were obtained in high diastereo-and enantiomeric purity. To rationalize the remarkably high and robust stereoselectivity observed in these reactions, we consider an enzyme–substrate-like mode of interaction involing a topographical match or mismatch of two geometric figures. Excellent chemical and stereochemical yields, combined with the simplicity and operational convenience of the experimental procedures, render the present method of immediate use for preparing various β-substituted pyroglutamic acids and related compounds. PMID:16248672

Michael addition reactions between chiral equivalents of a nucleophilic glycine and (S)- or (R)-3-[(E)-enoyl]-4-phenyl-1,3-oxazolidin-2-ones as a general method for efficient preparation of beta-substituted pyroglutamic acids. Case of topographically controlled stereoselectivity.

PubMed

Soloshonok, Vadim A; Cai, Chaozhong; Yamada, Takeshi; Ueki, Hisanori; Ohfune, Yasufumi; Hruby, Victor J

2005-11-02

This paper describes a systematic study of addition reactions between the chiral Ni(II) complex of the Schiff base of glycine with (S)-o-[N-(N-benzylprolyl)amino]benzophenone and (S)- or (R)-3-[(E)-enoyl]-4-phenyl-1,3-oxazolidin-2-ones as a general and synthetically efficient approach to beta-substituted pyroglutamic acids and relevant compounds. These reactions were shown to occur at room temperature in the presence of nonchelating organic bases and, most notably, with very high (>98% diastereomeric excess (de)) stereoselectivity at both newly formed stereogenic centers. The stereochemical outcome of the reactions was found to be overwhelmingly controlled by the stereochemical preferences of the Michael acceptors, and the chirality of the glycine complex influenced only the reaction rate. Thus, in the reactions of both the (S)-configured Ni(II) complex and the Michael acceptors, the reaction rates were exceptionally high, allowing preparation of the corresponding products with virtually quantitative (>98%) chemical and stereochemical yields. In contrast, reactions of the (S)-configured Ni(II) complex and (R)-configured Michael acceptors proceeded at noticeably lower rates, but the addition products were obtained in high diastereo- and enantiomeric purity. To rationalize the remarkably high and robust stereoselectivity observed in these reactions, we consider an enzyme-substrate-like mode of interaction involving a topographical match or mismatch of two geometric figures. Excellent chemical and stereochemical yields, combined with the simplicity and operational convenience of the experimental procedures, render the present method of immediate use for preparing various beta-substituted pyroglutamic acids and related compounds.

Diastereoselective Radical‐Type Cyclopropanation of Electron‐Deficient Alkenes Mediated by the Highly Active Cobalt(II) Tetramethyltetraaza[14]annulene Catalyst

PubMed Central

Chirila, Andrei; Gopal Das, Braja; Paul, Nanda D.

2017-01-01

Abstract A new protocol for the catalytic synthesis of cyclopropanes using electron‐deficient alkenes is presented, which is catalysed by a series of affordable, easy to synthesise and highly active substituted cobalt(II) tetraaza[14]annulenes. These catalysts are compatible with the use of sodium tosylhydrazone salts as precursors to diazo compounds in one‐pot catalytic transformations to afford the desired cyclopropanes in almost quantitative yields. The reaction takes advantage of the metalloradical character of the Co complexes to activate the diazo compounds. The reaction is practical and fast, and proceeds from readily available starting materials. It does not require the slow addition of diazo reagents or tosylhydrazone salts or heating and tolerates many solvents, which include protic ones such as MeOH. The CoII complexes derived from the tetramethyltetraaza[14]annulene ligand are easier to prepare than cobalt(II) porphyrins and present a similar catalytic carbene radical reactivity but are more active. The reaction proceeds at 20 °C in a matter of minutes and even at −78 °C in a few hours. The catalytic system is robust and can operate with either the alkene or the diazo reagent as the limiting reagent, which inhibits the dimerisation of diazo compounds totally. The protocol has been applied to synthesise a variety of substituted cyclopropanes. High yields and selectivities were achieved for various substrates with an intrinsic preference for trans cyclopropanes. PMID:28529668

Homogeneous catalytic hydrogenations of complex carbonaceous substrates. [16 references

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cox, J L; Wilcox, W A; Roberts, G L

1976-11-05

Results of homogeneous catalytic hydrogenation of complex unsaturated substrates including coal and coal-derived materials are reported, with organic soluble molecular complexes as catalysts. Among the substrates used were Hvab coal, solvent-refined coal, and COED pyrolysate. The hydrogenations were carried out in an autoclave. The results are summarized in tables.

Drosophila Longevity Assurance Conferred by Reduced Insulin Receptor Substrate Chico Partially Requires d4eBP.

PubMed

Bai, Hua; Post, Stephanie; Kang, Ping; Tatar, Marc

2015-01-01

Mutations of the insulin/IGF signaling (IIS) pathway extend Drosophila lifespan. Based on genetic epistasis analyses, this longevity assurance is attributed to downstream effects of the FOXO transcription factor. However, as reported FOXO accounts for only a portion of the observed longevity benefit, suggesting there are additional outputs of IIS to mediate aging. One candidate is target of rapamycin complex 1 (TORC1). Reduced TORC1 activity is reported to slow aging, whereas reduced IIS is reported to repress TORC1 activity. The eukaryotic translation initiation factor 4E binding protein (4E-BP) is repressed by TORC1, and activated 4E-BP is reported to increase Drosophila lifespan. Here we use genetic epistasis analyses to test whether longevity assurance mutants of chico, the Drosophila insulin receptor substrate homolog, require Drosophila d4eBP to slow aging. In chico heterozygotes, which are robustly long-lived, d4eBP is required but not sufficient to slow aging. Remarkably, d4eBP is not required or sufficient for chico homozygotes to extend longevity. Likewise, chico heterozygote females partially require d4eBP to preserve age-dependent locomotion, and both chico genotypes require d4eBP to improve stress-resistance. Reproduction and most measures of growth affected by either chico genotype are always independent of d4eBP. In females, chico heterozygotes paradoxically produce more rather than less phosphorylated 4E-BP (p4E-BP). Altered IRS function within the IIS pathway of Drosophila appears to have partial, conditional capacity to regulate aging through an unconventional interaction with 4E-BP.

Growth kinetics of disk-shaped copper islands in electrochemical deposition.

PubMed

Guo, Lian; Zhang, Shouliang; Searson, Peter

2009-05-01

The ability to independently dictate the shape and crystal orientation of islands in electrocrystallization remains a significant challenge. The main reason for this is that the complex interplay between the substrate, nucleation, and surface chemistry is not fully understood. Here we report on the kinetics of island growth for copper on ruthenium oxide. The small nucleation overpotential leads to enhanced lateral growth and the formation of hexagonal disk-shaped islands. The amorphous substrate allows the nuclei to achieve the thermodynamically favorable orientation, i.e., a 111 surface normal. Island growth follows power law kinetics in both lateral and vertical directions. At shorter times, the two growth exponents are equal to 1/2 whereas at longer times lateral growth slows down while vertical growth speeds up. We propose a growth mechanism, wherein the lateral growth of disk-shaped islands is initiated by attachment of Cu adatoms on the ruthenium oxide surface onto the island periphery while vertical growth is initiated by two-dimensional nucleation on the top terrace and followed by lateral step propagation. These results indicate three criteria for enhanced lateral growth in electrodeposition: (i) a substrate that leads to a small nucleation overpotential, (ii) fast adatom surface diffusion on substrate to promote lateral growth, and (iii) preferential anion adsorption to stabilize the basal plane.

In situ laser-induced photochemical silver substrate synthesis and sequential SERS detection in a flow cell.

PubMed

Herman, Krisztian; Szabó, László; Leopold, Loredana F; Chiş, Vasile; Leopold, Nicolae

2011-05-01

A new, simple, and effective approach for multianalyte sequential surface-enhanced Raman scattering (SERS) detection in a flow cell is reported. The silver substrate was prepared in situ by laser-induced photochemical synthesis. By focusing the laser on the 320 μm inner diameter glass capillary at 0.5 ml/min continuous flow of 1 mM silver nitrate and 10 mM sodium citrate mixture, a SERS active silver spot on the inner wall of the glass capillary was prepared in a few seconds. The test analytes, dacarbazine, 4-(2-pyridylazo)resorcinol (PAR) complex with Cu(II), and amoxicillin, were sequentially injected into the flow cell. Each analyte was adsorbed to the silver surface, enabling the recording of high intensity SERS spectra even at 2 s integration times, followed by desorption from the silver surface and being washed away from the capillary. Before and after each analyte passed the detection window, citrate background spectra were recorded, and thus, no "memory effects" perturbed the SERS detection. A good reproducibility of the SERS spectra obtained under flow conditions was observed. The laser-induced photochemically synthesized silver substrate enables high Raman enhancement, is characterized by fast preparation with a high success rate, and represents a valuable alternative for silver colloids as SERS substrate in flow approaches.

Conformational Dynamics, Ligand Binding and Effects of Mutations in NirE an S-Adenosyl-L-Methionine Dependent Methyltransferase

NASA Astrophysics Data System (ADS)

Singh, Warispreet; Karabencheva-Christova, Tatyana G.; Black, Gary W.; Ainsley, Jon; Dover, Lynn; Christov, Christo Z.

2016-01-01

Heme d1, a vital tetrapyrrol involved in the denitrification processes is synthesized from its precursor molecule precorrin-2 in a chemical reaction catalysed by an S-adenosyl-L-methionine (SAM) dependent Methyltransferase (NirE). The NirE enzyme catalyses the transfer of a methyl group from the SAM to uroporphyrinogen III and serves as a novel potential drug target for the pharmaceutical industry. An important insight into the structure-activity relationships of NirE has been revealed by elucidating its crystal structure, but there is still no understanding about how conformational flexibility influences structure, cofactor and substrate binding by the enzyme as well as the structural effects of mutations of residues involved in binding and catalysis. In order to provide this missing but very important information we performed a comprehensive atomistic molecular dynamics study which revealed that i) the binding of the substrate contributes to the stabilization of the structure of the full complex; ii) conformational changes influence the orientation of the pyrrole rings in the substrate, iii) more open conformation of enzyme active site to accommodate the substrate as an outcome of conformational motions; and iv) the mutations of binding and active site residues lead to sensitive structural changes which influence binding and catalysis.

Model-based Confirmation of Alternative Substrates of Mitochondrial Electron Transport Chain

PubMed Central

Kleessen, Sabrina; Araújo, Wagner L.; Fernie, Alisdair R.; Nikoloski, Zoran

2012-01-01

Discrimination of metabolic models based on high throughput metabolomics data, reflecting various internal and external perturbations, is essential for identifying the components that contribute to the emerging behavior of metabolic processes. Here, we investigate 12 different models of the mitochondrial electron transport chain (ETC) in Arabidopsis thaliana during dark-induced senescence in order to elucidate the alternative substrates to this metabolic pathway. Our findings demonstrate that the coupling of the proposed computational approach, based on dynamic flux balance analysis, with time-resolved metabolomics data results in model-based confirmations of the hypotheses that, during dark-induced senescence in Arabidopsis, (i) under conditions where the main substrate for the ETC are not fully available, isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase are able to donate electrons to the ETC, (ii) phytanoyl-CoA does not act even as an indirect substrate of the electron transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase complex, and (iii) the mitochondrial γ-aminobutyric acid transporter has functional significance in maintaining mitochondrial metabolism. Our study provides a basic framework for future in silico studies of alternative pathways in mitochondrial metabolism under extended darkness whereby the role of its components can be computationally discriminated based on available molecular profile data. PMID:22334689

Proteomic Interaction Patterns between Human Cyclins, the Cyclin-Dependent Kinase Ortholog pUL97 and Additional Cytomegalovirus Proteins

PubMed Central

Steingruber, Mirjam; Kraut, Alexandra; Socher, Eileen; Sticht, Heinrich; Reichel, Anna; Stamminger, Thomas; Amin, Bushra; Couté, Yohann; Hutterer, Corina; Marschall, Manfred

2016-01-01

The human cytomegalovirus (HCMV)-encoded cyclin-dependent kinase (CDK) ortholog pUL97 associates with human cyclin B1 and other types of cyclins. Here, the question was addressed whether cyclin interaction of pUL97 and additional viral proteins is detectable by mass spectrometry-based approaches. Proteomic data were validated by coimmunoprecipitation (CoIP), Western blot, in vitro kinase and bioinformatic analyses. Our findings suggest that: (i) pUL97 shows differential affinities to human cyclins; (ii) pUL97 inhibitor maribavir (MBV) disrupts the interaction with cyclin B1, but not with other cyclin types; (iii) cyclin H is identified as a new high-affinity interactor of pUL97 in HCMV-infected cells; (iv) even more viral phosphoproteins, including all known substrates of pUL97, are detectable in the cyclin-associated complexes; and (v) a first functional validation of pUL97-cyclin B1 interaction, analyzed by in vitro kinase assay, points to a cyclin-mediated modulation of pUL97 substrate preference. In addition, our bioinformatic analyses suggest individual, cyclin-specific binding interfaces for pUL97-cyclin interaction, which could explain the different strengths of interactions and the selective inhibitory effect of MBV on pUL97-cyclin B1 interaction. Combined, the detection of cyclin-associated proteins in HCMV-infected cells suggests a complex pattern of substrate phosphorylation and a role of cyclins in the fine-modulation of pUL97 activities. PMID:27548200

Dioxygenase-like reactivity of an isolable superoxo-nickel(II) complex.

PubMed

Company, Anna; Yao, Shenglai; Ray, Kallol; Driess, Matthias

2010-08-16

Although O(2) activation by metals such as iron and copper has been a matter of intensive research in the last decades, this type of chemistry for nickel systems is still in its infancy. Moreover, studies regarding the oxidizing ability of the resulting "Ni(n)-O(2)" species towards exogenous substrates are scarce. In this work, we report on the reactivity of an isolable and thermally stable mononuclear superoxo-nickel compound [Ni(II)(beta-diketiminato)(O(2))] (1) towards different types of organic substrates. In addition, we have been able to prove that the beta-diketiminato ligand can undergo partial intramolecular oxidation due to close proximity between the isopropyl groups of the beta-diketiminato-aryl and the superoxo subunits. Compound 1 performs hydrogen-atom abstraction from O-H and N-H groups and most importantly it shows an unprecedented dioxygenase-like reactivity in the oxidation of 2,4,6-tri-tert-butylphenol. The latter reaction most likely occurs through the mediation of a putative [Ni(III)-oxo] intermediate, affording an unprecedented oxidation product of the phenol that incorporates two oxygen atoms from a single O(2) subunit. Results presented herein provide evidence of the striking oxidizing ability of dioxygen-nickel species and further support the viability to use such systems as oxidation catalysts analogous to its heavy metal congener, palladium.

Understanding the fate of the oxyallyl cation following Nazarov electrocyclization: sequential Wagner-Meerwein migrations and the synthesis of spirocyclic cyclopentenones

PubMed Central

Huang, Jie; Lebœuf, David; Frontier, Alison J.

2011-01-01

A general reaction sequence is described that involves Nazarov cyclization followed by two sequential Wagner Meerwein migrations, to afford spirocyclic compounds from divinyl ketones in the presence of one equivalent of copper(II) complexes. A detailed investigation of this sequence is described including a study of substrate scope and limitations. It was found that after 4π electrocyclization, two different pathways are available to the oxyallyl cation intermediate: elimination of a proton can give the usual Nazarov cycloadduct, or ring contraction can give an alternative tertiary carbocation. After ring contraction, either [1,2]-hydride or carbon migration can occur, depending upon the substitution pattern of the substrate, to furnish spirocyclic products. The rearrangement pathway is favored over the elimination pathway when catalyst loading was high and the copper(II) counterion is noncoordinating. Several ligands were found to be effective for the reaction. Thus, the reaction sequence can be controlled by judicious choice of reaction conditions to allow selective generation of richly functionalized spirocycles. The three steps of the sequence are stereospecific: electrocyclization followed by two [1,2]-suprafacial Wagner-Meerwein shifts: the ring contraction and then an hydride, alkenyl or aryl shift. The method allows stereospecific installation of adjacent stereocenters or adjacent quaternary centers arrayed around a cyclopentenone ring. PMID:21466152

Structure of the unliganded form of the proprotein convertase furin suggests activation by a substrate-induced mechanism

PubMed Central

Dahms, Sven O.; Arciniega, Marcelino; Steinmetzer, Torsten; Huber, Robert; Than, Manuel E.

2016-01-01

Proprotein convertases (PCs) are highly specific proteases required for the proteolytic modification of many secreted proteins. An unbalanced activity of these enzymes is connected to pathologies like cancer, atherosclerosis, hypercholesterolaemia, and infectious diseases. Novel protein crystallographic structures of the prototypical PC family member furin in different functional states were determined to 1.8–2.0 Å. These, together with biochemical data and modeling by molecular dynamics calculations, suggest essential elements underlying its unusually high substrate specificity. Furin shows a complex activation mechanism and exists in at least four defined states: (i) the “off state,” incompatible with substrate binding as seen in the unliganded enzyme; (ii) the active “on state” seen in inhibitor-bound furin; and the respective (iii) calcium-free and (iv) calcium-bound forms. The transition from the off to the on state is triggered by ligand binding at subsites S1 to S4 and appears to underlie the preferential recognition of the four-residue sequence motif of furin. The molecular dynamics simulations of the four structural states reflect the experimental observations in general and provide approximations of the respective stabilities. Ligation by calcium at the PC-specific binding site II influences the active-site geometry and determines the rotamer state of the oxyanion hole-forming Asn295, and thus adds a second level of the activity modulation of furin. The described crystal forms and the observations of different defined functional states may foster the development of new tools and strategies for pharmacological intervention targeting furin. PMID:27647913

Dioxygen Reactivity of Biomimetic Fe(II) Complexes with Noninnocent Catecholate, o-Aminophenolate, and o-Phenylenediamine Ligands

PubMed Central

2015-01-01

This study describes the O2 reactivity of a series of high-spin mononuclear Fe(II) complexes each containing the facially coordinating tris(4,5-diphenyl-1-methylimidazol-2-yl)phosphine (Ph2TIP) ligand and one of the following bidentate, redox-active ligands: 4-tert-butylcatecholate (tBuCatH–), 4,6-di-tert-butyl-2-aminophenolate (tBu2APH–), or 4-tert-butyl-1,2-phenylenediamine (tBuPDA). The preparation and X-ray structural characterization of [Fe2+(Ph2TIP)(tBuCatH)]OTf, [3]OTf and [Fe2+(Ph2TIP)(tBuPDA)](OTf)2, [4](OTf)2 are described here, whereas [Fe2+(Ph2TIP)(tBu2APH)]OTf, [2]OTf was reported in our previous paper [Bittner et al., Chem.—Eur. J.2013,19, 9686–9698]. These complexes mimic the substrate-bound active sites of nonheme iron dioxygenases, which catalyze the oxidative ring-cleavage of aromatic substrates like catechols and aminophenols. Each complex is oxidized in the presence of O2, and the geometric and electronic structures of the resulting complexes were examined with spectroscopic (absorption, EPR, Mössbauer, resonance Raman) and density functional theory (DFT) methods. Complex [3]OTf reacts rapidly with O2 to yield the ferric-catecholate species [Fe3+(Ph2TIP)(tBuCat)]+ (3ox), which undergoes further oxidation to generate an extradiol cleavage product. In contrast, complex [4]2+ experiences a two-electron (2e–), ligand-based oxidation to give [Fe2+(Ph2TIP)(tBuDIBQ)]2+ (4ox), where DIBQ is o-diiminobenzoquinone. The reaction of [2]+ with O2 is also a 2e– process, yet in this case both the Fe center and tBu2AP ligand are oxidized; the resulting complex (2ox) is best described as [Fe3+(Ph2TIP)(tBu2ISQ)]+, where ISQ is o-iminobenzosemiquinone. Thus, the oxidized complexes display a remarkable continuum of electronic structures ranging from [Fe3+(L2–)]+ (3ox) to [Fe3+(L•–)]2+ (2ox) to [Fe2+(L0)]2+ (4ox). Notably, the O2 reaction rates vary by a factor of 105 across the series, following the order [3]+ > [2]+ > [4]2+, even though the complexes have similar structures and Fe3+/2+ redox potentials. To account for the kinetic data, we examined the relative abilities of the title complexes to bind O2 and participate in H-atom transfer reactions. We conclude that the trend in O2 reactivity can be rationalized by accounting for the role of proton transfer(s) in the overall reaction. PMID:24697567

EXAFS study of mercury(II) sorption to Fe- and Al-(hydr)oxides: I. Effects of pH

USGS Publications Warehouse

Kim, C.S.; Rytuba, J.J.; Brown, Gordon E.

2004-01-01

The study of mercury sorption products in model systems using appropriate in situ molecular-scale probes can provide detailed information on the modes of sorption at mineral/water interfaces. Such studies are essential for assessing the influence of sorption processes on the transport of Hg in contaminated natural systems. Macroscopic uptake of Hg(II) on goethite (??-FeOOH), ??-alumina (??-Al2O3), and bayerite (??-Al(OH)3) as a function of pH has been combined with Hg L III-edge EXAFS spectroscopy, FTIR spectroscopy, and bond valence analysis of possible sorption products to provide this type of information. Macroscopic uptake measurements show that Hg(II) sorbs strongly to fine-grained powders of synthetic goethite (Hg sorption density ??=0.39-0.42 ??mol/m2) and bayerite (??=0.39-0.44 ??mol/m2), while sorbing more weakly to ??-alumina (??=0.04-0.13 ??mol/m 2). EXAFS spectroscopy on the sorption samples shows that the dominant mode of Hg sorption on these phases is as monodentate and bidentate inner-sphere complexes. The mode of Hg(II) sorption to goethite was similar over the pH range 4.3-7.4, as were those of Hg(II) sorption to bayerite over the pH range 5.1-7.9. Conversion of the ??-Al2O3 sorbent to a bayerite-like phase in addition to the apparent reduction of Hg(II) to Hg(I), possibly by photoreduction during EXAFS data collection, resulted in enhanced Hg uptake from pH 5.2-7.8 and changes in the modes of sorption that correlate with the formation of the bayerite-like phase. Bond valence calculations are consistent with the sorption modes proposed from EXAFS analysis. EXAFS analysis of Hg(II) sorption products on a natural Fe oxyhydroxide precipitate and Al/Si-bearing flocculent material showed sorption products and modes of surface attachment similar to those for the model substrates, indicating that the model substrates are useful surrogates for the natural sediments. ?? 2003 Elsevier Inc. All rights reserved.

Modulation of GABAergic receptor binding by activation of calcium and calmodulin-dependent kinase II membrane phosphorylation.

PubMed

Churn, S B; DeLorenzo, R J

1998-10-26

gamma-Aminobutyric acid (GABA) is the primary inhibitory neurotransmitter in the central nervous system (CNS). Because of the important role that GABA plays in the CNS, alteration of GABAA receptor function would significantly affect neuronal excitability. Protein phosphorylation is a major mechanism for regulating receptor function in the brain and has been implicated in modulating GABAA receptor function. Therefore, this study was initiated to determine the role of calmodulin-dependent kinase II (CaM kinase II) membrane phosphorylation on GABAA receptor binding. Synaptosomal membrane fractions were tested for CaM kinase II activity towards endogenous substrates. In addition, muscimol binding was evaluated under equilibrium conditions in synaptosomal membrane fractions subjected to either basal (Mg2+ alone) or maximal CaM kinase II-dependent phosphorylation. Activation of endogenous CaM kinase II-dependent phosphorylation resulted in a significant enhancement of the apparent Bmax for muscimol binding without significantly altering the apparent binding affinity. The enhanced muscimol binding could be increased further by the addition of exogenous CaM kinase II to synaptosomal membrane fractions. Co-incubation with inhibitors of kinase activity during the phosphorylation reactions blocked the CaM kinase II-dependent increase in muscimol binding. The data support the hypothesis that activation of CaM kinase II-dependent phosphorylation caused an increased GABAA receptor binding and may play an important role in modulating the function of this inhibitory receptor/chloride ion channel complex. Copyright 1998 Elsevier Science B.V.

Near single-crystalline, high-carrier-mobility silicon thin film on a polycrystalline/amorphous substrate

DOEpatents

Findikoglu, Alp T [Los Alamos, NM; Jia, Quanxi [Los Alamos, NM; Arendt, Paul N [Los Alamos, NM; Matias, Vladimir [Santa Fe, NM; Choi, Woong [Los Alamos, NM

2009-10-27

A template article including a base substrate including: (i) a base material selected from the group consisting of polycrystalline substrates and amorphous substrates, and (ii) at least one layer of a differing material upon the surface of the base material; and, a buffer material layer upon the base substrate, the buffer material layer characterized by: (a) low chemical reactivity with the base substrate, (b) stability at temperatures up to at least about 800.degree. C. under low vacuum conditions, and (c) a lattice crystal structure adapted for subsequent deposition of a semiconductor material; is provided, together with a semiconductor article including a base substrate including: (i) a base material selected from the group consisting of polycrystalline substrates and amorphous substrates, and (ii) at least one layer of a differing material upon the surface of the base material; and, a buffer material layer upon the base substrate, the buffer material layer characterized by: (a) low chemical reactivity with the base substrate, (b) stability at temperatures up to at least about 800.degree. C. under low vacuum conditions, and (c) a lattice crystal structure adapted for subsequent deposition of a semiconductor material, and, a top-layer of semiconductor material upon the buffer material layer.

Copper(II) Carboxylate Promoted Intramolecular Diamination of Terminal Alkenes: Improved Reaction Conditions and Expanded Substrate Scope

PubMed Central

Zabawa, Thomas P.

2008-01-01

The copper(II) carboxylate promoted diamination reaction has been improved by the use of the organic soluble copper(II) neodecanoate [Cu(ND)2]. Cu(ND)2 allowed the less polar solvent, dichloroethane (DCE) to be used, and as a consequence, decomposition of less reactive substrates could be avoided. High diastereoselectivity was observed in the synthesis of 2,5-disubstituted pyrrolidines. Ureas, bis(anilines) and α-amido pyrroles derived from 2-allylaniline could also participate in the diamination reaction. PMID:17447781

Revisiting and re-engineering the classical zinc finger peptide: consensus peptide-1 (CP-1).

PubMed

Besold, Angelique N; Widger, Leland R; Namuswe, Frances; Michalek, Jamie L; Michel, Sarah L J; Goldberg, David P

2016-04-01

Zinc plays key structural and catalytic roles in biology. Structural zinc sites are often referred to as zinc finger (ZF) sites, and the classical ZF contains a Cys2His2 motif that is involved in coordinating Zn(II). An optimized Cys2His2 ZF, named consensus peptide 1 (CP-1), was identified more than 20 years ago using a limited set of sequenced proteins. We have reexamined the CP-1 sequence, using our current, much larger database of sequenced proteins that have been identified from high-throughput sequencing methods, and found the sequence to be largely unchanged. The CCHH ligand set of CP-1 was then altered to a CAHH motif to impart hydrolytic activity. This ligand set mimics the His2Cys ligand set of peptide deformylase (PDF), a hydrolytically active M(II)-centered (M = Zn or Fe) protein. The resultant peptide [CP-1(CAHH)] was evaluated for its ability to coordinate Zn(II) and Co(II) ions, adopt secondary structure, and promote hydrolysis. CP-1(CAHH) was found to coordinate Co(II) and Zn(II) and a pentacoordinate geometry for Co(II)-CP-1(CAHH) was implicated from UV-vis data. This suggests a His2Cys(H2O)2 environment at the metal center. The Zn(II)-bound CP-1(CAHH) was shown to adopt partial secondary structure by 1-D (1)H NMR spectroscopy. Both Zn(II)-CP-1(CAHH) and Co(II)-CP-1(CAHH) show good hydrolytic activity toward the test substrate 4-nitrophenyl acetate, exhibiting faster rates than most active synthetic Zn(II) complexes.

Custom fabrication of biomass containment devices using 3-D printing enables bacterial growth analyses with complex insoluble substrates.

PubMed

Nelson, Cassandra E; Beri, Nina R; Gardner, Jeffrey G

2016-11-01

Physiological studies of recalcitrant polysaccharide degradation are challenging for several reasons, one of which is the difficulty in obtaining a reproducibly accurate real-time measurement of bacterial growth using insoluble substrates. Current methods suffer from several problems including (i) high background noise due to the insoluble material interspersed with cells, (ii) high consumable and reagent cost and (iii) significant time delay between sampling and data acquisition. A customizable substrate and cell separation device would provide an option to study bacterial growth using optical density measurements. To test this hypothesis we used 3-D printing to create biomass containment devices that allow interaction between insoluble substrates and microbial cells but do not interfere with spectrophotometer measurements. Evaluation of materials available for 3-D printing indicated that UV-cured acrylic plastic was the best material, being superior to nylon or stainless steel when examined for heat tolerance, reactivity, and ability to be sterilized. Cost analysis of the 3-D printed devices indicated they are a competitive way to quantitate bacterial growth compared to viable cell counting or protein measurements, and experimental conditions were scalable over a 100-fold range. The presence of the devices did not alter growth phenotypes when using either soluble substrates or insoluble substrates. We applied biomass containment to characterize growth of Cellvibrio japonicus on authentic lignocellulose (non-pretreated corn stover), and found physiological evidence that xylan is a significant nutritional source despite an abundance of cellulose present. Copyright © 2016 Elsevier B.V. All rights reserved.

Hsl7 is a substrate-specific type II protein arginine methyltransferase in yeast

PubMed Central

Sayegh, Joyce; Clarke, Steven G.

2008-01-01

The Saccharomyces cerevisiae protein Hsl7 is a regulator of the Swe1 protein kinase in cell cycle checkpoint control. Hsl7 has been previously described as a type III protein arginine methyltransferase, catalyzing the formation of ω-monomethylarginine residues on non-physiological substrates. However, we show here that Hsl7 can also display type II activity, generating symmetric dimethylarginine residues on calf thymus histone H2A. Symmetric dimethylation is only observed when enzyme and the methyl-accepting substrate were incubated for extended times. We confirmed the Hsl7-dependent formation of symmetric dimethylarginine by amino acid analysis and thin layer chromatography with wild type and mutant recombinant enzymes expressed from both bacteria and yeast. This result is significant because no type II activity has been previously demonstrated in S. cerevisiae. We also show that Hsl7 has little or no activity on GST-GAR, a commonly used substrate for protein arginine methyltransferases, and only minimal activity on myelin basic protein. This enzyme thus may only recognize only a small subset of potential substrate proteins in yeast, in contrast to the situation with Rmt1, the major type I methyltransferase. PMID:18515076

Type II fatty acid synthesis is essential for the replication of Chlamydia trachomatis.

PubMed

Yao, Jiangwei; Abdelrahman, Yasser M; Robertson, Rosanna M; Cox, John V; Belland, Robert J; White, Stephen W; Rock, Charles O

2014-08-08

The major phospholipid classes of the obligate intracellular bacterial parasite Chlamydia trachomatis are the same as its eukaryotic host except that they also contain chlamydia-made branched-chain fatty acids in the 2-position. Genomic analysis predicts that C. trachomatis is capable of type II fatty acid synthesis (FASII). AFN-1252 was deployed as a chemical tool to specifically inhibit the enoyl-acyl carrier protein reductase (FabI) of C. trachomatis to determine whether chlamydial FASII is essential for replication within the host. The C. trachomatis FabI (CtFabI) is a homotetramer and exhibited typical FabI kinetics, and its expression complemented an Escherichia coli fabI(Ts) strain. AFN-1252 inhibited CtFabI by binding to the FabI·NADH complex with an IC50 of 0.9 μM at saturating substrate concentration. The x-ray crystal structure of the CtFabI·NADH·AFN-1252 ternary complex revealed the specific interactions between the drug, protein, and cofactor within the substrate binding site. AFN-1252 treatment of C. trachomatis-infected HeLa cells at any point in the infectious cycle caused a decrease in infectious titers that correlated with a decrease in branched-chain fatty acid biosynthesis. AFN-1252 treatment at the time of infection prevented the first cell division of C. trachomatis, although the cell morphology suggested differentiation into a metabolically active reticulate body. These results demonstrate that FASII activity is essential for C. trachomatis proliferation within its eukaryotic host and validate CtFabI as a therapeutic target against C. trachomatis. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Self-organized MBE growth of II VI epilayers on patterned GaSb substrates

NASA Astrophysics Data System (ADS)

Wissmann, H.; Tran Anh, T.; Rogaschewski, S.; von Ortenberg, M.

1999-05-01

We report on the self-organized MBE growth of II-VI epilayers on patterned and unpatterned GaSb substrates resulting in quantum wires and quantum wells, respectively. The HgSe : Fe quantum wires were grown on (0 0 1)GaSb substrates with a buffer of lattice-matched ZnTe 1- xSe x. Due to the anisotropic growth of HgSe on the A-oriented stripes roof-like overgrowth with a definite ridge was obtained. Additional Fe doping in the direct vicinity of the ridge results in a highly conductive quantum wire.

Nanoconduits and nanoreplicants

DOEpatents

Melechko, Anatoli V [Oak Ridge, TN; McKnight, Timothy E [Greenback, TN; Guillorn, Michael A [Ithaca, NY; Ilic, Bojan [Ithaca, NY; Merkulov, Vladimir I [Knoxville, TN; Doktycz, Mitchel J [Knoxville, TN; Lowndes, Douglas H [Knoxville, TN; Simpson, Michael L [Knoxville, TN

2007-06-12

Methods, manufactures, machines and compositions are described for nanotransfer and nanoreplication using deterministically grown sacrificial nanotemplates. An apparatus includes a substrate and a nanoconduit material coupled to a surface of the substrate, where the substrate defines an aperture and the nanoconduit material defines a nanoconduit that is i) contiguous with the aperture and ii) aligned substantially non-parallel to a plane defined by the surface of the substrate. An apparatus includes a substrate and a nanoreplicant structure coupled to a surface of the substrate.

Differential substrate behaviour of phenol and aniline derivatives during oxidation by horseradish peroxidase: kinetic evidence for a two-step mechanism.

PubMed

Gilabert, María Angeles; Hiner, Alexander N P; García-Ruiz, Pedro Antonio; Tudela, José; García-Molina, Francisco; Acosta, Manuel; García-Cánovas, Francisco; Rodríguez-López, José Neptuno

2004-06-01

The catalytic constant (k(cat)) and the second-order association constant of compound II with reducing substrate (k(5)) of horseradish peroxidase C (HRPC) acting on phenols and anilines have been determined from studies of the steady-state reaction velocities (V(0) vs. [S(0)]). Since k(cat)=k(2)k(6)/k(2)+k(6), and k(2) (the first-order rate constant for heterolytic cleavage of the oxygen-oxygen bond of hydrogen peroxide during compound I formation) is known, it has been possible to calculate the first-order rate constant for the transformation of each phenol or aniline by HRPC compound II (k(6)). The values of k(6) are quantitatively correlated to the sigma values (Hammett equation) and can be rationalized by an aromatic substrate oxidation mechanism in which the substrate donates an electron to the oxyferryl group in HRPC compound II, accompanied by two proton additions to the ferryl oxygen atom, one from the substrate and the other the protein or solvent. k(6) is also quantitatively correlated to the experimentally determined (13)C-NMR chemical shifts (delta(1)) and the calculated ionization potentials, E (HOMO), of the substrates. Similar dependencies were observed for k(cat) and k(5). From the kinetic analysis, the absolute values of the Michaelis constants for hydrogen peroxide and the reducing substrates (K(M)(H(2)O(2)) and K(M)(S)), respectively, were obtained.

Lessons from isolable nickel(I) precursor complexes for small molecule activation.

PubMed

Yao, Shenglai; Driess, Matthias

2012-02-21

Small-molecule activation by transition metals is essential to numerous organic transformations, both biological and industrial. Creating useful metal-mediated activation systems often depends on stabilizing the metal with uncommon low oxidation states and low coordination numbers. This provides a redox-active metal center with vacant coordination sites well suited for interacting with small molecules. Monovalent nickel species, with their d(9) electronic configuration, are moderately strong one-electron reducing agents that are synthetically attractive if they can be isolated. They represent suitable reagents for closing the knowledge gap in nickel-mediated activation of small molecules. Recently, the first strikingly stable dinuclear β-diketiminate nickel(I) precursor complexes were synthesized, proving to be suitable promoters for small-molecule binding and activation. They have led to many unprecedented nickel complexes bearing activated small molecules in different reduction stages. In this Account, we describe selected achievements in the activation of nitrous oxide (N(2)O), O(2), the heavier chalcogens (S, Se, and Te), and white phosphorus (P(4)) through this β-diketiminatonickel(I) precursor species. We emphasize the reductive activation of O(2), owing to its promise in oxidation processes. The one-electron-reduced O(2) activation product, that is, the corresponding β-diketiminato-supported Ni-O(2) complex, is a genuine superoxonickel(II) complex, representing an important intermediate in the early stages of O(2) activation. It selectively acts as an oxygen-atom transfer agent, hydrogen-atom scavenger, or both towards exogenous organic substrates to yield oxidation products. The one-electron reduction of the superoxonickel(II) moiety was examined by using elemental potassium, β-diketiminatozinc(II) chloride, and β-diketiminatoiron(I) complexes, affording the first heterobimetallic complexes featuring a [NiO(2)M] subunit (M is K, Zn, or Fe). Through density functional theory (DFT) calculations, the geometric and electronic structures of these complexes were established and their distinctive reactivity, including the unprecedented monooxygenase-like activity of a bis(μ-oxo)nickel-iron complex, was studied. The studies have further led to other heterobimetallic complexes containing a [NiO(2)M] core, which are useful for understanding the influence of the heterometal on structure-reactivity relationships. The activation of N(2)O led directly to the hydrogen-atom abstraction product bis(μ-hydroxo)nickel(II) species and prevented isolation of any intermediate. In contrast, the activation of elemental S, Se, and Te with the same nickel(I) reagent furnished activation products with superchalcogenido E(2)(-) (E is S, Se, or Te) and dichalcogenido E(2)(2-) ligand in different activation stages. The isolable supersulfidonickel(II) subunit may serve as a versatile building block for the synthesis of heterobimetallic disulfidonickel(II) complexes with a [NiS(2)M] core. In the case of white phosphorus, the P(4) molecule has been coordinated to the nickel(I) center of dinuclear β-diketiminatonickel(I) precursor complexes; however, the whole P(4) subunit is a weaker electron acceptor than the dichalcogen ligands E(2), thus remaining unreduced. This P(4) binding mode is rare and could open new doors for subsequent functionalization of P(4). Our advances in understanding how these small molecules are bound to a nickel(I) center and are activated for further transformation offer promise for designing new catalysts. These nickel-containing complexes offer exceptional potential for nickel-mediated transformations of organic molecules and as model compounds for mimicking active sites of nickel-containing metalloenzymes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mehboob, Shahila; Hevener, Kirk E.; Truong, Kent

Because of structural and mechanistic differences between eukaryotic and prokaryotic fatty acid synthesis enzymes, the bacterial pathway, FAS-II, is an attractive target for the design of antimicrobial agents. We have previously reported the identification of a novel series of benzimidazole compounds with particularly good antibacterial effect against Francisella tularensis, a Category A biowarfare pathogen. Herein we report the crystal structure of the F. tularensis FabI enzyme in complex with our most active benzimidazole compound bound with NADH. The structure reveals that the benzimidazole compounds bind to the substrate site in a unique conformation that is distinct from the binding motifmore » of other known FabI inhibitors. Detailed inhibition kinetics have confirmed that the compounds possess a novel inhibitory mechanism that is unique among known FabI inhibitors. These studies could have a strong impact on future antimicrobial design efforts and may reveal new avenues for the design of FAS-II active antibacterial compounds.« less

Ion-selective gold-thiol film on integrated screen-printed electrodes for analysis of Cu(II) ions.

PubMed

Li, Meng; Zhou, Hao; Shi, Lei; Li, Da-Wei; Long, Yi-Tao

2014-02-07

A novel type of ion-selective electrode (ISE) was manufactured for detecting trace amounts of Cu(II) ions. The basic substrates of ISE were fabricated using screen-printing technology, which could produce disposable electrodes on a large-scale with good repeatability. Moreover, the printed integrated three-electrode system of ISE could be directly used to read out the open-circuit potentials by a handheld device through a USB port. The ion-selective film was composed of gold nanorods (GNRs) and 6-(bis(pyridin-2-ylmethyl)amino)hexane-1-thiol (compound ), which were layer-by-layer modified on the electrode through an easily controlled self-assembly method. Compound contained the 2,2'-dipyridylamine (dpa) group that could coordinate with Cu(II) ions to form a 2 : 1 complex, therefore the screen-printed ISEs exhibited Nernstian potentiometric responses to Cu(II) ions with a detection limit of 6.3 × 10(-7) mol L(-1) over the range of 1.0 × 10(-6) to 1.0 × 10(-2) mol L(-1). The easily prepared screen-printed ion-selective electrode reported here was appropriate for in field analysis and pollutant detection in remote environments.

Self-assembly of InAs ring complexes on InP substrates by droplet epitaxy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noda, T.; Mano, T.; Jo, M.

We report the self-assembly of InAs ring complexes on InP (100) substrates by droplet epitaxy. Single-ring, ring-disk complex, and concentric double-ring structures were formed by controlling the As beam flux and substrate temperature. A clear photoluminescence signal was detected in a sample where InAs rings were embedded in InGaAs.

Coordination behavior of tetraaza [N4] ligand towards Co(II), Ni(II), Cu(II), Cu(I) and Pd(II) complexes: Synthesis, spectroscopic characterization and anticancer activity

NASA Astrophysics Data System (ADS)

El-Boraey, Hanaa A.

2012-11-01

Novel eight Co(II), Ni(II), Cu(II), Cu(I) and Pd(II) complexes with [N4] ligand (L) i.e. 2-amino-N-{2-[(2-aminobenzoyl)amino]ethyl}benzamide have been synthesized and structurally characterized by elemental analysis, spectral, thermal (TG/DTG), magnetic, and molar conductivity measurements. On the basis of IR, mass, electronic and EPR spectral studies an octahedral geometry has been proposed for Co(II), Ni(II) complexes and Cu(II) chloride complex, square-pyramidal for Cu(I) bromide complex. For Cu(II) nitrate complex (6), Pd(II) complex (8) square planar geometry was proposed. The EPR data of Cu(II) complexes in powdered form indicate dx2-y2 ground state of Cu(II) ion. The antitumor activity of the synthesized ligand and some selected metal complexes has been studied. The palladium(II) complex (8) was found to display cytotoxicity (IC50 = 25.6 and 41 μM) against human breast cancer cell line MCF-7 and human hepatocarcinoma HEPG2 cell line.

Analysis of substrate specificity of human DHHC protein acyltransferases using a yeast expression system

PubMed Central

Ohno, Yusuke; Kashio, Atsushi; Ogata, Ren; Ishitomi, Akihiro; Yamazaki, Yuki; Kihara, Akio

2012-01-01

Palmitoylation plays important roles in the regulation of protein localization, stability, and activity. The protein acyltransferases (PATs) have a common DHHC Cys-rich domain. Twenty-three DHHC proteins have been identified in humans. However, it is unclear whether all of these DHHC proteins function as PATs. In addition, their substrate specificities remain largely unknown. Here we develop a useful method to examine substrate specificities of PATs using a yeast expression system with six distinct model substrates. We identify 17 human DHHC proteins as PATs. Moreover, we classify 11 human and 5 yeast DHHC proteins into three classes (I, II, and III), based on the cellular localization of their respective substrates (class I, soluble proteins; class II, integral membrane proteins; class III, lipidated proteins). Our results may provide an important clue for understanding the function of individual DHHC proteins. PMID:23034182

Removal of GaAs growth substrates from II-VI semiconductor heterostructures

NASA Astrophysics Data System (ADS)

Bieker, S.; Hartmann, P. R.; Kießling, T.; Rüth, M.; Schumacher, C.; Gould, C.; Ossau, W.; Molenkamp, L. W.

2014-04-01

We report on a process that enables the removal of II-VI semiconductor epilayers from their GaAs growth substrate and their subsequent transfer to arbitrary host environments. The technique combines mechanical lapping and layer selective chemical wet etching and is generally applicable to any II-VI layer stack. We demonstrate the non-invasiveness of the method by transferring an all-II-VI magnetic resonant tunneling diode. High resolution x-ray diffraction proves that the crystal integrity of the heterostructure is preserved. Transport characterization confirms that the functionality of the device is maintained and even improved, which is ascribed to completely elastic strain relaxation of the tunnel barrier layer.

Novel metals and metal complexes as platforms for cancer therapy.

PubMed

Frezza, Michael; Hindo, Sarmad; Chen, Di; Davenport, Andrew; Schmitt, Sara; Tomco, Dajena; Dou, Q Ping

2010-06-01

Metals are essential cellular components selected by nature to function in several indispensable biochemical processes for living organisms. Metals are endowed with unique characteristics that include redox activity, variable coordination modes, and reactivity towards organic substrates. Due to their reactivity, metals are tightly regulated under normal conditions and aberrant metal ion concentrations are associated with various pathological disorders, including cancer. For these reasons, coordination complexes, either as drugs or prodrugs, become very attractive probes as potential anticancer agents. The use of metals and their salts for medicinal purposes, from iatrochemistry to modern day, has been present throughout human history. The discovery of cisplatin, cis-[Pt(II) (NH(3))(2)Cl(2)], was a defining moment which triggered the interest in platinum(II)- and other metal-containing complexes as potential novel anticancer drugs. Other interests in this field address concerns for uptake, toxicity, and resistance to metallodrugs. This review article highlights selected metals that have gained considerable interest in both the development and the treatment of cancer. For example, copper is enriched in various human cancer tissues and is a co-factor essential for tumor angiogenesis processes. However the use of copper-binding ligands to target tumor copper could provide a novel strategy for cancer selective treatment. The use of nonessential metals as probes to target molecular pathways as anticancer agents is also emphasized. Finally, based on the interface between molecular biology and bioinorganic chemistry the design of coordination complexes for cancer treatment is reviewed and design strategies and mechanisms of action are discussed.

A photochemical proposal for the preparation of ZnAl{sub 2}O{sub 4} and MgAl{sub 2}O{sub 4} thin films from β-diketonate complex precursors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cabello, G., E-mail: gerardocabelloguzman@hotmail.com; Lillo, L.; Caro, C.

2016-05-15

Highlights: • ZnAl{sub 2}O{sub 4} and MgAl{sub 2}O{sub 4} thin films were prepared by photo-chemical method. • The Zn(II), Mg(II) and Al(III) β-diketonate complexes were used as precursors. • The photochemical reaction was monitored by UV–vis and FT-IR spectroscopy. • The results reveal spinel oxide formation and the generation of intermediate products. - Abstract: ZnAl{sub 2}O{sub 4} and MgAl{sub 2}O{sub 4} thin films were grown on Si(100) and quartz plate substrates using a photochemical method in the solid phase with thin films of β-diketonate complexes as the precursors. The films were deposited by spin-coating and subsequently photolyzed at room temperaturemore » using 254 nm UV light. The photolysis of these films results in the deposition of metal oxide thin films and fragmentation of the ligands from the coordination sphere of the complexes. The obtained samples were post-annealed at different temperatures (350–1100 °C) for 2 h and characterized by FT-Infrared spectroscopy, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), atomic force miscroscopy (AFM), and UV–vis spectroscopy. The results indicate the formation of spinel-type structures and other phases. These characteristics determined the quality of the films, which were obtained from the photodeposition of ternary metal oxides.« less

The energy blockers 3-bromopyruvate and lonidamine: effects on bioenergetics of brain mitochondria.

PubMed

Macchioni, Lara; Davidescu, Magdalena; Roberti, Rita; Corazzi, Lanfranco

2014-10-01

Tumor cells favor abnormal energy production via aerobic glycolysis and show resistance to apoptosis, suggesting the involvement of mitochondrial dysfunction. The differences between normal and cancer cells in their energy metabolism provide a biochemical basis for developing new therapeutic strategies. The energy blocker 3-bromopyruvate (3BP) can eradicate liver cancer in animals without associated toxicity, and is a potent anticancer towards glioblastoma cells. Since mitochondria are 3BP targets, in this work the effects of 3BP on the bioenergetics of normal rat brain mitochondria were investigated in vitro, in comparison with the anticancer agent lonidamine (LND). Whereas LND impaired oxygen consumption dependent on any complex of the respiratory chain, 3BP was inhibitory to malate/pyruvate and succinate (Complexes I and II), but preserved respiration from glycerol-3-phosphate and ascorbate (Complex IV). Accordingly, although electron flow along the respiratory chain and ATP levels were decreased by 3BP in malate/pyruvate- and succinate-fed mitochondria, they were not significantly influenced from glycerol-3-phosphate- or ascorbate-fed mitochondria. LND produced a decrease in electron flow from all substrates tested. No ROS were produced from any substrate, with the exception of 3BP-induced H(2)O(2) release from succinate, which suggests an antimycin-like action of 3BP as an inhibitor of Complex III. We can conclude that 3BP does not abolish completely respiration and ATP synthesis in brain mitochondria, and has a limited effect on ROS production, confirming that this drug may have limited harmful effects on normal cells.

Predictive modelling of the dielectric response of plasmonic substrates: application to the interpretation of ellipsometric spectra

NASA Astrophysics Data System (ADS)

Pugliara, A.; Bayle, M.; Bonafos, C.; Carles, R.; Respaud, M.; Makasheva, K.

2018-03-01

A predictive modelling of plasmonic substrates appropriate to read ellipsometric spectra is presented in this work. We focus on plasmonic substrates containing a single layer of silver nanoparticles (AgNPs) embedded in silica matrices. The model uses the Abeles matrix formalism and is based on the quasistatic approximation of the classical Maxwell-Garnett mixing rule, however accounting for the electronic confinement effect through the damping parameter. It is applied on samples elaborated by: (i) RF-diode sputtering followed by Plasma Enhanced Chemical Vapor Deposition (PECVD) and (ii) Low Energy Ion Beam Synthesis (LE-IBS), and represents situations with increasing degree of complexity that can be accounted for by the model. It allows extraction of the main characteristics of the AgNPs population: average size, volume fraction and distance of the AgNPs layer from the matrix free surface. Model validation is achieved through comparison with results obtained from transmission electron microscopy approving for its applicability. The advantages and limitations of the proposed model are discussed after eccentricity-based statistical analysis along with further developments related to the quality of comparison between the model-generated spectra and the experimentally-recorded ellipsometric spectra.

Crystal structure of β1→6-galactosidase from Bifidobacterium bifidum S17: trimeric architecture, molecular determinants of the enzymatic activity and its inhibition by α-galactose.

PubMed

Godoy, Andre Schutzer; Camilo, Cesar Moises; Kadowaki, Marco Antonio; Muniz, Heloisa Dos S; Espirito Santo, Melissa; Murakami, Mario Tyago; Nascimento, Alessandro S; Polikarpov, Igor

2016-11-01

In a search for better comprehension of β-galactosidase function and specificity, we solved the crystal structures of the GH42 β-galactosidase BbgII from Bifidobacterium bifidum S17, a well-adapted probiotic microorganism from the human digestive tract, and its complex with d-α-galactose. BbgII is a three-domain molecule that forms barrel-shaped trimers in solution. BbgII interactions with d-α-galactose, a competitive inhibitor, showed a number of residues that are involved in the coordination of ligands. A combination of site-directed mutagenesis of these amino acid residues with enzymatic activity measurements confirmed that Glu161 and Glu320 are fundamental for catalysis and their substitution by alanines led to catalytically inactive mutants. Mutation Asn160Ala resulted in a two orders of magnitude decrease of the enzyme k cat without significant modification in its K m , whereas mutations Tyr289Phe and His371Phe simultaneously decreased k cat and increased K m values. Enzymatic activity of Glu368Ala mutant was too low to be detected. Our docking and molecular dynamics simulations showed that the enzyme recognizes and tightly binds substrates with β1→6 and β1→3 bonds, while binding of the substrates with β1→4 linkages is less favorable. Structural data are available in the PDB under the accession numbers 4UZS and 4UCF. © 2016 Federation of European Biochemical Societies.

Quantum mechanics/molecular mechanics study of the catalytic cycle of water splitting in photosystem II.

PubMed

Sproviero, Eduardo M; Gascón, José A; McEvoy, James P; Brudvig, Gary W; Batista, Victor S

2008-03-19

This paper investigates the mechanism of water splitting in photosystem II (PSII) as described by chemically sensible models of the oxygen-evolving complex (OEC) in the S0-S4 states. The reaction is the paradigm for engineering direct solar fuel production systems since it is driven by solar light and the catalyst involves inexpensive and abundant metals (calcium and manganese). Molecular models of the OEC Mn3CaO4Mn catalytic cluster are constructed by explicitly considering the perturbational influence of the surrounding protein environment according to state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, in conjunction with the X-ray diffraction (XRD) structure of PSII from the cyanobacterium Thermosynechococcus elongatus. The resulting models are validated through direct comparisons with high-resolution extended X-ray absorption fine structure spectroscopic data. Structures of the S3, S4, and S0 states include an additional mu-oxo bridge between Mn(3) and Mn(4), not present in XRD structures, found to be essential for the deprotonation of substrate water molecules. The structures of reaction intermediates suggest a detailed mechanism of dioxygen evolution based on changes in oxidization and protonation states and structural rearrangements of the oxomanganese cluster and surrounding water molecules. The catalytic reaction is consistent with substrate water molecules coordinated as terminal ligands to Mn(4) and calcium and requires the formation of an oxyl radical by deprotonation of the substrate water molecule ligated to Mn(4) and the accumulation of four oxidizing equivalents. The oxyl radical is susceptible to nucleophilic attack by a substrate water molecule initially coordinated to calcium and activated by two basic species, including CP43-R357 and the mu-oxo bridge between Mn(3) and Mn(4). The reaction is concerted with water ligand exchange, swapping the activated water by a water molecule in the second coordination shell of calcium.

A case of mitochondrial encephalomyopathy associated with a muscle coenzyme Q10 deficiency.

PubMed

Boitier, E; Degoul, F; Desguerre, I; Charpentier, C; François, D; Ponsot, G; Diry, M; Rustin, P; Marsac, C

1998-01-01

We report severe coenzyme Q10 deficiency of muscle in a 4-year-old boy presenting with progressive muscle weakness, seizures, cerebellar syndrome, and a raised cerebro-spinal fluid lactate concentration. State-3 respiratory rates of muscle mitochondria with glutamate, pyruvate, palmitoylcarnitine, and succinate as respiratory substrates were markedly reduced, whereas ascorbate/N,N,N',N'-tetramethyl-p-phenylenediamine were oxidized normally. The activities of complexes I, II, III and IV of the electron transport chain were normal, but the activities of complexes I+III and II+III, both systems requiring coenzyme Q10 as an electron carrier, were dramatically decreased. These results suggested a defect in the mitochondrial coenzyme Q10 content. This was confirmed by the direct assessment of coenzyme Q10 level by high-performance liquid chromatography in patient's muscle homogenate and isolated mitochondria, revealing levels of 16% and 6% of the control values, respectively. We did not find any impairment of the respiratory chain either in a lymphoblastoid cell line or in skin cultured fibroblasts from the patient, suggesting that the coenzyme Q10 depletion was tissue-specific. This is a new case of a muscle deficiency of mitochondrial coenzyme Q in a patient suffering from an encephalomyopathy.

3-Nitropropionic Acid is a Suicide Inhibitor of MitochondrialRespiration that, Upon Oxidation by Complex II, Forms a Covalent AdductWith a Catalytic Base Arginine in the Active Site of the Enzyme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Li-shar; Sun, Gang; Cobessi, David

We report three new structures of mitochondrial respiratory Complex II (succinate ubiquinone oxidoreductase, E.C. 1.3.5.1) at up to 2.1 {angstrom} resolution, with various inhibitors. The structures define the conformation of the bound inhibitors and suggest the residues involved in substrate binding and catalysis at the dicarboxylate site. In particular they support the role of Arg297 as a general base catalyst accepting a proton in the dehydrogenation of succinate. The dicarboxylate ligand in oxaloacetate-containing crystals appears to be the same as that reported for Shewanella flavocytochrome c treated with fumarate. The plant and fungal toxin 3-nitropropionic acid, an irreversible inactivator ofmore » succinate dehydrogenase, forms a covalent adduct with the side chain of Arg297. The modification eliminates a trypsin cleavage site in the flavoprotein, and tandem mass spectroscopic analysis of the new fragment shows the mass of Arg 297 to be increased by 83 Da and to have potential of losing 44 Da, consistent with decarboxylation, during fragmentation.« less

[Streptoverticillium griseoviridum n. sp., a producer of the candidin-amphotericin B group, antifungal heptaene nonaromatic antibiotic 0185].

PubMed

Konev, Iu E; Efimova, V M; Etingov, E D; Zaval'naia, N M

1978-02-01

An actinomyceteous strain LIA-0185 producing a heptaenic non-aromatic antibiotic of the candidin type was isolated from a soil sample taken in the Georgian SSR under the programme of screening antifungal antibiotics. The taxonomic study of the strain showed that it belonged to the series of viridoflavum and had the following main taxonomic features: the sporophores in the whorls, straight, remote: the aerial mycelium from yellow to dark-olive-grey; the substrate mycelium olive; the soluble pigment absent; the melanine pigment was produced on the peptone medium; the culture formed H2S; assimilated glucose, mannose, inozide and to a lesser extent fructose; did not assimilate arabinose, xylose, sucrose, lactose, ramnose and raffinose. The strain inhibited the growth of yeast and fungi, grampositive bacteria and actinomycetes and produced a complex of non-aromatic heptaenic antibiotics. The actinomycete differed from the other whorl cultures. It was classified as a new species Sv. griseoviridum sp. nov. The antibiotic complex was a mixture of 2 components, i. e. I and II present approximately in equal amounts. Component II was analogous to candidin. Component I was a new original substance.

Two Tropinone Reductases with Distinct Stereospecificities from Cultured Roots of Hyoscyamus niger1

PubMed Central

Hashimoto, Takashi; Nakajima, Keiji; Ongena, Godelieve; Yamada, Yasuyuki

1992-01-01

Tropinone is an alkamine intermediate at the branch point of biosynthetic pathways leading to various tropane alkaloids. Two stereospecifically distinct NADPH-dependent oxidoreductases, TR-I and TR-II, which, respectively, reduce tropinone to 3α-hydroxytropane (tropine) and 3β-hydroxytropane (ψ-tropine), were detected mainly in the root of tropane alkaloid-producing plants but not in nonproducing cultured root. Both reductases were purified to near homogeneity from cultured root of Hyoscyamus niger and characterized. The TR-I reaction was reversible, whereas the TR-II reaction was essentially irreversible, reduction of the ketone being highly favored over oxidation of the alcohol ψ-tropine. Marked differences were found between the two reductase in their affinities for tropinone substrate and in the effects of amino acid modification reagents. Some differences in substrate specificity were apparent. For example, N-propyl-4-piperidone was reduced by TR-II but not by TR-I. Conversely, 3-quinuclidinone and 8-thiabicyclo[3,2,1]octane-3-one were accepted as substrates by TR-I but hardly at all by TR-II. Both enzymes were shown to be class B oxidoreductases, which transfer the pro-S hydrogen of NAD(P)H to their substrates. Possible roles of these tropinone reductases in alkaloid biosynthesis are discussed. Images Figure 6 PMID:16653065

Crystallographic and Molecular Dynamics Simulation Analysis of Escherichia Coli Dihydroneopterin Aldolase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blaszczyk, Jaroslaw; Lu, Zhenwei; Li, Yue

2014-09-01

To understand the structural basis for the biochemical differences and further investigate the catalytic mechanism of DHNA, we have determined the structure of EcDHNA complexed with NP at 1.07-Å resolution [PDB:2O90], built an atomic model of EcDHNA complexed with the substrate DHNP, and performed molecular dynamics (MD) simulation analysis of the substrate complex. EcDHNA has the same fold as SaDHNA and also forms an octamer that consists of two tetramers, but the packing of one tetramer with the other is significantly different between the two enzymes. Furthermore, the structures reveal significant differences in the vicinity of the active site, particularlymore » in the loop that connects strands β3 and β4, mainly due to the substitution of nearby residues. The building of an atomic model of the complex of EcDHNA and the substrate DHNP and the MD simulation of the complex show that some of the hydrogen bonds between the substrate and the enzyme are persistent, whereas others are transient. The substrate binding model and MD simulation provide the molecular basis for the biochemical behaviors of the enzyme, including noncooperative substrate binding, indiscrimination of a pair of epimers as the substrates, proton wire switching during catalysis, and formation of epimerization product.« less

Contractility in type III cochlear fibrocytes is dependent on non-muscle myosin II and intercellular gap junctional coupling.

PubMed

Kelly, John J; Forge, Andrew; Jagger, Daniel J

2012-08-01

The cochlear spiral ligament is a connective tissue that plays diverse roles in normal hearing. Spiral ligament fibrocytes are classified into functional sub-types that are proposed to carry out specialized roles in fluid homeostasis, the mediation of inflammatory responses to trauma, and the fine tuning of cochlear mechanics. We derived a secondary sub-culture from guinea pig spiral ligament, in which the cells expressed protein markers of type III or "tension" fibrocytes, including non-muscle myosin II (nmII), α-smooth muscle actin (αsma), vimentin, connexin43 (cx43), and aquaporin-1. The cells formed extensive stress fibers containing αsma, which were also associated intimately with nmII expression, and the cells displayed the mechanically contractile phenotype predicted by earlier modeling studies. cx43 immunofluorescence was evident within intercellular plaques, and the cells were coupled via dye-permeable gap junctions. Coupling was blocked by meclofenamic acid (MFA), an inhibitor of cx43-containing channels. The contraction of collagen lattice gels mediated by the cells could be prevented reversibly by blebbistatin, an inhibitor of nmII function. MFA also reduced the gel contraction, suggesting that intercellular coupling modulates contractility. The results demonstrate that these cells can impart nmII-dependent contractile force on a collagenous substrate, and support the hypothesis that type III fibrocytes regulate tension in the spiral ligament-basilar membrane complex, thereby determining auditory sensitivity.

Modeling of substrate and inhibitor binding to phospholipase A2.

PubMed

Sessions, R B; Dauber-Osguthorpe, P; Campbell, M M; Osguthorpe, D J

1992-09-01

Molecular graphics and molecular mechanics techniques have been used to study the mode of ligand binding and mechanism of action of the enzyme phospholipase A2. A substrate-enzyme complex was constructed based on the crystal structure of the apoenzyme. The complex was minimized to relieve initial strain, and the structural and energetic features of the resultant complex analyzed in detail, at the molecular and residue level. The minimized complex was then used as a basis for examining the action of the enzyme on modified substrates, binding of inhibitors to the enzyme, and possible reaction intermediate complexes. The model is compatible with the suggested mechanism of hydrolysis and with experimental data about stereoselectivity, efficiency of hydrolysis of modified substrates, and inhibitor potency. In conclusion, the model can be used as a tool in evaluating new ligands as possible substrates and in the rational design of inhibitors, for the therapeutic treatment of diseases such as rheumatoid arthritis, atherosclerosis, and asthma.

The Effects of Zebra Mussels (Dreissena polymorpha) on the Foraging Success of Eurasian Perch (Perca fluviatilis) and Ruffe (Gymnocephalus cernuus)

NASA Astrophysics Data System (ADS)

Dieterich, Axel; Mörtl, Martin; Eckmann, Reiner

2004-07-01

Complex habitat structures can influence the foraging success of fish. Competition for food between fish species can therefore depend on the competitors' abilities to cope with structural complexity. In laboratory experiments, we comparatively assessed effects of zebra mussels (Dreissena polymorpha Pall.) on the foraging success of Eurasian perch (Perca fluviatilis L.) and ruffe (Gymnocephalus cernuus (L.)). In single-species and mixed-species experiments, the fish were fed caddisfly larvae (Tinodes waeneri (L.)) over complex (mussel-covered stones) and less-complex (bare stones) substrates. With intraspecific competition, food consumption by perch and ruffe decreased significantly when the complex substrate was used. With interspecific competition, food consumption by perch and ruffe did not change with substrate complexity, but perch clearly out-competed ruffe on both substrates. Zebra mussel beds provide a refuge for macrozoobenthos against predation by ruffe and probably also by perch. (

Activation of the DnaK-ClpB Complex is Regulated by the Properties of the Bound Substrate.

PubMed

Fernández-Higuero, Jose Angel; Aguado, Alejandra; Perales-Calvo, Judit; Moro, Fernando; Muga, Arturo

2018-04-11

The chaperone ClpB in bacteria is responsible for the reactivation of aggregated proteins in collaboration with the DnaK system. Association of these chaperones at the aggregate surface stimulates ATP hydrolysis, which mediates substrate remodeling. However, a question that remains unanswered is whether the bichaperone complex can be selectively activated by substrates that require remodeling. We find that large aggregates or bulky, native-like substrates activates the complex, whereas a smaller, permanently unfolded protein or extended, short peptides fail to stimulate it. Our data also indicate that ClpB interacts differently with DnaK in the presence of aggregates or small peptides, displaying a higher affinity for aggregate-bound DnaK, and that DnaK-ClpB collaboration requires the coupled ATPase-dependent remodeling activities of both chaperones. Complex stimulation is mediated by residues at the β subdomain of DnaK substrate binding domain, which become accessible to the disaggregase when the lid is allosterically detached from the β subdomain. Complex activation also requires an active NBD2 and the integrity of the M domain-ring of ClpB. Disruption of the M-domain ring allows the unproductive stimulation of the DnaK-ClpB complex in solution. The ability of the DnaK-ClpB complex to discrimínate different substrate proteins might allow its activation when client proteins require remodeling.

Metal (II) Complexes Derived from Naphthofuran-2-carbohydrazide and Diacetylmonoxime Schiff Base: Synthesis, Spectroscopic, Electrochemical, and Biological Investigation

PubMed Central

Sumathi, R. B.; Halli, M. B.

2014-01-01

A new Schiff base and a new series of Co(II), Ni(II), Cu(II), Cd(II), and Hg(II) complexes were synthesized by the condensation of naphthofuran-2-carbohydrazide and diacetylmonoxime. Metal complexes of the Schiff base were prepared from their chloride salts of Co(II), Ni(II), Cu(II), Cd(II), and Hg(II) in ethanol. The ligand along with its metal complexes have been characterized on the basis of analytical data, IR, electronic, mass, 1HNMR, ESR spectral data, thermal studies, magnetic susceptibility, and molar conductance measurements. The nonelectrolytic behaviour of the complexes was assessed from the measured low conductance data. The elemental analysis of the complexes confirm the stoichiometry of the type CuL2Cl2 and MLCl2 where M = Ni(II), Co(II), Cd(II), and Hg(II) and L = Schiff base. The redox property of the Cu(II) complex was investigated by electrochemical method using cyclic voltammetry. In the light of these results, Co(II), Ni(II), and Cu(II) complexes are assigned octahedral geometry, Cd(II), and Hg(II) complexes tetrahedral geometry. In order to evaluate the effect of metal ions upon chelation, both the ligand and its metal complexes were screened for their antibacterial and antifungal activities by minimum inhibitory concentration (MIC) method. The DNA cleaving capacity of all the complexes was analysed by agarose gel electrophoresis method. PMID:24592203

TFIIH and P-TEFb Coordinate Transcription with Capping Enzyme Recruitment at Specific Genes in Fission Yeast

PubMed Central

Viladevall, Laia; St. Amour, Courtney V.; Rosebrock, Adam; Schneider, Susanne; Zhang, Chao; Allen, Jasmina J.; Shokat, Kevan M.; Schwer, Beate; Leatherwood, Janet K.; Fisher, Robert P.

2009-01-01

Summary Cyclin-dependent kinases (CDKs) are subunits of transcription factor (TF) IIH and positive transcription elongation factor b (P-TEFb). To define their functions, we mutated the TFIIH-associated kinase Mcs6 and P-TEFb homologs Cdk9 and Lsk1 of fission yeast, making them sensitive to bulky purine analogs. Selective inhibition of Mcs6 or Cdk9 blocks cell division, alters RNA polymerase (Pol) II carboxyl-terminal domain (CTD) phosphorylation and represses specific, overlapping subsets of transcripts. At a common target gene, both CDKs must be active for normal Pol II occupancy, and Spt5—a CDK substrate and regulator of elongation—accumulates disproportionately to Pol II when either kinase is inhibited. In contrast, Mcs6 activity is sufficient, and necessary, to recruit the Cdk9/Pcm1 (mRNA cap methyltransferase) complex. In vitro, phosphorylation of the CTD by Mcs6 stimulates subsequent phosphorylation by Cdk9. We propose that TFIIH primes the CTD and promotes recruitment of P-TEFb/Pcm1, serving to couple elongation and capping of select pre-mRNAs. PMID:19328067

In situ Silver Spot Preparation and on-Plate Surface-Enhanced Raman Scattering Detection in Thin Layer Chromatography Separation

NASA Astrophysics Data System (ADS)

Herman, K.; Mircescu, N. E.; Szabo, L.; Leopold, L. F.; Chiş, V.; Leopold, N.

2013-05-01

An improved approach for surface-enhanced Raman scattering (SERS) detection of mixture constituents after thin layer chromatography (TLC) separation is presented. A SERS active silver substrate was prepared under open air conditions, directly on the thin silica film by photo-reduction of silver nitrate, allowing the detection of binary mixtures of cresyl violet, bixine, crystal violet, and Cu(II) complex of 4-(2-pyridylazo)resorcinol. The recorded SERS spectrum provides a unique spectral fingerprint for each molecule; therefore the use of analyte standards is avoided, thus rendering the presented procedure advantageous compared to the conventional detection methodology in TLC.

Crystallization and crystal manipulation of a steric chaperone in complex with its lipase substrate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pauwels, Kris, E-mail: krpauwel@vub.ac.be; Loris, Remy; Vandenbussche, Guy

2005-08-01

Crystals of the lipase of B. glumae in complex with its specific foldase were obtained in two forms. Crystallization, crystal manipulation and preliminary X-ray diffraction analysis are described. Bacterial lipases that are secreted via the type II secretion pathway require a lipase-specific foldase in order to obtain their native and biologically active conformation in the periplasmic space. The lipase–foldase complex from Burkholderia glumae (319 and 333 residues, respectively) was crystallized in two crystal forms. One crystal form belongs to space group P3{sub 1}21 (P3{sub 2}21), with unit-cell parameters a = b = 122.3, c = 98.2 Å. A procedure ismore » presented which improved the diffraction of these crystals from ∼5 to 2.95 Å. For the second crystal form, which belonged to space group C2 with unit-cell parameters a = 183.0, b = 75.7, c = 116.6 Å, X-ray data were collected to 1.85 Å.« less

Biochemical Characterization of Glutamate Racemase-A New Candidate Drug Target against Burkholderia cenocepacia Infections.

PubMed

Israyilova, Aygun; Buroni, Silvia; Forneris, Federico; Scoffone, Viola Camilla; Shixaliyev, Namiq Q; Riccardi, Giovanna; Chiarelli, Laurent Roberto

2016-01-01

The greatest obstacle for the treatment of cystic fibrosis patients infected with the Burkholderia species is their intrinsic antibiotic resistance. For this reason, there is a need to develop new effective compounds. Glutamate racemase, an essential enzyme for the biosynthesis of the bacterial cell wall, is an excellent candidate target for the design of new antibacterial drugs. To this aim, we recombinantly produced and characterized glutamate racemase from Burkholderia cenocepacia J2315. From the screening of an in-house library of compounds, two Zn (II) and Mn (III) 1,3,5-triazapentadienate complexes were found to efficiently inhibit the glutamate racemase activity with IC50 values of 35.3 and 10.0 μM, respectively. Using multiple biochemical approaches, the metal complexes have been shown to affect the enzyme activity by binding to the enzyme-substrate complex and promoting the formation of an inhibited dimeric form of the enzyme. Our results corroborate the value of glutamate racemase as a good target for the development of novel inhibitors against Burkholderia.

Complex oxides useful for thermoelectric energy conversion

DOEpatents

Majumdar, Arunava [Orinda, CA; Ramesh, Ramamoorthy [Moraga, CA; Yu, Choongho [College Station, TX; Scullin, Matthew L [Berkeley, CA; Huijben, Mark [Enschede, NL

2012-07-17

The invention provides for a thermoelectric system comprising a substrate comprising a first complex oxide, wherein the substrate is optionally embedded with a second complex oxide. The thermoelectric system can be used for thermoelectric power generation or thermoelectric cooling.

Synthesis, characterization and antimicrobial studies of Schiff base complexes

NASA Astrophysics Data System (ADS)

Zafar, Hina; Ahmad, Anis; Khan, Asad U.; Khan, Tahir Ali

2015-10-01

The Schiff base complexes, MLCl2 [M = Fe(II), Co(II), Ni(II), Cu(II) and Zn(II)] have been synthesized by the template reaction of respective metal ions with 2-acetylpyrrole and 1,3-diaminopropane in 1:2:1 M ratio. The complexes have been characterized by elemental analyses, ESI - mass, NMR (1H and 13C), IR, XRD, electronic and EPR spectral studies, magnetic susceptibility and molar conductance measurements. These studies show that all the complexes have octahedral arrangement around the metal ions. The molar conductance measurements of all the complexes in DMSO indicate their non-electrolytic nature. The complexes were screened for their antibacterial activity in vitro against Gram-positive (Streptococcus pyogenes) and Gram-negative (Klebsiella pneumoniae) bacteria. Among the metal complexes studied the copper complex [CuLCl2], showed highest antibacterial activity nearly equal to standard drug ciprofloxacin. Other complexes also showed considerable antibacterial activity. The relative order of activity against S. Pyogenes is as Cu(II) > Zn(II) > Co(II) = Fe(II) > Ni(II) and with K. Pneumonia is as Cu(II) > Co(II) > Zn(II) > Fe(II) > Ni(II).

C–H and O 2 activation at a Pt(II) center enabled by a novel sulfonated CNN pincer ligand

DOE PAGES

Watts, David; Wang, Daoyong; Adelberg, Mackenzie; ...

2016-09-21

A novel sulfonated CNN pincer ligand has been designed to support CH and O 2 activation at a Pt(II) center. The derived cycloplatinated aqua complex 7 was found to be one of the most active reported homogeneous Pt catalysts for H/D exchange between studied arenes (benzene, benzene-d 6, toluene-d 8, p-xylene, and mesitylene) and 2,2,2-trifluoroethanol (TFE) or 2,2,2-trifluoroethanol-d; the TON for C 6D 6 as a substrate is >250 after 48 h at 80 °C. The reaction is very selective; no benzylic CH bond activation was observed. The per-CH-bond reactivity diminishes in the series benzene (19) > toluene ( p-CH:more » m-CH: o-CH = 1:0.9:0.2) > xylene (2.9) > mesitylene (1.1). The complex 7 reacts slowly in TFE solutions under ambient light but not in the dark with O 2 to selectively produce a Pt(IV) trifluoroethoxo derivative. The H/D exchange reaction kinetics and results of the DFT study suggest that complex 7, and not its TFE derivatives, is the major species responsible for the arene CH bond activation. Lastly, the reaction deuterium kinetic isotope effect, k H/k D = 1.7, the reaction selectivity, and reaction kinetics modeling suggest that the CH bond cleavage step is rate-determining.« less

Initial nitrogen enrichment conditions determines variations in nitrogen substrate utilization by heterotrophic bacterial isolates.

PubMed

Ghosh, Suchismita; Ayayee, Paul A; Valverde-Barrantes, Oscar J; Blackwood, Christopher B; Royer, Todd V; Leff, Laura G

2017-04-04

The nitrogen (N) cycle consists of complex microbe-mediated transformations driven by a variety of factors, including diversity and concentrations of N compounds. In this study, we examined taxonomic diversity and N substrate utilization by heterotrophic bacteria isolated from streams under complex and simple N-enrichment conditions. Diversity estimates differed among isolates from the enrichments, but no significant composition were detected. Substrate utilization and substrate range of bacterial assemblages differed within and among enrichments types, and not simply between simple and complex N-enrichments. N substrate use patterns differed between isolates from some complex and simple N-enrichments while others were unexpectedly similar. Taxonomic composition of isolates did not differ among enrichments and was unrelated to N use suggesting strong functional redundancy. Ultimately, our results imply that the available N pool influences physiology and selects for bacteria with various abilities that are unrelated to their taxonomic affiliation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Resch, M.

Enzymatic depolymerization of polysaccharides is a key step in the production of fuels and chemicals from lignocellulosic biomass, and discovery of synergistic biomass-degrading enzyme paradigms will enable improved conversion processes. Historically, revealing insights into enzymatic saccharification mechanisms on plant cell walls has been hindered by uncharacterized substrates and low resolution imaging techniques. Also, translating findings between model substrates to intact biomass is critical for evaluating enzyme performance. Here we employ a fungal free enzyme cocktail, a complexed cellulosomal system, and a combination of the two to investigate saccharification mechanisms on cellulose I, II and III along with corn stover frommore » Clean Fractionation (CF), which is an Organosolv pretreatment. The insoluble Cellulose Enriched Fraction (CEF) from CF contains mainly cellulose with minor amounts of residual hemicellulose and lignin, the amount of which depends on the CF pretreatment severity. Enzymatic digestions at both low and high-solids loadings demonstrate that CF reduces the amount of enzyme required to depolymerize polysaccharides relative to deacetylated, dilute acid pretreated corn stover. Transmission and scanning electron microscopy of the biomass provides evidence for the different mechanisms of enzymatic deconstruction between free and complexed enzyme systems, and reveals the basis for the synergistic relationship between the two enzyme paradigms on a process-relevant substrate for the first time. These results also demonstrate that the presence of lignin, rather than cellulose morphology, is more detrimental to cellulosome action than to free cellulases. As enzyme costs are a major economic driver for biorefineries, this study provides key inputs for the evaluation of CF as a pretreatment method for biomass conversion.« less

CD, MCD and VTVH MCD Studies of Biferrous and Mixed-Valent myo-Inositol Oxygenase: Insights into Substrate Activation of O2 Reactivity

PubMed Central

Snyder, Rae Ana; Bell, Caleb B.; Diao, Yinghui; Krebs, Carsten; Bollinger, J. Martin; Solomon, Edward I.

2013-01-01

Myo-inositol oxygenase (MIOX) catalyzes the 4e− oxidation of myo-inositol (MI) to D-glucuronate using a substrate activated Fe(II)Fe(III) site. The biferrous and Fe(II)Fe(III) forms of MIOX were studied with circular dichroism (CD), magnetic circular dichroism (MCD), and variable temperature variable field (VTVH) MCD spectroscopies. The MCD spectrum of biferrous MIOX shows two ligand field (LF) transitions near 10,000 cm−1, split by ~2,000 cm−1, characteristic of 6 coordinate (6C) Fe(II) sites, indicating that the modest reactivity of the biferrous form toward O2 can be attributed to the saturated coordination of both irons. Upon oxidation to the Fe(II)Fe(III) state, MIOX shows two LF transitions in the ~10,000 cm−1 region, again implying a coordinatively saturated Fe(II) site. Upon MI binding, these split in energy to 5,200 cm−1 and 11,200 cm−1, showing that MI binding causes the Fe(II) to become coordinately unsaturated. VTVH MCD magnetization curves of unbound and MI-bound Fe(II)Fe(III) forms show that upon substrate binding, the isotherms become more nested, requiring that the exchange coupling and ferrous zero field splitting (ZFS) both decrease in magnitude. These results imply that MI binds to the ferric site, weakening the Fe(III)-μ-OH bond and strengthening the Fe(II)-μ-OH bond. This perturbation results in the release of a coordinated water from the Fe(II) that enables its O2 activation. PMID:24066857

Ammonia release method for depositing metal oxides

DOEpatents

Silver, Gary L.; Martin, Frank S.

1994-12-13

A method of depositing metal oxides on substrates which is indifferent to the electrochemical properties of the substrates and which comprises forming ammine complexes containing metal ions and thereafter effecting removal of ammonia from the ammine complexes so as to permit slow precipitation and deposition of metal oxide on the substrates.

Mod5 protein binds to tRNA gene complexes and affects local transcriptional silencing

PubMed Central

Pratt-Hyatt, Matthew; Pai, Dave A.; Haeusler, Rebecca A.; Wozniak, Glenn G.; Good, Paul D.; Miller, Erin L.; McLeod, Ian X.; Yates, John R.; Hopper, Anita K.; Engelke, David R.

2013-01-01

The tRNA gene-mediated (tgm) silencing of RNA polymerase II promoters is dependent on subnuclear clustering of the tRNA genes, but genetic analysis shows that the silencing requires additional mechanisms. We have identified proteins that bind tRNA gene transcription complexes and are required for tgm silencing but not required for gene clustering. One of the proteins, Mod5, is a tRNA modifying enzyme that adds an N6-isopentenyl adenosine modification at position 37 on a small number of tRNAs in the cytoplasm, although a subpopulation of Mod5 is also found in the nucleus. Recent publications have also shown that Mod5 has tumor suppressor characteristics in humans as well as confers drug resistance through prion-like misfolding in yeast. Here, we show that a subpopulation of Mod5 associates with tRNA gene complexes in the nucleolus. This association occurs and is required for tgm silencing regardless of whether the pre-tRNA transcripts are substrates for Mod5 modification. In addition, Mod5 is bound to nuclear pre-tRNA transcripts, although they are not substrates for the A37 modification. Lastly, we show that truncation of the tRNA transcript to remove the normal tRNA structure also alleviates silencing, suggesting that synthesis of intact pre-tRNAs is required for the silencing mechanism. These results are discussed in light of recent results showing that silencing near tRNA genes also requires chromatin modification. PMID:23898186

Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase

PubMed Central

Chang, Wei-chen; Layne, Andrew P; Miles, Linde A; Krebs, Carsten

2014-01-01

Iron-dependent halogenases employ cis-halo-Fe(IV)-oxo (haloferryl) complexes to functionalize unactivated aliphatic carbon centers, a capability elusive to synthetic chemists. Halogenation requires (1) coordination of a halide anion (Cl− or Br−) to the enzyme's Fe(II) cofactor; (2) coupled activation of O2 and decarboxylation of α-ketoglutarate to generate the haloferryl intermediate; (3) abstraction of hydrogen (H•) from the substrate by the ferryl oxo group; and (4) transfer of the cis halogen as Cl• or Br• to the substrate radical. This enzymatic solution to an unsolved chemical challenge is potentially generalizable to installation of other functional groups, provided that the corresponding anions can support the four requisite steps. We show here that the wild-type halogenase SyrB2 can indeed direct aliphatic nitration and azidation reactions by the same chemical logic. The discovery and enhancement by mutagenesis of these previously unknown reaction types suggests unrecognized or untapped versatility in ferryl-mediated enzymatic C–H-bond activation. PMID:24463698

The Power of Integrating Kinetic Isotope Effects into the Formalism of the Michaelis-Menten Equation

PubMed Central

Klinman, Judith P.

2014-01-01

The final arbiter of enzyme mechanism is the ability to establish and test a kinetic mechanism. Isotope effects play a major role in expanding the scope and insight derived from the Michaelis-Menten equation. The integration of isotope effects into the formalism of the Michaelis-Menten equation began in the 1970s and has continued to this day. This review discusses a family of eukaryotic copper proteins that includes dopamine β-monooxygenase, tyramine β-monooxygenase, and peptidylglycine α-amidating enzyme, responsible for the synthesis of the neuro-active compounds, norepinephrine, octopamine and C-terminally carboxamidated peptides, respectively. Highlighted are results that show how combining kinetic isotope effects with initial rate parameters permits an evaluation of: (i) the order of substrate binding to multi-substrate enzymes; (ii) the magnitude of individual rate constants in complex, multi-step reactions; (iii) the identification of chemical intermediates; and (iv) the role of non-classical (tunneling) behavior in C–H activation. PMID:23937475

Evaluation of optical excitation conditions for ruthenium complex for biosensor optodes

NASA Astrophysics Data System (ADS)

Pieper, Sean; Zhong, Zhong; Lear, Kevin L.; Reardon, Ken

2007-03-01

Development of a fiber optic biosensor incorporating genetically engineered enzymes which catalyze chlorinated ethenes in an oxygen-consuming reaction for in situ monitoring of groundwater contaminants motivates optimization of optode excitation conditions. These conditions affect the sensitivity, signal-to-noise, and optode service life impacting the quality of the overall biosensor. Optodes are generally comprised of a fluorophore conjugated with a polymer as a substrate cross linked at the distal end of a fiber optic. We investigate the excitation conditions of tris(4,7-diphenyl-1,10-phenanthroline) ruthenium(II) chloride (Ru(dpp)3) conjugated with poly(vinyl alcohol) (PVOH) as an optode. A reported advantage of Ru(dpp)3 is that it has no emission spectral shift occurring under varying chemical and environmental conditions. Photostability degradation due to photobleaching of Ru(dpp)3 with PVOH as a substrate is explored by varying the optical irradiance of the fluorophore containing optode. Other issues relating to practical implementation of Ru(dpp)3 as oxygen sensitive biosensors will be discussed.

A contractile and counterbalancing adhesion system controls the 3D shape of crawling cells.

PubMed

Burnette, Dylan T; Shao, Lin; Ott, Carolyn; Pasapera, Ana M; Fischer, Robert S; Baird, Michelle A; Der Loughian, Christelle; Delanoe-Ayari, Helene; Paszek, Matthew J; Davidson, Michael W; Betzig, Eric; Lippincott-Schwartz, Jennifer

2014-04-14

How adherent and contractile systems coordinate to promote cell shape changes is unclear. Here, we define a counterbalanced adhesion/contraction model for cell shape control. Live-cell microscopy data showed a crucial role for a contractile meshwork at the top of the cell, which is composed of actin arcs and myosin IIA filaments. The contractile actin meshwork is organized like muscle sarcomeres, with repeating myosin II filaments separated by the actin bundling protein α-actinin, and is mechanically coupled to noncontractile dorsal actin fibers that run from top to bottom in the cell. When the meshwork contracts, it pulls the dorsal fibers away from the substrate. This pulling force is counterbalanced by the dorsal fibers' attachment to focal adhesions, causing the fibers to bend downward and flattening the cell. This model is likely to be relevant for understanding how cells configure themselves to complex surfaces, protrude into tight spaces, and generate three-dimensional forces on the growth substrate under both healthy and diseased conditions.

A contractile and counterbalancing adhesion system controls the 3D shape of crawling cells

PubMed Central

Burnette, Dylan T.; Shao, Lin; Ott, Carolyn; Pasapera, Ana M.; Fischer, Robert S.; Baird, Michelle A.; Der Loughian, Christelle; Delanoe-Ayari, Helene; Paszek, Matthew J.; Davidson, Michael W.; Betzig, Eric

2014-01-01

How adherent and contractile systems coordinate to promote cell shape changes is unclear. Here, we define a counterbalanced adhesion/contraction model for cell shape control. Live-cell microscopy data showed a crucial role for a contractile meshwork at the top of the cell, which is composed of actin arcs and myosin IIA filaments. The contractile actin meshwork is organized like muscle sarcomeres, with repeating myosin II filaments separated by the actin bundling protein α-actinin, and is mechanically coupled to noncontractile dorsal actin fibers that run from top to bottom in the cell. When the meshwork contracts, it pulls the dorsal fibers away from the substrate. This pulling force is counterbalanced by the dorsal fibers’ attachment to focal adhesions, causing the fibers to bend downward and flattening the cell. This model is likely to be relevant for understanding how cells configure themselves to complex surfaces, protrude into tight spaces, and generate three-dimensional forces on the growth substrate under both healthy and diseased conditions. PMID:24711500

Structure of the detoxification catalyst mercuric ion reductase from Bacillus sp. strain RC607

NASA Astrophysics Data System (ADS)

Schiering, N.; Kabsch, W.; Moore, M. J.; Distefano, M. D.; Walsh, C. T.; Pai, E. F.

1991-07-01

SEVERAL hundred million tons of toxic mercurials are dispersed in the biosphere1. Microbes can detoxify organo-mercurials and mercury salts through sequential action of two enzymes, organomercury lyase2 and mercuric ion reductase (MerA) 3-5. The latter, a homodimer with homology to the FAD-dependent disulphide oxidoreductases6, catalyses the reaction NADPH + Hg(II) --> NADP+ + H+Hg(0), one of the very rare enzymic reactions with metal substrates. Human glutathione reductase7,8 serves as a reference molecule for FAD-dependent disulphide reductases and between its primary structure9 and that of MerA from Tn501 (Pseudomonas), Tn21 (Shigella), pI258 (Staphylococcus) and Bacillus, 25-30% of the residues have been conserved10,11. All MerAs have a C-terminal extension about 15 residues long but have very varied N termini. Although the enzyme from Streptomyces lividans has no addition, from Pseudomonas aeruginosa Tn5Ol and Bacillus sp. strain RC607 it has one and two copies respectively of a domain of 80-85 residues, highly homologous to MerP, the periplasmic component of proteins encoded by the mer operon11. These domains can be proteolytically cleaved off without changing the catalytic efficiency3. We report here the crystal structure of MerA from the Gram-positive bacterium Bacillus sp. strain RC607. Analysis of its complexes with nicotinamide dinucleotide substrates and the inhibitor Cd(II) reveals how limited structural changes enable an enzyme to accept as substrate what used to be a dangerous inhibitor. Knowledge of the mode of mercury ligation is a prerequisite for understanding this unique detoxification mechanism.

Surface stability and the selection rules of substrate orientation for optimal growth of epitaxial II-VI semiconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yin, Wan-Jian; Department of Physics & Astronomy, and Wright Center for Photovoltaics Innovation and Commercialization, The University of Toledo, Toledo, Ohio 43606; Yang, Ji-Hui

2015-10-05

The surface structures of ionic zinc-blende CdTe (001), (110), (111), and (211) surfaces are systematically studied by first-principles density functional calculations. Based on the surface structures and surface energies, we identify the detrimental twinning appearing in molecular beam epitaxy (MBE) growth of II-VI compounds as the (111) lamellar twin boundaries. To avoid the appearance of twinning in MBE growth, we propose the following selection rules for choosing optimal substrate orientations: (1) the surface should be nonpolar so that there is no large surface reconstructions that could act as a nucleation center and promote the formation of twins; (2) the surfacemore » structure should have low symmetry so that there are no multiple equivalent directions for growth. These straightforward rules, in consistent with experimental observations, provide guidelines for selecting proper substrates for high-quality MBE growth of II-VI compounds.« less

A Cdc48 “Retrochaperone” Function Is Required for the Solubility of Retrotranslocated, Integral Membrane Endoplasmic Reticulum-associated Degradation (ERAD-M) Substrates*

PubMed Central

Neal, Sonya; Mak, Raymond; Bennett, Eric J.; Hampton, Randolph

2017-01-01

A surprising feature of endoplasmic reticulum (ER)-associated degradation (ERAD) is the movement, or retrotranslocation, of ubiquitinated substrates from the ER lumen or membrane to the cytosol where they are degraded by the 26S proteasome. Multispanning ER membrane proteins, called ERAD-M substrates, are retrotranslocated to the cytosol as full-length intermediates during ERAD, and we have investigated how they maintain substrate solubility. Using an in vivo assay, we show that retrotranslocated ERAD-M substrates are moved to the cytoplasm as part of the normal ERAD pathway, where they are part of a solely proteinaceous complex. Using proteomics and direct biochemical confirmation, we found that Cdc48 serves as a critical “retrochaperone” for these ERAD-M substrates. Cdc48 binding to retrotranslocated, ubiquitinated ERAD-M substrates is required for their solubility; removal of the polyubiquitin chains or competition for binding by addition of free polyubiquitin liberated Cdc48 from retrotranslocated proteins and rendered them insoluble. All components of the canonical Cdc48 complex Cdc48-Npl4-Ufd1 were present in solubilized ERAD-M substrates. This function of the complex was observed for both HRD and DOA pathway substrates. Thus, in addition to the long known ATP-dependent extraction of ERAD substrates during retrotranslocation, the Cdc48 complex is generally and critically needed for the solubility of retrotranslocated ERAD-M intermediates. PMID:28077573

A Cdc48 "Retrochaperone" Function Is Required for the Solubility of Retrotranslocated, Integral Membrane Endoplasmic Reticulum-associated Degradation (ERAD-M) Substrates.

PubMed

Neal, Sonya; Mak, Raymond; Bennett, Eric J; Hampton, Randolph

2017-02-24

A surprising feature of endoplasmic reticulum (ER)-associated degradation (ERAD) is the movement, or retrotranslocation, of ubiquitinated substrates from the ER lumen or membrane to the cytosol where they are degraded by the 26S proteasome. Multispanning ER membrane proteins, called ERAD-M substrates, are retrotranslocated to the cytosol as full-length intermediates during ERAD, and we have investigated how they maintain substrate solubility. Using an in vivo assay, we show that retrotranslocated ERAD-M substrates are moved to the cytoplasm as part of the normal ERAD pathway, where they are part of a solely proteinaceous complex. Using proteomics and direct biochemical confirmation, we found that Cdc48 serves as a critical "retrochaperone" for these ERAD-M substrates. Cdc48 binding to retrotranslocated, ubiquitinated ERAD-M substrates is required for their solubility; removal of the polyubiquitin chains or competition for binding by addition of free polyubiquitin liberated Cdc48 from retrotranslocated proteins and rendered them insoluble. All components of the canonical Cdc48 complex Cdc48-Npl4-Ufd1 were present in solubilized ERAD-M substrates. This function of the complex was observed for both HRD and DOA pathway substrates. Thus, in addition to the long known ATP-dependent extraction of ERAD substrates during retrotranslocation, the Cdc48 complex is generally and critically needed for the solubility of retrotranslocated ERAD-M intermediates. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Synthesis, spectroscopic characterization, first order nonlinear optical properties and DFT calculations of novel Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) complexes with 1,3-diphenyl-4-phenylazo-5-pyrazolone ligand

NASA Astrophysics Data System (ADS)

Abdel-Latif, Samir A.; Mohamed, Adel A.

2018-02-01

Novel Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) metal ions with 1,3-diphenyl-4-phenylazo-5-pyrazolone (L) have been prepared and characterized using different analytical and spectroscopic techniques. 1:1 Complexes of Mn(II), Co(II) and Zn(II) are distorted octahedral whereas Ni(II) complex is square planar and Cu(II) is distorted trigonal bipyramid. 1:2 Complexes of Mn(II), Co(II), Cu(II) and Zn(II) are distorted trigonal bipyramid whereas Ni(II) complex is distorted tetrahedral. All complexes behave as non-ionic in dimethyl formamide (DMF). The electronic structure and nonlinear optical parameters (NLO) of the complexes were investigated theoretically at the B3LYP/GEN level of theory. Molecular stability and bond strengths have been investigated by applying natural bond orbital (NBO) analysis. The geometries of the studied complexes are non-planner. DFT calculations have been also carried out to calculate the global properties; hardness (η), global softness (S) and electronegativity (χ). The calculated small energy gap between HOMO and LUMO energies shows that the charge transfer occurs within the complexes. The total static dipole moment (μtot), the mean polarizability (<α>), the anisotropy of the polarizability (Δα) and the mean first-order hyperpolarizability (<β>) were calculated and compared with urea as a reference material. The complexes show implying optical properties.

Computational (DFT) and Experimental (EXAFS) Study of the Interaction of [Ir(IMes)(H)2 (L)3 ] with Substrates and Co-substrates Relevant for SABRE in Dilute Systems.

PubMed

van Weerdenburg, Bram J A; Engwerda, Anthonius H J; Eshuis, Nan; Longo, Alessandro; Banerjee, Dipanjan; Tessari, Marco; Guerra, Célia Fonseca; Rutjes, Floris P J T; Bickelhaupt, F Matthias; Feiters, Martin C

2015-07-13

Signal amplification by reversible exchange (SABRE) is an emerging hyperpolarization method in NMR spectroscopy, in which hyperpolarization is transferred through the scalar coupling network of para-hydrogen derived hydrides in a metal complex to a reversibly bound substrate. Substrates can even be hyperpolarized at concentrations below that of the metal complex by addition of a suitable co-substrate. Here we investigate the catalytic system used for trace detection in NMR spectroscopy with [Ir(IMes)(H)2 (L)3 ](+) (IMes=1,3-dimesitylimidazol-2-ylidene) as catalyst, pyridine as a substrate and 1-methyl-1,2,3-triazole as co-substrate in great detail. With density functional theory (DFT), validated by extended X-ray absorption fine structure (EXAFS) experiments, we provide explanations for the relative abundance of the observed metal complexes, as well as their contribution to SABRE. We have established that the interaction between iridium and ligands cis to IMes is weaker than that with the trans ligand, and that in mixed complexes with pyridine and triazole, the latter preferentially takes up the trans position. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coupling Oxygen Consumption with Hydrocarbon Oxidation in Bacterial Multicomponent Monooxygenases.

PubMed

Wang, Weixue; Liang, Alexandria D; Lippard, Stephen J

2015-09-15

A fundamental goal in catalysis is the coupling of multiple reactions to yield a desired product. Enzymes have evolved elegant approaches to address this grand challenge. A salient example is the biological conversion of methane to methanol catalyzed by soluble methane monooxygenase (sMMO), a member of the bacterial multicomponent monooxygenase (BMM) superfamily. sMMO is a dynamic protein complex of three components: a hydroxylase, a reductase, and a regulatory protein. The active site, a carboxylate-rich non-heme diiron center, is buried inside the 251 kDa hydroxylase component. The enzyme processes four substrates: O2, protons, electrons, and methane. To couple O2 activation to methane oxidation, timely control of substrate access to the active site is critical. Recent studies of sMMO, as well as its homologues in the BMM superfamily, have begun to unravel the mechanism. The emerging and unifying picture reveals that each substrate gains access to the active site along a specific pathway through the hydroxylase. Electrons and protons are delivered via a three-amino-acid pore located adjacent to the diiron center; O2 migrates via a series of hydrophobic cavities; and hydrocarbon substrates reach the active site through a channel or linked set of cavities. The gating of these pathways mediates entry of each substrate to the diiron active site in a timed sequence and is coordinated by dynamic interactions with the other component proteins. The result is coupling of dioxygen consumption with hydrocarbon oxidation, avoiding unproductive oxidation of the reductant rather than the desired hydrocarbon. To initiate catalysis, the reductase delivers two electrons to the diiron(III) center by binding over the pore of the hydroxylase. The regulatory component then displaces the reductase, docking onto the same surface of the hydroxylase. Formation of the hydroxylase-regulatory component complex (i) induces conformational changes of pore residues that may bring protons to the active site; (ii) connects hydrophobic cavities in the hydroxylase leading from the exterior to the diiron active site, providing a pathway for O2 and methane, in the case of sMMO, to the reduced diiron center for O2 activation and substrate hydroxylation; (iii) closes the pore, as well as a channel in the case of four-component BMM enzymes, restricting proton access to the diiron center during formation of "Fe2O2" intermediates required for hydrocarbon oxidation; and (iv) inhibits undesired electron transfer to the Fe2O2 intermediates by blocking reductase binding during O2 activation. This mechanism is quite different from that adopted by cytochromes P450, a large class of heme-containing monooxygenases that catalyze reactions very similar to those catalyzed by the BMM enzymes. Understanding the timed enzyme control of substrate access has implications for designing artificial catalysts. To achieve multiple turnovers and tight coupling, synthetic models must also control substrate access, a major challenge considering that nature requires large, multimeric, dynamic protein complexes to accomplish this feat.

A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II.

PubMed

Parua, Pabitra K; Booth, Gregory T; Sansó, Miriam; Benjamin, Bradley; Tanny, Jason C; Lis, John T; Fisher, Robert P

2018-06-13

The end of the RNA polymerase II (Pol II) transcription cycle is strictly regulated to prevent interference between neighbouring genes and to safeguard transcriptome integrity 1 . The accumulation of Pol II downstream of the cleavage and polyadenylation signal can facilitate the recruitment of factors involved in mRNA 3'-end formation and termination 2 , but how this sequence is initiated remains unclear. In a chemical-genetic screen, human protein phosphatase 1 (PP1) isoforms were identified as substrates of positive transcription elongation factor b (P-TEFb), also known as the cyclin-dependent kinase 9 (Cdk9)-cyclin T1 (CycT1) complex 3 . Here we show that Cdk9 and PP1 govern phosphorylation of the conserved elongation factor Spt5 in the fission yeast Schizosaccharomyces pombe. Cdk9 phosphorylates both Spt5 and a negative regulatory site on the PP1 isoform Dis2 4 . Sites targeted by Cdk9 in the Spt5 carboxy-terminal domain can be dephosphorylated by Dis2 in vitro, and dis2 mutations retard Spt5 dephosphorylation after inhibition of Cdk9 in vivo. Chromatin immunoprecipitation and sequencing analysis indicates that Spt5 is dephosphorylated as transcription complexes traverse the cleavage and polyadenylation signal, concomitant with the accumulation of Pol II phosphorylated at residue Ser2 of the carboxy-terminal domain consensus heptad repeat 5 . A conditionally lethal Dis2-inactivating mutation attenuates the drop in Spt5 phosphorylation on chromatin, promotes transcription beyond the normal termination zone (as detected by precision run-on transcription and sequencing 6 ) and is genetically suppressed by the ablation of Cdk9 target sites in Spt5. These results suggest that the transition of Pol II from elongation to termination coincides with a Dis2-dependent reversal of Cdk9 signalling-a switch that is analogous to a Cdk1-PP1 circuit that controls mitotic progression 4 .

Surface Electrochemical Modification of a Nickel Substrate to Prepare a NiFe-based Electrode for Water Oxidation.

PubMed

Guo, Dingyi; Qi, Jing; Zhang, Wei; Cao, Rui

2017-01-20

The slow kinetics of water oxidation greatly jeopardizes the efficiency of water electrolysis for H 2 production. Developing highly active water oxidation electrodes with affordable fabrication costs is thus of great importance. Herein, a Ni II Fe III surface species on Ni metal substrate was generated by electrochemical modification of Ni in a ferrous solution by a fast, simple, and cost-effective procedure. In the prepared Ni II Fe III catalyst film, Fe III was incorporated uniformly through controlled oxidation of Fe II cations on the electrode surface. The catalytically active Ni II originated from the Ni foam substrate, which ensured the close contact between the catalyst and the support toward improved charge-transfer efficiency. The as-prepared electrode exhibited high activity and long-term stability for electrocatalytic water oxidation. The overpotentials required to reach water oxidation current densities of 50, 100, and 500 mA cm -2 are 276, 290, and 329 mV, respectively. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Novel Bioinformatics-Based Approach for Proteomic Biomarkers Prediction of Calpain-2 & Caspase-3 Protease Fragmentation: Application to βII-Spectrin Protein

NASA Astrophysics Data System (ADS)

El-Assaad, Atlal; Dawy, Zaher; Nemer, Georges; Kobeissy, Firas

2017-01-01

The crucial biological role of proteases has been visible with the development of degradomics discipline involved in the determination of the proteases/substrates resulting in breakdown-products (BDPs) that can be utilized as putative biomarkers associated with different biological-clinical significance. In the field of cancer biology, matrix metalloproteinases (MMPs) have shown to result in MMPs-generated protein BDPs that are indicative of malignant growth in cancer, while in the field of neural injury, calpain-2 and caspase-3 proteases generate BDPs fragments that are indicative of different neural cell death mechanisms in different injury scenarios. Advanced proteomic techniques have shown a remarkable progress in identifying these BDPs experimentally. In this work, we present a bioinformatics-based prediction method that identifies protease-associated BDPs with high precision and efficiency. The method utilizes state-of-the-art sequence matching and alignment algorithms. It starts by locating consensus sequence occurrences and their variants in any set of protein substrates, generating all fragments resulting from cleavage. The complexity exists in space O(mn) as well as in O(Nmn) time, where N, m, and n are the number of protein sequences, length of the consensus sequence, and length per protein sequence, respectively. Finally, the proposed methodology is validated against βII-spectrin protein, a brain injury validated biomarker.

Structural, spectroscopic and thermal characterization of 2-tert-butylaminomethylpyridine-6-carboxylic acid methylester and its Fe(III), Co(II), Ni(II), Cu(II), Zn(II) and UO(2)(II) complexes.

PubMed

Mohamed, Gehad G; El-Gamel, Nadia E A

2005-04-01

Fe(III), Co(II), Ni(II), Cu(II), Zn(II) and UO(2)(II) complexes with the ligand 2-tert-butylaminomethylpyridine-6-carboxylic acid methylester (HL(2)) have been prepared and characterized by elemental analyses, molar conductance, magnetic moment, thermal analysis and spectral data. 1:1 M:HL(2) complexes, with the general formula [M(HL(2))X(2)].nH(2)O (where M = Co(II) (X = Cl, n = 0), Ni(II) (X = Cl, n = 3), Cu(II) (grey colour, X = AcO, n = 1), Cu(II) (yellow colour, X = Cl, n = 0) and Zn(II) (X = Br, n = 0). In addition, the Fe(III) and UO(2)(II) complexes of the type 1:2 M:HL(2) and with the formulae [Fe(L(2))(2)]Cl and [UO(2)(HL(2))(2)](NO(3))(2) are prepared. From the IR data, it is seen that HL(2) ligand behaves as a terdentate ligand coordinated to the metal ions via the pyridyl N, carboxylate O and protonated NH group; except the Fe(III) complex, it coordinates via the deprotonated NH group. This is supported by the molar conductance data, which show that all the complexes are non-electrolytes, while the Fe(III) and UO(2)(II) complexes are 1:1 electrolytes. IR and H1-NMR spectral studies suggest a similar behaviour of the Zn(II) complex in solid and solution states. From the solid reflectance spectral data and magnetic moment measurements, the complexes have a trigonal bipyramidal (Co(II), Ni(II), Cu(II) and Zn(II) complexes) and octahedral (Fe(III), UO(2)(II) complexes) geometrical structures. The thermal behaviour of the complexes is studied and the different dynamic parameters are calculated applying Coats-Redfern equation.

Steric and Electronic Influence on Proton-Coupled Electron-Transfer Reactivity of a Mononuclear Mn(III)-Hydroxo Complex.

PubMed

Rice, Derek B; Wijeratne, Gayan B; Burr, Andrew D; Parham, Joshua D; Day, Victor W; Jackson, Timothy A

2016-08-15

A mononuclear hydroxomanganese(III) complex was synthesized utilizing the N5 amide-containing ligand 2-[bis(pyridin-2-ylmethyl)]amino-N-2-methyl-quinolin-8-yl-acetamidate (dpaq(2Me) ). This complex is similar to previously reported [Mn(III)(OH)(dpaq(H))](+) [Inorg. Chem. 2014, 53, 7622-7634] but contains a methyl group adjacent to the hydroxo moiety. This α-methylquinoline group in [Mn(III)(OH)(dpaq(2Me))](+) gives rise to a 0.1 Å elongation in the Mn-N(quinoline) distance relative to [Mn(III)(OH)(dpaq(H))](+). Similar bond elongation is observed in the corresponding Mn(II) complex. In MeCN, [Mn(III)(OH)(dpaq(2Me))](+) reacts rapidly with 2,2',6,6'-tetramethylpiperidine-1-ol (TEMPOH) at -35 °C by a concerted proton-electron transfer (CPET) mechanism (second-order rate constant k2 of 3.9(3) M(-1) s(-1)). Using enthalpies and entropies of activation from variable-temperature studies of TEMPOH oxidation by [Mn(III)(OH)(dpaq(2Me))](+) (ΔH(‡) = 5.7(3) kcal(-1) M(-1); ΔS(‡) = -41(1) cal M(-1) K(-1)), it was determined that [Mn(III)(OH)(dpaq(2Me))](+) oxidizes TEMPOH ∼240 times faster than [Mn(III)(OH)(dpaq(H))](+). The [Mn(III)(OH)(dpaq(2Me))](+) complex is also capable of oxidizing the stronger O-H and C-H bonds of 2,4,6-tri-tert-butylphenol and xanthene, respectively. However, for these reactions [Mn(III)(OH)(dpaq(2Me))](+) displays, at best, modest rate enhancement relative to [Mn(III)(OH)(dpaq(H))](+). A combination of density function theory (DFT) and cyclic voltammetry studies establish an increase in the Mn(III)/Mn(II) reduction potential of [Mn(III)(OH)(dpaq(2Me))](+) relative to [Mn(III)(OH)(dpaq(H))](+), which gives rise to a larger driving force for CPET for the former complex. Thus, more favorable thermodynamics for [Mn(III)(OH)(dpaq(2Me))](+) can account for the dramatic increase in rate with TEMPOH. For the more sterically encumbered substrates, DFT computations suggest that this effect is mitigated by unfavorable steric interactions between the substrate and the α-methylquinoline group of the dpaq(2Me) ligand. The DFT calculations, which reproduce the experimental activation free energies quite well, provide the first examination of the transition-state structure of mononuclear Mn(III)(OH) species during a CPET reaction.

Effect of chronic pre-treatment with angiotensin converting enzyme inhibition on skeletal muscle mitochondrial recovery after ischemia/reperfusion.

PubMed

Thaveau, Fabien; Zoll, Joffrey; Bouitbir, Jamal; N'guessan, Benoît; Plobner, Philippe; Chakfe, Nabil; Kretz, Jean-Georges; Richard, Ruddy; Piquard, François; Geny, Bernard

2010-06-01

Impaired skeletal muscle energetic participates in peripheral arterial disease (PAD) patient's morbidity and mortality. Angiotensin converting enzyme inhibition (ACEi), cornerstone for pharmacologic risk factor management in PAD patients, might also be interesting by protecting skeletal muscle energetic. We therefore determined whether chronic ACEi might reduce ischemia-induced mitochondrial respiratory chain dysfunction in the frequent setting of hindlimb ischemia-reperfusion. Ischemic legs of rats submitted to 5 h ischemia induced by a rubber band tourniquet applied on the root of the hindlimb followed by reperfusion without (IR, n = 11) or after ACEi (n = 14; captopril 40 mg/kg per day during 28 days before surgery) were studied and compared to that of sham-operated animals (n = 11). The effect of ACEi on the non-ischemic contralateral leg was also determined in the ACEi group. Maximal oxidative capacities (V(max)) and complexes I, II and IV activities of the mitochondrial respiratory chain of the gastrocnemius muscle were determined using glutamate-malate, succinate and TMPD-ascorbate substrates. Arterial blood pressure was significantly decreased after ACEi (124 +/- 2.8 vs. 108 +/- 4.19 mmHg; P = 0.01). Ischemia-reperfusion reduced V(max) (4.4 +/- 0.4 vs. 8.7 +/- 0.5 micromol O2/min/g dry weight, -49%, P < 0.001), affecting mitochondrial complexes I, II and IV activities. ACEi failed to modulate ischemia-induced dysfunction (V(max) 5.1 +/- 0.7 micromol O2/min/g dry weight) or the non-ischemic contralateral muscle respiratory rate. Ischemia-reperfusion significantly impaired the mitochondrial respiratory chain I, II and IV complexes of skeletal muscle. Pharmacologic pre-treatment with ACEi did not prevent or increase such alterations. Further studies might be useful to improve the pharmacologic conditioning of PAD patients needing arterial revascularization.

The O2-Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data.

PubMed

Askerka, Mikhail; Brudvig, Gary W; Batista, Victor S

2017-01-17

Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn 4 O 5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage "S" states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves through the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O 2 evolution. The structure of the dark-stable S 1 state has been a target for X-ray crystallography for the past 15 years. However, traditional X-ray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S 1 state. However, the atom positions in this crystal structure are still not consistent with high-resolution EXAFS spectroscopy, partially due to the poorly resolved oxygen positions next to Mn centers and partial reduction due to extended dark adaptation of the sample. These inconsistencies led to the new models of the OEC with an alternative low oxidation state and raised questions on the protonation state of the cluster, especially the O5 μ-oxo bridge. This Account summarizes the most recent models of the OEC that emerged from QM/MM, EXAFS and femtosecond X-ray crystallography methods. When PSII in the S 1 state is exposed to light, the S 1 state is advanced to the higher oxidation states and eventually binds substrate water molecules. Identifying the substrate waters is of paramount importance for establishing the water-oxidation mechanism but is complicated by a large number of spectroscopically similar waters. Water analogues can, therefore, be helpful because they serve as spectroscopic markers that help to track the motion of the substrate waters. Due to a close structural and electronic similarity to water, ammonia has been of particular interest. We review three competing hypotheses on substrate water/ammonia binding and compile theoretical and experimental evidence to support them. Binding of ammonia as a sixth ligand to Mn4 during the S 1 → S 2 transition seems to satisfy most of the criteria, especially the most compelling recent EPR data on D1-D61A mutated PSII. Such a binding mode suggests delivery of water from the "narrow" channel through a "carousel" rearrangement of waters around Mn4 upon the S 2 → S 3 transition. An alternative hypothesis suggests water delivery through the "large" channel on the Ca side. However, both water delivery paths lead to a similar S 3 structure, seemingly reaching consensus on the nature of the last detectable S-state intermediate in the Kok cycle before O 2 evolution.

The O 2 -Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data

DOE PAGES

Askerka, Mikhail; Brudvig, Gary W.; Batista, Victor S.

2016-12-21

Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn 4O 5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage “S” states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves throughmore » the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/ MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O 2 evolution. The structure of the dark-stable S1 state has been a target for X-ray crystallography for the past 15 years. However, traditional Xray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S 1 state. However, the atom positions in this crystal structure are still not consistent with high-resolution EXAFS spectroscopy, partially due to the poorly resolved oxygen positions next to Mn centers and partial reduction due to extended dark adaptation of the sample. These inconsistencies led to the new models of the OEC with an alternative low oxidation state and raised questions on the protonation state of the cluster, especially the O5 μ-oxo bridge. This Account summarizes the most recent models of the OEC that emerged from QM/MM, EXAFS and femtosecond X-ray crystallography methods. When PSII in the S 1 state is exposed to light, the S 1 state is advanced to the higher oxidation states and eventually binds substrate water molecules. Identifying the substrate waters is of paramount importance for establishing the water-oxidation mechanism but is complicated by a large number of spectroscopically similar waters. Water analogues can, therefore, be helpful because they serve as spectroscopic markers that help to track the motion of the substrate waters. Due to a close structural and electronic similarity to water, ammonia has been of particular interest. We review three competing hypotheses on substrate water/ammonia binding and compile theoretical and experimental evidence to support them. Binding of ammonia as a sixth ligand to Mn4 during the S 1 → S 2 transition seems to satisfy most of the criteria, especially the most compelling recent EPR data on D1-D61A mutated PSII. Such a binding mode suggests delivery of water from the “narrow” channel through a “carousel” rearrangement of waters around Mn4 upon the S 2 → S 3 transition. An alternative hypothesis suggests water delivery through the “large” channel on the Ca side. However, both water delivery paths lead to a similar S 3 structure, seemingly reaching consensus on the nature of the last detectable S-state intermediate in the Kok cycle before O 2 evolution.« less

The O 2 -Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Askerka, Mikhail; Brudvig, Gary W.; Batista, Victor S.

Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn 4O 5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage “S” states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves throughmore » the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/ MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O 2 evolution. The structure of the dark-stable S1 state has been a target for X-ray crystallography for the past 15 years. However, traditional Xray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S 1 state. However, the atom positions in this crystal structure are still not consistent with high-resolution EXAFS spectroscopy, partially due to the poorly resolved oxygen positions next to Mn centers and partial reduction due to extended dark adaptation of the sample. These inconsistencies led to the new models of the OEC with an alternative low oxidation state and raised questions on the protonation state of the cluster, especially the O5 μ-oxo bridge. This Account summarizes the most recent models of the OEC that emerged from QM/MM, EXAFS and femtosecond X-ray crystallography methods. When PSII in the S 1 state is exposed to light, the S 1 state is advanced to the higher oxidation states and eventually binds substrate water molecules. Identifying the substrate waters is of paramount importance for establishing the water-oxidation mechanism but is complicated by a large number of spectroscopically similar waters. Water analogues can, therefore, be helpful because they serve as spectroscopic markers that help to track the motion of the substrate waters. Due to a close structural and electronic similarity to water, ammonia has been of particular interest. We review three competing hypotheses on substrate water/ammonia binding and compile theoretical and experimental evidence to support them. Binding of ammonia as a sixth ligand to Mn4 during the S 1 → S 2 transition seems to satisfy most of the criteria, especially the most compelling recent EPR data on D1-D61A mutated PSII. Such a binding mode suggests delivery of water from the “narrow” channel through a “carousel” rearrangement of waters around Mn4 upon the S 2 → S 3 transition. An alternative hypothesis suggests water delivery through the “large” channel on the Ca side. However, both water delivery paths lead to a similar S 3 structure, seemingly reaching consensus on the nature of the last detectable S-state intermediate in the Kok cycle before O 2 evolution.« less

Ammonia release method for depositing metal oxides

DOEpatents

Silver, G.L.; Martin, F.S.

1994-12-13

A method is described for depositing metal oxides on substrates which is indifferent to the electrochemical properties of the substrates and which comprises forming ammine complexes containing metal ions and thereafter effecting removal of ammonia from the ammine complexes so as to permit slow precipitation and deposition of metal oxide on the substrates. 1 figure.

Open-ended half-mode substrate integrated waveguide sensor with ground flange for complex permittivity measurement

USDA-ARS?s Scientific Manuscript database

A novel open-ended half-mode substrate integrated waveguide (HMSIW) sensor with ground flange for measuring complex permittivity of liquids, semisolids, and granular and particulate materials is presented. The open-ended HMSIW is designed and fabricated on FR4 substrate. The ground flange was custo...

DICER-ARGONAUTE2 Complex in Continuous Fluorogenic Assays of RNA Interference Enzymes

PubMed Central

Bernard, Mark A.; Wang, Leyu; Tachado, Souvenir D.

2015-01-01

Mechanistic studies of RNA processing in the RNA-Induced Silencing Complex (RISC) have been hindered by lack of methods for continuous monitoring of enzymatic activity. “Quencherless” fluorogenic substrates of RNAi enzymes enable continuous monitoring of enzymatic reactions for detailed kinetics studies. Recombinant RISC enzymes cleave the fluorogenic substrates targeting human thymidylate synthase (TYMS) and hypoxia-inducible factor 1-α subunit (HIF1A). Using fluorogenic dsRNA DICER substrates and fluorogenic siRNA, DICER+ARGONAUTE2 mixtures exhibit synergistic enzymatic activity relative to either enzyme alone, and addition of TRBP does not enhance the apparent activity. Titration of AGO2 and DICER in enzyme assays suggests that AGO2 and DICER form a functional high-affinity complex in equimolar ratio. DICER and DICER+AGO2 exhibit Michaelis-Menten kinetics with DICER substrates. However, AGO2 cannot process the fluorogenic siRNA without DICER enzyme, suggesting that AGO2 cannot self-load siRNA into its active site. The DICER+AGO2 combination processes the fluorogenic siRNA substrate (K m=74 nM) with substrate inhibition kinetics (K i=105 nM), demonstrating experimentally that siRNA binds two different sites that affect Dicing and AGO2-loading reactions in RISC. This result suggests that siRNA (product of DICER) bound in the active site of DICER may undergo direct transfer (as AGO2 substrate) to the active site of AGO2 in the DICER+AGO2 complex. Competitive substrate assays indicate that DICER+AGO2 cleavage of fluorogenic siRNA is specific, since unlabeled siRNA and DICER substrates serve as competing substrates that cause a concentration-dependent decrease in fluorescent rates. Competitive substrate assays of a series of DICER substrates in vitro were correlated with cell-based assays of HIF1A mRNA knockdown (log-log slope=0.29), suggesting that improved DICER substrate designs with 10-fold greater processing by the DICER+AGO2 complex can provide a strong (~2800-fold) improvement in potency for mRNA knockdown. This study lays the foundation of a systematic biochemical approach to optimize nucleic acid-based therapeutics for Dicing and ARGONAUTE2-loading for improving efficacy. PMID:25793518

Comparison of different substrates for laser-induced electron transfer desorption/ionization of metal complexes

NASA Astrophysics Data System (ADS)

Grechnikov, A. A.; Georgieva, V. B.; Donkov, N.; Borodkov, A. S.; Pento, A. V.; Raicheva, Z. G.; Yordanov, Tc A.

2016-03-01

Four different substrates, namely, graphite, tungsten, amorphous silicon (α-Si) and titanium dioxide (TiO2) films, were compared in view of the laser-induced electron transfer desorption/ionization (LETDI) of metal coordination complexes. A rhenium complex with 8-mercaptoquinoline, a copper complex with diphenylthiocarbazone and chlorophyll A were studied as the test analytes. The dependencies of the ion yield and the surface temperature on the incident radiation fluence were investigated experimentally and theoretically. The temperature was estimated using the numerical solution of a one-dimensional heat conduction problem with a heat source distributed in time and space. It was found that at the same temperature, the ion yield from the different substrates varies in the range of three orders of magnitude. The direct comparison of all studied substrates revealed that LETDI from the TiO2 and α-Si films offer a better choice for producing molecular ions of metal coordination complexes.

Nano transfer and nanoreplication using deterministically grown sacrificial nanotemplates

DOEpatents

Melechko, Anatoli V [Oak Ridge, TN; McKnight, Timothy E [Greenback, TN; Guillorn, Michael A [Ithaca, NY; Ilic, Bojan [Ithaca, NY; Merkulov, Vladimir I [Knoxville, TX; Doktycz, Mitchel J [Knoxville, TN; Lowndes, Douglas H [Knoxville, TN; Simpson, Michael L [Knoxville, TN

2012-03-27

Methods, manufactures, machines and compositions are described for nanotransfer and nanoreplication using deterministically grown sacrificial nanotemplates. An apparatus, includes a substrate and a nanoconduit material coupled to a surface of the substrate. The substrate defines an aperture and the nanoconduit material defines a nanoconduit that is i) contiguous with the aperture and ii) aligned substantially non-parallel to a plane defined by the surface of the substrate.

Controlled Acceleration and Inhibition of Bergman Cyclization by Metal Chlorides

NASA Astrophysics Data System (ADS)

Warner, Benjamin P.; Millar, Susan P.; Broene, Richard D.; Buchwald, Stephen L.

1995-08-01

The Bergman cyclization has been the subject of renewed interest with the discovery of naturally occurring enediyne-based antitumor agents that cleave DNA by means of an aromatic diradical. These natural substrates have a means to trigger this cycloaromatization process. Control of this reaction by substrate modification would allow aromatic diradicals to be generated selectively. In the studies presented here it is disclosed that the Bergman cyclization of 1,2-bis(diphenyl phosphinoethynyl)benzene was accelerated by a factor of >30,000 by the addition of palladium(II) chloride or platinum(II) chloride and was inhibited by the addition of mercury(II) chloride.

Characterization and Reactivity of a Terminal Nickel(III)-Oxygen Adduct

PubMed Central

Pirovano, Paolo; Farquhar, Erik R.; Swart, Marcel; Fitzpatrick, Anthony J.; Morgan, Grace G.; McDonald, Aidan R.

2015-01-01

High-valent terminal metal-oxygen adducts are hypothesized to be the potent oxidising reactants in late transition metal oxidation catalysis. In particular, examples of high-valent terminal nickel-oxygen adducts are sparse, meaning there is a dearth in the understanding of such oxidants. In this study, a monoanionic NiII-bicarbonate complex was found to react in a 1:1 ratio with the one-electron oxidant tris(4-bromophenyl)ammoniumyl hexachloroantimonate, yielding a thermally unstable intermediate in high yield (~95%). Electronic absorption, electronic paramagnetic resonance and X-ray absorption spectroscopies and density functional theory calculations confirm its description as a low-spin (S = ½), square planar NiIII-oxygen adduct. This rare example of a high-valent terminal nickel-oxygen complex performs oxidations of organic substrates, including 2,6-ditertbutylphenol and triphenylphosphine, which are indicative of hydrogen atom abstraction and oxygen atom transfer reactivity, respectively. PMID:25612563

Trapping of the Enoyl-Acyl Carrier Protein Reductase–Acyl Carrier Protein Interaction

PubMed Central

Tallorin, Lorillee; Finzel, Kara; Nguyen, Quynh G.; Beld, Joris; La Clair, James J.; Burkart, Michael D.

2016-01-01

An ideal target for metabolic engineering, fatty acid biosynthesis remains poorly understood on a molecular level. These carrier protein-dependent pathways require fundamental protein–protein interactions to guide reactivity and processivity, and their control has become one of the major hurdles in successfully adapting these biological machines. Our laboratory has developed methods to prepare acyl carrier proteins (ACPs) loaded with substrate mimetics and cross-linkers to visualize and trap interactions with partner enzymes, and we continue to expand the tools for studying these pathways. We now describe application of the slow-onset, tight-binding inhibitor triclosan to explore the interactions between the type II fatty acid ACP from Escherichia coli, AcpP, and its corresponding enoyl-ACP reductase, FabI. We show that the AcpP–triclosan complex demonstrates nM binding, inhibits in vitro activity, and can be used to isolate FabI in complex proteomes. PMID:26938266

Characterization and Reactivity of a Terminal Nickel(III)-Oxygen Adduct

DOE PAGES

Pirovano, Paolo; Farquhar, Erik R.; Swart, Marcel; ...

2015-01-22

Here, high-valent terminal metal–oxygen adducts are hypothesized to be the potent oxidizing reactants in late transition metal oxidation catalysis. In particular, examples of high-valent terminal nickel–oxygen adducts are scarce, meaning there is a dearth in the understanding of such oxidants. A monoanionic Ni II-bicarbonate complex has been found to react in a 1:1 ratio with the one-electron oxidant tris(4-bromophenyl)ammoniumyl hexachloroantimonate, yielding a thermally unstable intermediate in high yield (ca. 95%). Electronic absorption, electronic paramagnetic resonance, and X-ray absorption spectroscopies and density functional theory calculations confirm its description as a low-spin (S=1/2), square planar Ni III–oxygen adduct. Moreover, this rare examplemore » of a high-valent terminal nickel–oxygen complex performs oxidations of organic substrates, including 2,6-di-tert-butylphenol and triphenylphosphine, which are indicative of hydrogen atom abstraction and oxygen atom transfer reactivity, respectively.« less

An Iron(II)(1,3-bis(2'-pyridylimino)isoindoline) Complex as a Catalyst for Substrate Oxidation with H2O2. Evidence for a Transient Peroxodiiron(III) Species.

PubMed

Pap, József S; Cranswick, Matthew A; Balogh-Hergovich, E; Baráth, Gábor; Giorgi, Michel; Rohde, Gregory T; Kaizer, József; Speier, Gábor; Que, Lawrence

2013-08-01

The complex [Fe(indH)(solvent) 3 ](ClO 4 ) 2 ( 1 ) has been isolated from the reaction of equimolar amounts of 1,3-bis(2'-pyridylimino)isoindoline (indH) and Fe(ClO 4 ) 2 in acetonitrile and characterized by X-ray crystallography and several spectroscopic techniques. It is a suitable catalyst for the oxidation of thioanisoles and benzyl alcohols with H 2 O 2 as the oxidant. Hammett correlations and kinetic isotope effect experiments support the involvement of an electrophilic metal-based oxidant. A metastable green species ( 2 ) is observed when 1 is reacted with H 2 O 2 at -40 °C, which has been characterized to have a Fe III ( μ -O)( μ -O 2 )Fe III core on the basis of UV-Vis, electron paramagnetic resonance, resonance Raman, and X-ray absorption spectroscopic data.

Human and rat liver phenol sulfotransferase: structure-activity relationships for phenolic substrates.

PubMed

Campbell, N R; Van Loon, J A; Sundaram, R S; Ames, M M; Hansch, C; Weinshilboum, R

1987-12-01

Phenol sulfotransferase (PST) catalyzes the sulfate conjugation of many phenolic drugs. Human liver contains thermostable (TS) and thermolabile forms of PST. Ion exchange chromatography shows that two isozymes of TS PST (peaks I and II) are present in human liver preparations. Rat liver contains four forms of PST that can be separated by ion exchange chromatography. Quantitative structure-activity relationship (QSAR) analysis was used to study phenolic substrates for both human and rat liver PST. Thirty-six substituted phenols were tested as substrates for partially purified human liver TS PST peak I. QSAR analysis resulted in derivation of the following equation: log 1/Km = 0.92 (+/- 0.18)log P - 1.48 (+/- 0.38)MR'4 - 0.64 (+/- 0.41)MR3 + 1.04 (+/- 0.63)MR2 + 0.67(+/- 0.44) sigma- + 4.03 (+/- 0.42). In this equation Km is the Michaelis constant, P is the octanol-water partition coefficient, MR is the molar refractivity of substituents at the 2-, 3-, and 4-positions, and sigma- is the Hammett constant. Values of log 1/Km calculated with this equation were highly correlated with log 1/Km values (r = 0.950) that were observed experimentally. Nine phenols were also tested as substrates for partially purified human liver TS PST peak II. Log 1/Km values for these compounds were significantly correlated for the two isozymes of TS PST (r = 0.992, p less than 0.001). QSAR analysis was also used to derive equations that described the behavior of phenolic substrates for rat liver PST forms I and II. These equations differed substantially from the equation derived for compounds tested with human liver TS PST peak I. Therefore, the characteristics of the active sites of human liver TS PST peak I and rat liver PST forms I and II appear to differ. Application of these equations may make it possible to predict Km values of phenolic substrates for human liver TS PST and for rat liver PST forms I and II.

Angiotensin-converting enzyme: I. New strategies for assay

PubMed Central

Ryan, James W.; Chung, Alfred; Ryan, Una S.

1980-01-01

The disposition of converting enzyme (kininase II) on the luminal surface of pulmonary endothelial cells is well established. Further, it is known that there is a net conversion of angiotensin I into angiotensin II as blood passes through the lungs. However, little is known about modulations of converting enzyme activity that may arise through, e.g., changes in the quality of inhalants, blood flow, or blood oxygenation. There are few data on the effects of lung disease. A major barrier to studies to examine for pathophysiologic modulations of converting enzyme is that of assay. The enzyme can be measured in terms of the rate of formation of angiotensin II from a known quantity of angiotensin I. However, both peptides are biologically active, and lungs contain other enzymes capable of degrading them. We have developed a series of radiolabeled, acylated tripeptides to improve our ability to examine for changes in the net converting enzyme of intact lungs. The enzyme, a dipeptidyl carboxypeptidase, is capable of removing C-terminal dipeptides from a variety of oligopeptides. We have prepared benzoyl-Gly-Gly-Gly (I), benzoyl-Pro-Phe-Arg (II), benzoyl-Gly-His-Leu (III), benzoyl-Phe-Ala-Pro (IV), and benzoyl-Phe-His-Leu (V), each containing a 3H-atom in the para position of the benzoyl moiety. Substrates I and III have been used previously in photometric assays of low sensitivity. II is the acylated C-terminal tripeptide of bradykinin, IV is an acylated tripeptide analog of BPP5a (

Synthesis, characterization and molecular modeling of some transition metal complexes of Schiff base derived from 5-aminouracil and 2-benzoyl pyridine

NASA Astrophysics Data System (ADS)

Abdel-Monem, Yasser K.; Abouel-Enein, Saeyda A.; El-Seady, Safa M.

2018-01-01

Multidentate Schiff base (H2L) ligand results from condensation of 5-aminouracil and 2-benzoyl pyridine and its metal chloride (Mn(II), Co(II), Ni(II), Cu(II), Zn(II), Pd(II), Fe(III), Cr(III), Ru(III), Zr(IV) and Hf(IV)) complexes were prepared. The structural features of the ligand and its metal complexes were confirmed by elemental analyses, spectroscopic methods (IR, UV-Vis, 1H NMR, mass), magnetic moment measurements and thermal studies. The data refer to the ligand coordinates with metal ions in a neutral form and shows different modes of chelation toward the metal atom. All complexes have octahedral skeleton structure, tetrahedrally Mn(II), Ni(II), trigonalbipyramidal Co(II) and square planner Pd(II). Thermal decomposition of complexes as well as the interaction of different types of solvent of crystallization are assigned by thermogravimetric analysis. Molecular modeling of prepared complexes were investigated to study the expected anticancer activities of the prepared complexes. All metal complexes have no interaction except the complexes of Pd(II), Fe(III) and Mn(II).

An unexpected phosphate binding site in Glyceraldehyde 3-Phosphate Dehydrogenase: Crystal structures of apo, holo and ternary complex of Cryptosporidium parvum enzyme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cook, William J; Senkovich, Olga; Chattopadhyay, Debasish

2009-06-08

The structure, function and reaction mechanism of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) have been extensively studied. Based on these studies, three anion binding sites have been identified, one 'Ps' site (for binding the C-3 phosphate of the substrate) and two sites, 'Pi' and 'new Pi', for inorganic phosphate. According to the original flip-flop model, the substrate phosphate group switches from the 'Pi' to the 'Ps' site during the multistep reaction. In light of the discovery of the 'new Pi' site, a modified flip-flop mechanism, in which the C-3 phosphate of the substrate binds to the 'new Pi' site and flips tomore » the 'Ps' site before the hydride transfer, was proposed. An alternative model based on a number of structures of B. stearothermophilus GAPDH ternary complexes (non-covalent and thioacyl intermediate) proposes that in the ternary Michaelis complex the C-3 phosphate binds to the 'Ps' site and flips from the 'Ps' to the 'new Pi' site during or after the redox step. We determined the crystal structure of Cryptosporidium parvum GAPDH in the apo and holo (enzyme + NAD) state and the structure of the ternary enzyme-cofactor-substrate complex using an active site mutant enzyme. The C. parvum GAPDH complex was prepared by pre-incubating the enzyme with substrate and cofactor, thereby allowing free movement of the protein structure and substrate molecules during their initial encounter. Sulfate and phosphate ions were excluded from purification and crystallization steps. The quality of the electron density map at 2{angstrom} resolution allowed unambiguous positioning of the substrate. In three subunits of the homotetramer the C-3 phosphate group of the non-covalently bound substrate is in the 'new Pi' site. A concomitant movement of the phosphate binding loop is observed in these three subunits. In the fourth subunit the C-3 phosphate occupies an unexpected site not seen before and the phosphate binding loop remains in the substrate-free conformation. Orientation of the substrate with respect to the active site histidine and serine (in the mutant enzyme) also varies in different subunits. The structures of the C. parvum GAPDH ternary complex and other GAPDH complexes demonstrate the plasticity of the substrate binding site. We propose that the active site of GAPDH can accommodate the substrate in multiple conformations at multiple locations during the initial encounter. However, the C-3 phosphate group clearly prefers the 'new Pi' site for initial binding in the active site.« less

The Structure of Lombricine Kinase

PubMed Central

Bush, D. Jeffrey; Kirillova, Olga; Clark, Shawn A.; Davulcu, Omar; Fabiola, Felcy; Xie, Qing; Somasundaram, Thayumanasamy; Ellington, W. Ross; Chapman, Michael S.

2011-01-01

Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309–317, which is disordered in substrate-free structures of homologs and is known from the NMR of arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His178. Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates. PMID:21212263

Synthesis of Optode Thin Layer using Sol Gel Hybrid of Trietoxysiloxane monomer and 3-(Trimethoxysilyl) Propilamine with Ionophore 4-(2-Pyridilazo)-1,3-Benzenadiol (PAR)

NASA Astrophysics Data System (ADS)

Wahyuningsih, S.; Rahmawati, F.; Kamal, S.; Slamet, S.; Yunianto, M.; Rahmawati, P.; Aini, F. N.

2018-03-01

Optode (Optical sensors) is one of the modern chemical sensors in the field of analytical chemistry that has utilized of inorganic polymers. The optode based on MLCT (Metal to Ligand Charge Transfer) (or MMLL’CT, Mixing Metal-Ligand to Ligand Charge Transfer) or LMCT (Ligand to Metal Charge Transfer) phenomenons have beed generated from oktyltrietxysilane, aminopropyltrimethoxysilane and 4-(2-pyrydilazo) resorcinol (abbreviated as OTES-APTS-PAR) for Cu(II), Cr(III), Ni(II), Fe(III), Cd(II), and Zn(II) ions target. The syntheses of thin layer optode were performed by sol gel method followed by evaporation in glass substrat. The formation of 4-(2-pyrydilazo) resorcinol complexes with ions target have gained strong absorption spectras in visible region because of charge transfer phenomenons. The optical sensor of OTES-APTS-PAR was analysed thermal properties using Differential Thermal Analysis (DTA). DTA thermogram showed a glass transition peaks at a temperature of 315.5 °C. Fourier transform Infrared (FTIR) spectras have showed that the optode materials consisted NH aryl groups indicated IR absorption at 1577.7 cm-1 and also –CH aromatic at 1469.0 cm-1. Synthesized optode materials have strong broad visible absorption with the maximum wavelengths (λmax) = 405 nm and 508.5 nm, respectively. This material have excellent optical responds to several metal ions such as Cu(II), Cr(III), Ni(II), Fe(III), Cd(II), and Zn(II) that was showed from huge Δλmax and the increase of Ktotal

Synthesis, characterization and biological activity of complexes of 2-hydroxy-3,5-dimethylacetophenoneoxime (HDMAOX) with copper(II), cobalt(II), nickel(II) and palladium(II)

NASA Astrophysics Data System (ADS)

Singh, Bibhesh K.; Jetley, Umesh K.; Sharma, Rakesh K.; Garg, Bhagwan S.

2007-09-01

A new series of complexes of 2-hydroxy-3,5-dimethyl acetophenone oxime (HDMAOX) with Cu(II), Co(II), Ni(II) and Pd(II) have been prepared and characterized by different physical techniques. Infrared spectra of the complexes indicate deprotonation and coordination of the phenolic OH. It also confirms that nitrogen atom of the oximino group contributes to the complexation. Electronic spectra and magnetic susceptibility measurements reveal square planar geometry for Cu(II), Ni(II) and Pd(II) complexes and tetrahedral geometry for Co(II) complex. The elemental analyses and mass spectral data have justified the ML 2 composition of complexes. Kinetic and thermodynamic parameters were computed from the thermal decomposition data using Coats and Redfern method. The geometry of the metal complexes has been optimized with the help of molecular modeling. The free ligand (HDMAOX) and its metal complexes have been tested in vitro against Alternarie alternate, Aspergillus flavus, Aspergillus nidulans and Aspergillus niger fungi and Streptococcus, Staph, Staphylococcus and Escherchia coli bacteria in order to assess their antimicrobial potential. The results indicate that the ligand and its metal complexes possess antimicrobial properties.

Synthesis, characterization and biological activity of complexes of 2-hydroxy-3,5-dimethylacetophenoneoxime (HDMAOX) with copper(II), cobalt(II), nickel(II) and palladium(II).

PubMed

Singh, Bibhesh K; Jetley, Umesh K; Sharma, Rakesh K; Garg, Bhagwan S

2007-09-01

A new series of complexes of 2-hydroxy-3,5-dimethyl acetophenone oxime (HDMAOX) with Cu(II), Co(II), Ni(II) and Pd(II) have been prepared and characterized by different physical techniques. Infrared spectra of the complexes indicate deprotonation and coordination of the phenolic OH. It also confirms that nitrogen atom of the oximino group contributes to the complexation. Electronic spectra and magnetic susceptibility measurements reveal square planar geometry for Cu(II), Ni(II) and Pd(II) complexes and tetrahedral geometry for Co(II) complex. The elemental analyses and mass spectral data have justified the ML(2) composition of complexes. Kinetic and thermodynamic parameters were computed from the thermal decomposition data using Coats and Redfern method. The geometry of the metal complexes has been optimized with the help of molecular modeling. The free ligand (HDMAOX) and its metal complexes have been tested in vitro against Alternarie alternate, Aspergillus flavus, Aspergillus nidulans and Aspergillus niger fungi and Streptococcus, Staph, Staphylococcus and Escherchia coli bacteria in order to assess their antimicrobial potential. The results indicate that the ligand and its metal complexes possess antimicrobial properties.

Effects of the type and thickness of ceramic, substrate, and cement on the optical color of a lithium disilicate ceramic.

PubMed

Pires, Laís A; Novais, Pollyanna M R; Araújo, Vinícius D; Pegoraro, Luiz F

2017-01-01

Reproducing the characteristics of natural teeth in ceramic crowns remains a complex and difficult process. The purpose of this in vitro study was to evaluate the effect of the substrate, cement, type, and thickness of the ceramic on the resulting color of a lithium disilicate ceramic. Forty ceramic disks were prepared from IPS e.max Press LT (low translucency) and HO (high opacity) in 2 different thicknesses (1.5 and 2 mm). The LT groups were composed of monolithic ceramic disks, and the HO groups were composed of disks fabricated with a 0.5-mm thickness combined with a 1- or 1.5-mm veneering ceramic thickness. Disks made of composite resin (R) and alloy (A) were used as substrate structures. The resin cement used was Variolink II. Color was measured with a spectrophotometer and expressed in CIELAB coordinates. Color differences (ΔE) were calculated. The data were analyzed with ANOVA and the Tukey HSD test (α=.05). When the ΔE of ceramic disks with both substrates, with and without cement, were compared, the lowest value (3) was obtained for ceramic HO with a 2-mm thickness/alloy substrate/without cement; the highest value (10) was obtained for ceramic LT with a1.5-mm thickness/alloy substrate/with cement. This difference was statistically significant. When the effect of cement on the ΔE of ceramics in both substrates was compared, the lowest value (1.1) occurred with ceramic HO with a 1.5-mm thickness/resin substrate, and the highest was observed for ceramic LT with a 1.5-mm thickness/alloy substrate (6.4). This difference was statistically significant. The substrate color, type and thickness of ceramic, and presence of the cement significantly influenced the resulting optical color. The ΔE values of cemented HO ceramics were lower than that of the LT ceramic. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

The influence of ozone on atmospheric emissions of gaseous elemental mercury and reactive gaseous mercury from substrates

USGS Publications Warehouse

Engle, M.A.; Sexauer, Gustin M.; Lindberg, S.E.; Gertler, A.W.; Ariya, P.A.

2005-01-01

Experiments were performed to investigate the effect of ozone (O 3) on mercury (Hg) emission from a variety of Hg-bearing substrates. Substrates with Hg(II) as the dominant Hg phase exhibited a 1.7 to 51-fold increase in elemental Hg (Hgo) flux and a 1.3 to 8.6-fold increase in reactive gaseous mercury (RGM) flux in the presence of O3-enriched clean (50 ppb O3; 8 substrates) and ambient air (up to ???70 ppb O3; 6 substrates), relative to clean air (oxidant and Hg free air). In contrast, Hgo fluxes from two artificially Hgo-amended substrates decreased by more than 75% during exposure to O3-enriched clean air relative to clean air. Reactive gaseous mercury emissions from Hg o-amended substrates increased immediately after exposure to O 3 but then decreased rapidly. These experimental results demonstrate that O3 is very important in controlling Hg emissions from substrates. The chemical mechanisms that produced these trends are not known but potentially involve heterogenous reactions between O3, the substrate, and Hg. Our experiments suggest they are not homogenous gas-phase reactions. Comparison of the influence of O3 versus light on increasing Hgo emissions from dry Hg(II)-bearing substrates demonstrated that they have a similar amount of influence although O3 appeared to be slightly more dominant. Experiments using water-saturated substrates showed that the presence of high-substrate moisture content minimizes reactions between atmospheric O3 and substrate-bound Hg. Using conservative calculations developed in this paper, we conclude that because O3 concentrations have roughly doubled in the last 100 years, this could have increased Hgo emissions from terrestrial substrates by 65-72%. ?? 2005 Elsevier Ltd. All rights reserved.

Structural and Functional Analysis of Phytotoxin Toxoflavin-Degrading Enzyme

PubMed Central

Kim, Myung-Il; Ma, Jun; Nagamatsu, Tomohisa; Goo, Eunhye; Kim, Hongsup; Hwang, Ingyu; Han, Jaehong; Rhee, Sangkee

2011-01-01

Pathogenic bacteria synthesize and secrete toxic low molecular weight compounds as virulence factors. These microbial toxins play essential roles in the pathogenicity of bacteria in various hosts, and are emerging as targets for antivirulence strategies. Toxoflavin, a phytotoxin produced by Burkholderia glumae BGR1, has been known to be the key factor in rice grain rot and wilt in many field crops. Recently, toxoflavin-degrading enzyme (TxDE) was identified from Paenibacillus polymyxa JH2, thereby providing a possible antivirulence strategy for toxoflavin-mediated plant diseases. Here, we report the crystal structure of TxDE in the substrate-free form and in complex with toxoflavin, along with the results of a functional analysis. The overall structure of TxDE is similar to those of the vicinal oxygen chelate superfamily of metalloenzymes, despite the lack of apparent sequence identity. The active site is located at the end of the hydrophobic channel, 9 Å in length, and contains a Mn(II) ion interacting with one histidine residue, two glutamate residues, and three water molecules in an octahedral coordination. In the complex, toxoflavin binds in the hydrophobic active site, specifically the Mn(II)-coordination shell by replacing a ligating water molecule. A functional analysis indicated that TxDE catalyzes the degradation of toxoflavin in a manner dependent on oxygen, Mn(II), and the reducing agent dithiothreitol. These results provide the structural features of TxDE and the early events in catalysis. PMID:21799856

Fe (III), Co(II), Ni(II), Cu(II) and Zn(II) complexes of schiff bases based-on glycine and phenylalanine: Synthesis, magnetic/thermal properties and antimicrobial activity

NASA Astrophysics Data System (ADS)

Sevgi, Fatih; Bagkesici, Ugur; Kursunlu, Ahmed Nuri; Guler, Ersin

2018-02-01

Zinc (II), copper (II), nickel (II), cobalt (II) and iron (III) complexes of Schiff bases (LG, LP) derived from 2-hydroxynaphthaldehyde with glycine and phenylalanine were reported and characterized by 1H NMR, 13C NMR, elemental analyses, melting point, FT-IR, magnetic susceptibility and thermal analyses (TGA). TGA data show that iron and cobalt include to the coordinated water and metal:ligand ratio is 1:2 while the complex stoichiometry for Ni (II), Cu (II) and Zn (II) complexes is 1:1. As expected, Ni (II) and Zn (II) complexes are diamagnetic; Cu (II), Co (II) and Fe (III) complexes are paramagnetic character due to a strong ligand of LG and LP. The LG, LP and their metal complexes were screened for their antimicrobial activities against five Gram-positive (Staphylococcus aureus, Methicillin resistant Staphylococcus aureus (MRSA), Bacillus cereus, Streptococcus mutans and Enterococcus faecalis) and three Gram-negative (Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa) and one fungi (Candida albicans) by using broth microdilution techniques. The activity data show that ligands and their metal complexes exhibited moderate to good activity against Gram-positive bacteria and fungi.

Synthesis and characterization of new complexes of nickel (II), palladium (II) and platinum(II) with derived sulfonamide ligand: Structure, DFT study, antibacterial and cytotoxicity activities

NASA Astrophysics Data System (ADS)

Bouchoucha, Afaf; Zaater, Sihem; Bouacida, Sofiane; Merazig, Hocine; Djabbar, Safia

2018-06-01

The synthesis, characterization and biological study of new nickel (II), palladium (II), and platinum (II) complexes with sulfamethoxazole ligand used in pharmaceutical field, were reported. [MLCl2].nH2O is the general formula obtained for Pd(II) and Pt(II) complexes. These complexes have been prepared and characterized by elemental analysis, FTIR, 1HNMR spectral, magnetic measurements, UV-Visible spectra, and conductivity. The DFT calculation was applied to optimize the geometric structure of the Pd(II) and Pt(II) complexes. A new single-crystal X-ray structure of the Ni(II) complex has been determined. It crystallized in monoclinic system with P 21/c space group and Z = 8. The invitro antibacterial activity of ligand and complexes against Escherichia coli, P. aeruginosa, Klebsiella pneumoniae, S. aureus, Bacillus subtilis species has been carried out and compared using agar-diffusion method. The Pd(II) and Pt(II) complexes showed a remarkable inhibition against bacteria tested. The invitro cytotoxicity assay of the complexes against three cell lines chronic myelogenous leukaemia (K562), human colon adenocarcinoma (HT-29) and breast cancer (MCF-7) was also reported.

1,2,3-Triazole-Heme Interactions in Cytochrome P450: Functionally Competent Triazole-Water- Heme Complexes

PubMed Central

Conner, Kip P.; Vennam, Preethi; Woods, Caleb M.; Krzyaniak, Matthew D.; Bowman, Michael K.; Atkins, William M.

2012-01-01

In comparison to imidazole (IMZ) and 1,2,4-triazole (1,2,4-TRZ) the isosteric 1,2,3-triazole (1,2,3-TRZ) is unrepresented among CYP inhibitors. This is surprising because 1,2,3-TRZs are easily obtained via ‘click’ chemistry. To understand this underrepresentation of 1,2,3-TRZs among CYP inhibitors, thermodynamic and DFT computational studies were performed with unsusbstituted IMZ, 1,2,4-TRZ, and 1,2,3-TRZ. The results indicate that the lower affinity of 1,2,3-TRZ for the heme iron includes a large unfavorable entropy term likely originating in solvent – 1,2,3-TRZ interactions; the difference is not solely due to differences in the enthalpy of heme – ligand interactions. In addition, the 1,2,3-TRZ fragment was incorporated into a well-established CYP3A4 substrate and mechanism based inactivator, 17-α-ethynylestradiol (17EE), via click chemistry. This derivative, 17-click, yielded optical spectra consistent with low spin ferric heme iron (type II) in contrast to 17EE, which yields a high spin complex (type I). Furthermore, the rate of CYP3A4-mediated metabolism of 17-click was comparable to 17EE, and with different regioselectivity. Surprisingly, CW EPR and HYSCORE EPR spectroscopy indicate that the 17-click does not displace water from the 6th axial ligand position of CYP3A4 as expected for a type II ligand. We propose a binding model where 17-click pendant 1,2,3-TRZ hydrogen bonds with the 6th axial water ligand. The results demonstrate the potential for 1,2,3-TRZ to form metabolically labile water-bridged low spin heme complexes, consistent with recent evidence that nitrogenous type II ligands of CYPs can be efficiently metabolized. The specific case of [CYP3A4•17-click] highlights the risk of interpreting CYP-ligand complex structure on the basis of optical spectra. PMID:22809252

Functional characterization of recombinant prefoldin complexes from a hyperthermophilic archaeon, Thermococcus sp. strain KS-1.

PubMed

Iizuka, Ryo; Sugano, Yuri; Ide, Naoki; Ohtaki, Akashi; Yoshida, Takao; Fujiwara, Shinsuke; Imanaka, Tadayuki; Yohda, Masafumi

2008-03-28

Prefoldin is a heterohexameric molecular chaperone complex that is found in the eukaryotic cytosol and also in archaea. It captures a nonnative protein and subsequently delivers it to a group II chaperonin for proper folding. Archaeal prefoldin is a heterocomplex containing two alpha subunits and four beta subunits with the structure of a double beta-barrel assembly, with six long coiled coils protruding from it like a jellyfish with six tentacles. We have studied the protein folding mechanism of group II chaperonin using those of Thermococcus sp. strain KS-1 (T. KS-1) because they exhibit high protein folding activity in vitro. We have also demonstrated functional cooperation between T. KS-1 chaperonins and prefoldin from Pyrococcus horikoshii OT3. Recent genome analysis has shown that Thermococcus kodakaraensis KOD1 contains two pairs of prefoldin subunit genes, correlating with the existence of two different chaperonin subunits. In this study, we characterized four different recombinant prefoldin complexes composed of two pairs of prefoldin subunits (alpha1, alpha2, beta1, and beta2) from T. KS-1. All of them (alpha1-beta1, alpha2-beta1, alpha1-beta2, and alpha2-beta2) exist as alpha(2)beta(4) heterohexamers and can protect several proteins from forming aggregates with different activities. We have also compared the collaborative activity between the prefoldin complexes and the cognate chaperonins. Prefoldin complexes containing the beta1 subunit interacted with the chaperonins more strongly than those with the beta2 subunit. The results suggest that Thermococcus spp. express different prefoldins for different substrates or conditions as chaperonins.

Synthesis, structure and catechol-oxidase activity of copper(II) complexes of 17-hydroxy-16-(N-3-oxo-prop-1-enyl)amino steroids.

PubMed

Wegner, Rainer; Dubs, Manuela; Görls, Helmar; Robl, Christian; Schönecker, Bruno; Jäger, Ernst-G

2002-09-01

Copper is next to iron the most important element in the biological transport, storage and in redox reactions of dioxygen. A bioanalogous activation of dioxygen with copper complexes is used for catalytical epoxidation, allylic hydroxylation and oxidative coupling of aromatic substrates, for example. With stereochemical information in form of chiral ligands, enantioselective reactions may be possible. Another aspect of interest on copper catalyzed reactions with dioxygen is that the exact mechanism and biological function of some enzymes (especially catechol oxidase) is yet not fully clear. For studies mimicking the copper-containing catechol oxidase appropriate chiral steroid ligands with defined stereochemistry and conformation have been synthesized. The four diastereomeric 16,17-aminoalcohols of the 3-methoxy-estra-1,3,5(10)-triene series have been condensed with salicylic aldehyde and different beta-ketoenols to the chiral ligand types 1-5. These compounds with different steric and electronic properties and different arrangements of the neighboring hydroxy and nitrogen functions were reacted with copper(II) acetate to copper complexes. The structure of these complexes will be discussed. The bioanalogous oxidation of 3,5-di-tbutyl-catechol (dtbc) to the corresponding quinone was catalyzed by most of the complexes, indicating their ability to activate dioxygen. The trans configurations c and d showed an activity one magnitude higher than the cis configurations a and b. Comparing compounds with the same diastereomeric configuration, the main influence was that of the peripheral R(1-3) substituents at the beta-ketoenaminic group which are useful for the fine-tuning of the properties of the copper atoms like redox potential and Lewis acidity.

Epileptogenesis causes an N-methyl-d-aspartate receptor/Ca2+-dependent decrease in Ca2+/calmodulin-dependent protein kinase II activity in a hippocampal neuronal culture model of spontaneous recurrent epileptiform discharges.

PubMed

Blair, Robert E; Sombati, Sompong; Churn, Severn B; Delorenzo, Robert J

2008-06-24

Alterations in the function of Ca2+/calmodulin-dependent protein kinase II (CaM kinase II) have been observed in both in vivo and in vitro models of epileptogenesis; however the molecular mechanism mediating the effects of epileptogenesis on CaM kinase II has not been elucidated. This study was initiated to evaluate the molecular pathways involved in causing the long-lasting decrease in CaM kinase II activity in the hippocampal neuronal culture model of low Mg2+-induced spontaneous recurrent epileptiform discharges (SREDs). We show here that the decrease in CaM kinase II activity associated with SREDs in hippocampal cultures involves a Ca2+/N-methyl-d-aspartate (NMDA) receptor-dependent mechanism. Low Mg2+-induced SREDs result in a significant decrease in Ca2+/calmodulin-dependent substrate phosphorylation of the synthetic peptide autocamtide-2. Reduction of extracellular Ca2+ levels (0.2 mM in treatment solution) or the addition of dl-2-amino-5-phosphonovaleric acid (APV) 25 microM blocked the low Mg2+-induced decrease in CaM kinase II-dependent substrate phosphorylation. Antagonists of the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)/kainic acid receptor or L-type voltage sensitive Ca2+ channel had no effect on the low Mg2+-induced decrease in CaM kinase II-dependent substrate phosphorylation. The results of this study demonstrate that the decrease in CaM kinase II activity associated with this model of epileptogenesis involves a selective Ca2+/NMDA receptor-dependent mechanism and may contribute to the production and maintenance of SREDs in this model.

Epileptogenesis causes an N-methyl-d-aspartate receptor/Ca2+-dependent decrease in Ca2+/calmodulin-dependent protein kinase II activity in a hippocampal neuronal culture model of spontaneous recurrent epileptiform discharges

PubMed Central

Blair, Robert E.; Sombati, Sompong; Churn, Severn B.; DeLorenzo, Robert J.

2008-01-01

Alterations in the function of Ca2+/calmodulin-dependent protein kinase II (CaM Kinase II) have been observed in both in vivo and in vitro models of epileptogenesis; however the molecular mechanism mediating the effects of epileptogenesis on CaM Kinase II have not been elucidated. This study was initiated to evaluate the molecular pathways involved in causing the long lasting decrease in CaM Kinase II activity in the hippocampal neuronal culture model of low Mg2+ induced spontaneous recurrent epileptiform discharges (SREDs). We show here that the decrease in CaM kinase II activity associated with SREDs in hippocampal cultures involves a Ca2+/N-methyl-d-aspartate (NMDA) receptor-dependent mechanism. Low Mg2+ induced SREDs results in a significant decrease in Ca2+/calmodulin-dependent substrate phosphorylation of the synthetic peptide autocamtide-2. Reduction of extracellular Ca2+ levels (0.2 mM in treatment solution) or the addition of DL-2-amino-5-phosphonovaleric acid (APV) 25 µM blocked the low Mg2+ induced decrease in CaM kinase II-dependent substrate phosphorylation. Antagonists of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)/kainic acid receptor or L-type voltage sensitive Ca2+ channel had no effect on the low Mg2+ induced decrease in CaM kinase II-dependent substrate phosphorylation. The results of this study demonstrate that the decrease in CaM kinase II activity associated with this model of epileptogenesis involves a selective Ca2+/NMDA receptor-dependent mechanism and may contribute to the production and maintenance of SREDs in this model. PMID:18495112

Tripeptidyl-peptidase II: a multi-purpose peptidase.

PubMed

Tomkinson, Birgitta; Lindås, Ann-Christin

2005-10-01

Tripeptidyl-peptidase II is a high-molecular weight peptidase with a widespread distribution in eukaryotic cells. The enzyme sequentially removes tripeptides from a free N-terminus of longer peptides and also displays a low endopeptidase activity. A role for tripeptidyl-peptidase II in the formation of peptides for antigen presentation has recently become evident, and the enzyme also appears to be important for the degradation of some specific substrates, e.g. the neuropeptide cholecystokinin. However, it is likely that the main biological function of tripeptidyl-peptidase II is to participate in a general intracellular protein turnover. This peptidase may act on oligopeptides generated by the proteasome, or other endopeptidases, and the tripeptides formed would subsequently be good substrates for other exopeptidases. The fact that tripeptidyl-peptidase II activity is increased in sepsis-induced muscle wasting, a situation of enhanced protein turnover, corroborates this biological role.

Heterobimetallic Complexes with MIII-(μ-OH)-MII Cores (MIII = Fe, Mn, Ga; MII = Ca, Sr, and Ba): Structural, Kinetic, and Redox Properties.

PubMed

Park, Young Jun; Cook, Sarah A; Sickerman, Nathaniel S; Sano, Yohei; Ziller, Joseph W; Borovik, A S

2013-02-01

The effects of redox-inactive metal ions on dioxygen activation were explored using a new Fe II complex containing a tripodal ligand with 3 sulfonamido groups. This iron complex exhibited a faster initial rate for the reduction of O 2 than its Mn II analog. Increases in initial rates were also observed in the presence of group 2 metal ions for both the Fe II and Mn II complexes, which followed the trend NMe 4 + < Ba II < Ca II = Sr II . These studies led to the isolation of heterobimetallic complexes containing Fe III -( μ -OH)-M II cores (M II = Ca, Sr, and Ba) and one with a [Sr II (OH)Mn III ] + motif. The analogous [Ca II (OH)Ga III ] + complex was also prepared and its solid state molecular structure is nearly identical to that of the [Ca II (OH)Fe III ] + system. Nuclear magnetic resonance studies indicated that the diamagnetic [Ca II (OH)Ga III ] + complex retained its structure in solution. Electrochemical measurements on the heterobimetallic systems revealed similar one-electron reduction potentials for the [Ca II (OH)Fe III ] + and [Sr II (OH)Fe III ] + complexes, which were more positive than the potential observed for [Ba II (OH)Fe III ] + . Similar results were obtained for the heterobimetallic Mn II complexes. These findings suggest that Lewis acidity is not the only factor to consider when evaluating the effects of group 2 ions on redox processes, including those within the oxygen-evolving complex of Photosystem II.

Metallohydrolase biomimetics with catalytic and structural flexibility.

PubMed

Mendes, Luisa L; Englert, Daniel; Fernandes, Christiane; Gahan, Lawrence R; Schenk, Gerhard; Horn, Adolfo

2016-11-22

The structural and functional properties of zinc(ii) complexes of two nitrogen rich polydentate ligands, HTPDP = 1,3-bis(bis-pyridin-2-ylmethylamino)propan-2-ol and HTPPNOL = N,N,N'-tris-(2-pyridylmethyl)-1,3-diaminopropan-2-ol, are compared. HTPDP is a hepta-dentate ligand with four pyridyl groups attached to a 1,3-diaminopropan-2-ol backbone while HTPPNOL contains only three pyridyl groups. In reactions with Zn(ClO 4 ) 2 , HTPDP forms a dinuclear zinc compound [Zn 2 (TPDP)(OAc)](ClO 4 ) 2 , 1. On the other hand, mononuclear [Zn(HTPPNOL)](ClO 4 ) 2 , 2, and tetranuclear [Zn 4 (TPPNOL) 2 (OAc) 3 ](ClO 4 ) 3 , 3, complexes were isolated with the ligand HTPPNOL. Kinetic measurements with the substrate bis(2,4-dinitrophenyl)phosphate (BDNPP) revealed that compound 1 (k cat = 31.4 × 10 -3 min -1 ) is more reactive than 3 (k cat = 7.7 × 10 -3 min -1 ) at pH = 8.5, whilst the mononuclear compound 2 is inactive. Compound 1 displays a typical steady-state kinetic behaviour, while compound 3 exhibits steady-state behaviour only ∼120 s after starting the reaction, preceded by a burst-phase. 31 P NMR studies confirm that 1 can promote the hydrolysis of both ester bonds in BDNPP, generating the monoester DNPP and inorganic phosphate in the process. In contrast, DNPP is not a substrate for 3. The crystal structure of the complex formed by 3 and DNPP reveals the formation of a tetranuclear zinc complex [Zn 4 (TPPNOL) 2 (DNPP) 2 ](ClO 4 ) 2 , 4, in which the phosphate moiety of DNPP adopts an unusual tridentate μ-η 1 :η 1 :η 1 coordination mode.

Templated synthesis of cyclic [4]rotaxanes consisting of two stiff rods threaded through two bis-macrocycles with a large and rigid central plate as spacer.

PubMed

Collin, Jean-Paul; Durola, Fabien; Frey, Julien; Heitz, Valérie; Reviriego, Felipe; Sauvage, Jean-Pierre; Trolez, Yann; Rissanen, Kari

2010-05-19

Two related cyclic [4]rotaxanes consisting of double macrocycles and rigid rods incorporating two bidentate chelates have each been prepared in high yield. The first step is a multigathering and threading reaction driven by coordination of two different bidentate chelates (part of either the rings or the rods) to each copper(I) center so as to afford the desired precursor. In both cases, the assembly step is done under very mild conditions, and it is quantitative. The second key reaction is the stopper-attaching reaction, based on click chemistry. Even if the quadruple stoppering reaction is not quantitative, it is relatively high-yielding (60% and 95%), and the copper-driven assembly process is carried out at room temperature without any aggressive reagent. The final copper-complexed [4]rotaxanes obtained contain two aromatic plates roughly parallel to one another located at the center of each bis-macrocycle. In the most promising case in terms of host-guest properties, the plates are zinc(II) porphyrins of the tetra-aryl series. The compounds have been fully characterized by various spectroscopic techniques ((1)H NMR, mass spectrometry, and electronic absorption spectroscopy). Unexpectedly, the copper-complexed porphyrinic [4]rotaxane could be crystallized as its 4PF(6)(-) salt to afford X-ray quality crystals. The structure obtained is in perfect agreement with the postulated chemical structure of the compound. It is particularly attractive in terms of symmetry and molecular aesthetics. The distance between the zinc atoms of the two porphyrins is 8.673 A, which is sufficient to allow insertion between the two porphyrinic plates of small ditopic basic substrates able to interact with the central porphyrinic Zn atoms. This prediction has been confirmed by absorption spectroscopy measurements in the presence of various organic substrates. However, large substrates cannot be introduced in the corresponding recognition site and are thus complexed mostly in an exo fashion, being located outside the receptor cavity. Noteworthy, the stability constants of the 1:1 host-guest complexes are high (10(7) M(-1)).

The hydrolysis and biogas production of complex cellulosic substrates using three anaerobic biomass sources.

PubMed

Keating, C; Cysneiros, D; Mahony, T; O'Flaherty, V

2013-01-01

In this study, the ability of various sludges to digest a diverse range of cellulose and cellulose-derived substrates was assessed at different temperatures to elucidate the factors affecting hydrolysis. For this purpose, the biogas production was monitored and the specific biogas activity (SBA) of the sludges was employed to compare the performance of three anaerobic sludges on the degradation of a variety of complex cellulose sources, across a range of temperatures. The sludge with the highest performance on complex substrates was derived from a full-scale bioreactor treating sewage at 37 °C. Hydrolysis was the rate-limiting step during the degradation of complex substrates. No activity was recorded for the synthetic cellulose compound carboxymethylcellulose (CMC) using any of the sludges tested. Increased temperature led to an increase in hydrolysis rates and thus SBA values. The non-granular nature of the mesophilic sludge played a positive role in the hydrolysis of solid substrates, while the granular sludges proved more effective on the degradation of soluble compounds.

Ferryl Protonation in Oxoiron(IV) Porphyrins and Its Role in Oxygen Transfer

DOE PAGES

Boaz, Nicholas C.; Bell, Seth R.; Groves, John T.

2015-02-04

Ferryl porphyrins, P–Fe IVmore » $=$O, are central reactive intermediates in the catalytic cycles of numerous heme proteins and a variety of model systems. There has been considerable interest in elucidating factors, such as terminal oxo basicity, that may control ferryl reactivity. Here in this study, the sulfonated, water-soluble ferryl porphyrin complexes tetramesitylporphyrin, oxoFe IVTMPS (FeTMPS-II), its 2,6-dichlorophenyl analogue, oxoFe IVTDClPS (FeTDClPS-II), and two other analogues are shown to be protonated under turnover conditions to produce the corresponding bis-aqua-iron(III) porphyrin cation radicals. The results reveal a novel internal electromeric equilibrium, P–Fe IV$=$O $$\\leftrightarrows$$ P +–Fe III(OH 2) 2. Reversible pKa values in the range of 4–6.3 have been measured for this process by pH-jump, UV–vis spectroscopy. Ferryl protonation has important ramifications for C–H bond cleavage reactions mediated by oxoiron(IV) porphyrin cation radicals in protic media. Both solvent O–H and substrate C–H deuterium kinetic isotope effects are observed for these reactions, indicating that hydrocarbon oxidation by these oxoiron(IV) porphyrin cation radicals occurs via a solvent proton-coupled hydrogen atom transfer from the substrate that has not been previously described. The effective FeO–H bond dissociation energies for FeTMPS-II and FeTDClPS-II were estimated from similar kinetic reactivities of the corresponding oxoFe IVTMPS + and oxoFe IVTDClPS + species to be ~92–94 kcal/mol. Similar values were calculated from the two-proton P +–Fe III(OH 2) 2 pK a obs and the porphyrin oxidation potentials, despite a 230 mV range for the iron porphyrins examined. Thus, the iron porphyrin with the lower ring oxidation potential has a compensating higher basicity of the ferryl oxygen. The solvent-derived proton adds significantly to the driving force for C–H bond scission.« less

Novel Metals and Metal Complexes as Platforms for Cancer Therapy

PubMed Central

Frezza, Michael; Hindo, Sarmad; Chen, Di; Davenport, Andrew; Schmitt, Sara; Tomco, Dajena; Dou, Q. Ping

2013-01-01

Metals are essential cellular components selected by nature to function in several indispensable biochemical processes for living organisms. Metals are endowed with unique characteristics that include redox activity, variable coordination modes, and reactivity towards organic substrates. Due to their reactivity, metals are tightly regulated under normal conditions and aberrant metal ion concentrations are associated with various pathological disorders, including cancer. For these reasons, coordination complexes, either as drugs or prodrugs, become very attractive probes as potential anticancer agents. The use of metals and their salts for medicinal purposes, from iatrochemistry to modern day, has been present throughout human history. The discovery of cisplatin, cis-[PtII(NH3)2Cl2], was a defining moment which triggered the interest in platinum(II)- and other metal-containing complexes as potential novel anticancer drugs. Other interests in this field address concerns for uptake, toxicity, and resistance to metallodrugs. This review article highlights selected metals that have gained considerable interest in both the development and the treatment of cancer. For example, copper is enriched in various human cancer tissues and is a co-factor essential for tumor angiogenesis processes. However the use of copper-binding ligands to target tumor copper could provide a novel strategy for cancer selective treatment. The use of nonessential metals as probes to target molecular pathways as anticancer agents is also emphasized. Finally, based on the interface between molecular biology and bioinorganic chemistry the design of coordination complexes for cancer treatment is reviewed and design strategies and mechanisms of action are discussed. PMID:20337575

Uncoupling metallonuclease metal ion binding sites via nudge mutagenesis.

PubMed

Papadakos, Grigorios A; Nastri, Horacio; Riggs, Paul; Dupureur, Cynthia M

2007-05-01

The hydrolysis of phosphodiester bonds by nucleases is critical to nucleic acid processing. Many nucleases utilize metal ion cofactors, and for a number of these enzymes two active-site metal ions have been detected. Testing proposed mechanistic roles for individual bound metal ions has been hampered by the similarity between the sites and cooperative behavior. In the homodimeric PvuII restriction endonuclease, the metal ion dependence of DNA binding is sigmoidal and consistent with two classes of coupled metal ion binding sites. We reasoned that a conservative active-site mutation would perturb the ligand field sufficiently to observe the titration of individual metal ion binding sites without significantly disturbing enzyme function. Indeed, mutation of a Tyr residue 5.5 A from both metal ions in the enzyme-substrate crystal structure (Y94F) renders the metal ion dependence of DNA binding biphasic: two classes of metal ion binding sites become distinct in the presence of DNA. The perturbation in metal ion coordination is supported by 1H-15N heteronuclear single quantum coherence spectra of enzyme-Ca(II) and enzyme-Ca(II)-DNA complexes. Metal ion binding by free Y94F is basically unperturbed: through multiple experiments with different metal ions, the data are consistent with two alkaline earth metal ion binding sites per subunit of low millimolar affinity, behavior which is very similar to that of the wild type. The results presented here indicate a role for the hydroxyl group of Tyr94 in the coupling of metal ion binding sites in the presence of DNA. Its removal causes the affinities for the two metal ion binding sites to be resolved in the presence of substrate. Such tuning of metal ion affinities will be invaluable to efforts to ascertain the contributions of individual bound metal ions to metallonuclease function.

Kinetics and binding sites for interaction of the prefoldin with a group II chaperonin: contiguous non-native substrate and chaperonin binding sites in the archaeal prefoldin.

PubMed

Okochi, Mina; Nomura, Tomoko; Zako, Tamotsu; Arakawa, Takatoshi; Iizuka, Ryo; Ueda, Hiroshi; Funatsu, Takashi; Leroux, Michel; Yohda, Masafumi

2004-07-23

Prefoldin is a jellyfish-shaped hexameric co-chaperone of the group II chaperonins. It captures a protein folding intermediate and transfers it to a group II chaperonin for completion of folding. The manner in which prefoldin interacts with its substrates and cooperates with the chaperonin is poorly understood. In this study, we have examined the interaction between a prefoldin and a chaperonin from hyperthermophilic archaea by immunoprecipitation, single molecule observation, and surface plasmon resonance. We demonstrate that Pyrococcus prefoldin interacts most tightly with its cognate chaperonin, and vice versa, suggesting species specificity in the interaction. Using truncation mutants, we uncovered by kinetic analyses that this interaction is multivalent in nature, consistent with multiple binding sites between the two chaperones. We present evidence that both N- and C-terminal regions of the prefoldin beta sub-unit are important for molecular chaperone activity and for the interaction with a chaperonin. Our data are consistent with substrate and chaperonin binding sites on prefoldin that are different but in close proximity, which suggests a possible handover mechanism of prefoldin substrates to the chaperonin.

Electron spin echo envelope modulation studies of the Cu(II)-substituted derivative of isopenicillin N synthase: A structural and spectroscopic model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng Jiang; Peisach, J.; Lijune Ming

Electron spin echo envelope modulation spectroscopy (ESEEM) was used to study the active site structure of isopenicillin N synthase (IPNS) from Cephalosporium acremonium with Cu(II) as a spectroscopic probe. Fourier transform of the simulated electron spin-echo envelope for the Cu(II)-substituted enzyme, Cu(II)IPNS, revealed two nearly magnetically equivalent, equatorially coordinated His imidazoles. The superhyperfine coupling constant, A{sub iso}, for the remote {sup 14}N of each imidazole was 1.65 MHz. The binding of substrate to the enzyme altered the magnetic coupling so that A{sub iso} is 1.30 MHz for one nitrogen and 2.16 MHz for the other. From a comparison of themore » ESSEM of Cu(II)IPNS in D{sub 2}O and H{sub 2}O, it is suggested that water is a ligand of Cu(II) and this is displaced upon the addition of substrate.« less

Removal of Ca 2+ from the Oxygen-Evolving Complex in Photosystem II Has Minimal Effect on the Mn 4O 5 Core Structure: A Polarized Mn X-ray Absorption Spectroscopy Study

DOE PAGES

Lohmiller, Thomas; Shelby, Megan L.; Long, Xi; ...

2015-05-19

We studied Ca 2+ -depleted and Ca 2+ -reconstituted spinach photosystem II using polarized X-ray absorption spectroscopy of oriented PS II preparations to investigate the structural and functional role of the Ca 2+ ion in the Mn 4O 5Ca cluster of the oxygen-evolving complex (OEC). Samples were prepared by low pH/citrate treatment as one-dimensionally ordered membrane layers and poised in the Ca 2+ -depleted S 1 (S 1') and S 2 (S 2') states, the S 2'Y Z• state, at which point the catalytic cycle of water oxidation is inhibited, and the Ca 2+ -reconstituted S 1 state. Polarized Mnmore » K-edge XANES and EXAFS spectra exhibit pronounced dichroism. Polarized EXAFS data of all states of Ca 2+ -depleted PS II investigated show only minor changes in distances and orientations of the Mn-Mn vectors compared to the Ca 2+ -containing OEC, which may be attributed to some loss of rigidity of the core structure. Thus, removal of the Ca 2+ ion does not lead to fundamental distortion or rearrangement of the tetranuclear Mn cluster, which indicates that the Ca 2+ ion in the OEC is not critical for structural maintenance of the cluster, at least in the S 1 and S 2 states, but fulfills a crucial catalytic function in the mechanism of the water oxidation reaction. On the basis of this structural information, reasons for the inhibitory effect of Ca 2+ removal are discussed, attributing to the Ca 2+ ion a fundamental role in organizing the surrounding (substrate) water framework and in proton-coupled electron transfer to Y Z• (D1-Tyr161).« less

Removal of Ca(2+) from the Oxygen-Evolving Complex in Photosystem II Has Minimal Effect on the Mn4O5 Core Structure: A Polarized Mn X-ray Absorption Spectroscopy Study.

PubMed

Lohmiller, Thomas; Shelby, Megan L; Long, Xi; Yachandra, Vittal K; Yano, Junko

2015-10-29

Ca(2+)-depleted and Ca(2+)-reconstituted spinach photosystem II was studied using polarized X-ray absorption spectroscopy of oriented PS II preparations to investigate the structural and functional role of the Ca(2+) ion in the Mn4O5Ca cluster of the oxygen-evolving complex (OEC). Samples were prepared by low pH/citrate treatment as one-dimensionally ordered membrane layers and poised in the Ca(2+)-depleted S1 (S1') and S2 (S2') states, the S2'YZ(•) state, at which point the catalytic cycle of water oxidation is inhibited, and the Ca(2+)-reconstituted S1 state. Polarized Mn K-edge XANES and EXAFS spectra exhibit pronounced dichroism. Polarized EXAFS data of all states of Ca(2+)-depleted PS II investigated show only minor changes in distances and orientations of the Mn-Mn vectors compared to the Ca(2+)-containing OEC, which may be attributed to some loss of rigidity of the core structure. Thus, removal of the Ca(2+) ion does not lead to fundamental distortion or rearrangement of the tetranuclear Mn cluster, which indicates that the Ca(2+) ion in the OEC is not critical for structural maintenance of the cluster, at least in the S1 and S2 states, but fulfills a crucial catalytic function in the mechanism of the water oxidation reaction. On the basis of this structural information, reasons for the inhibitory effect of Ca(2+) removal are discussed, attributing to the Ca(2+) ion a fundamental role in organizing the surrounding (substrate) water framework and in proton-coupled electron transfer to YZ(•) (D1-Tyr161).

Mechanical ventilation causes pulmonary mitochondrial dysfunction and delayed alveolarization in neonatal mice.

PubMed

Ratner, Veniamin; Sosunov, Sergey A; Niatsetskaya, Zoya V; Utkina-Sosunova, Irina V; Ten, Vadim S

2013-12-01

Hyperoxia inhibits pulmonary bioenergetics, causing delayed alveolarization in mice. We hypothesized that mechanical ventilation (MV) also causes a failure of bioenergetics to support alveolarization. To test this hypothesis, neonatal mice were ventilated with room air for 8 hours (prolonged) or for 2 hours (brief) with 15 μl/g (aggressive) tidal volume (Tv), or for 8 hours with 8 μl/g (gentle) Tv. After 24 hours or 10 days of recovery, lung mitochondria were examined for adenosine diphosphate (ADP)-phosphorylating respiration, using complex I (C-I)-dependent, complex II (C-II)-dependent, or cytochrome C oxidase (C-IV)-dependent substrates, ATP production rate, and the activity of C-I and C-II. A separate cohort of mice was exposed to 2,4-dinitrophenol (DNP), a known uncoupler of oxidative phosphorylation. At 10 days of recovery, pulmonary alveolarization and the expression of vascular endothelial growth factor (VEGF) were assessed. Sham-operated littermates were used as control mice. At 24 hours after aggressive MV, mitochondrial ATP production rates and the activity of C-I and C-II were significantly decreased compared with control mice. However, at 10 days of recovery, only mice exposed to prolonged-aggressive MV continued to exhibit significantly depressed mitochondrial respiration. This was associated with significantly poorer alveolarization and VEGF expression. In contrast, mice exposed to brief-aggressive or prolonged-gentle MV exhibited restored mitochondrial ADP-phosphorylation, normal alveolarization and pulmonary VEGF content. Exposure to DNP fully replicated the phenotype consistent with alveolar developmental arrest. Our data suggest that the failure of bioenergetics to support normal lung development caused by aggressive and prolonged ventilation should be considered a fundamental mechanism for the development of bronchopulmonary dysplasia in premature neonates.

Synthesis, spectroscopic characterization and biological activities of N4O2 Schiff base ligand and its metal complexes of Co(II), Ni(II), Cu(II) and Zn(II)

NASA Astrophysics Data System (ADS)

Al-Resayes, Saud I.; Shakir, Mohammad; Abbasi, Ambreen; Amin, Kr. Mohammad Yusuf; Lateef, Abdul

The Schiff base ligand, bis(indoline-2-one)triethylenetetramine (L) obtained from condensation of triethylenetetramine and isatin was used to synthesize the complexes of type, [ML]Cl2 [M = Co(II), Ni(II), Cu(II) and Zn(II)]. L was characterized on the basis of the results of elemental analysis, FT-IR, 1H and 13C NMR, mass spectroscopic studies. The stoichiometry, bonding and stereochemistries of complexes were ascertained on the basis of results of elemental analysis, magnetic susceptibility values, molar conductance and various spectroscopic studies. EPR, UV-vis and magnetic moments revealed an octahedral geometry for complexes. L and its Cu(II) and Zn(II) complexes were screened for their antibacterial activity. Analgesic activity of Cu(II) and Zn(II) complexes was also tested in rats by tail flick method. Both complexes were found to possess good antibacterial and moderate analgesic activity.

Synthesis, spectroscopic characterization, thermal analysis and electrical conductivity studies of Mg(II), Ca(II), Sr(II) and Ba(II) vitamin B2 complexes

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Moussa, Mohamed A. A.; Mohamed, Soha F.

2011-05-01

Riboflavin (RF) complexes of Mg(II), Ca(II), Sr(II) and Ba(II) were successfully synthesized. Structures of metal complexes obtained were confirmed and characterized by elemental analysis, molar conductance, and infrared spectra. DC electrical conductivity measurements indicated that the alkaline earth metal (II) complexes of RF ligand are non-electrolytes. Elemental analysis of chelates suggest that the metal(II) ligand ratio is 1:2 with structure formula as [M(RF) 2( X) 2]· nH 2O. Infrared assignments clearly show that RF ligand coordinated as a bidentate feature through azomethine nitrogen of pyrazine ring and C dbnd O of pyrimidine-2,4-dione. Thermal analyses of Mg(II), Ca(II), Sr(II) and Ba(II) complexes were investigated using (TG/DSC) under atmospheric nitrogen between 30 and 800 °C. The surface morphology of the complexes was studied by SEM. The electrical conductivities of RF and its metal complexes were also measured with DC electrical conductivity in the temperature range from room to 483 K.

Fabrication of complex nanoscale structures on various substrates

NASA Astrophysics Data System (ADS)

Han, Kang-Soo; Hong, Sung-Hoon; Lee, Heon

2007-09-01

Polymer based complex nanoscale structures were fabricated and transferred to various substrates using reverse nanoimprint lithography. To facilitate the fabrication and transference of the large area of the nanostructured layer to the substrates, a water-soluble polyvinyl alcohol mold was used. After generation and transference of the nanostructured layer, the polyvinyl alcohol mold was removed by dissolving in water. A residue-free, UV-curable, glue layer was formulated and used to bond the nanostructured layer onto the substrates. As a result, nanometer scale patterned polymer layers were bonded to various substrates and three-dimensional nanostructures were also fabricated by stacking of the layers.

Dense protective coatings, methods for their preparation and coated articles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tulyani, Sonia; Bhatia, Tania; Smeggil, John G.

A method for depositing a protective coating on a complex shaped substrate includes the steps of: (1) dipping a complex shaped substrate into a slurry to form a base coat thereon, the slurry comprising an aqueous solution, at least one refractory metal oxide, and at least one transient fluid additive present in an amount of about 0.1 percent to 10 percent by weight of the slurry; (2) curing the dipped substrate; (3) dipping the substrate into a precursor solution to form a top barrier coat thereon; and (4) heat treating the dipped, cured substrate to form a protective coating.

Strong Inhibition of O-Atom Transfer Reactivity for Mn(IV)(O)(π-Radical-Cation)(Lewis Acid) versus Mn(V)(O) Porphyrinoid Complexes.

PubMed

Zaragoza, Jan Paulo T; Baglia, Regina A; Siegler, Maxime A; Goldberg, David P

2015-05-27

The oxygen atom transfer (OAT) reactivity of two valence tautomers of a Mn(V)(O) porphyrinoid complex was compared. The OAT kinetics of Mn(V)(O)(TBP8Cz) (TBP8Cz = octakis(p-tert-butylphenyl)corrolazinato(3-)) reacting with a series of triarylphosphine (PAr3) substrates were monitored by stopped-flow UV-vis spectroscopy, and revealed second-order rate constants ranging from 16(1) to 1.43(6) × 10(4) M(-1) s(-1). Characterization of the OAT transition state analogues Mn(III)(OPPh3)(TBP8Cz) and Mn(III)(OP(o-tolyl)3)(TBP8Cz) was carried out by single-crystal X-ray diffraction (XRD). A valence tautomer of the closed-shell Mn(V)(O)(TBP8Cz) can be stabilized by the addition of Lewis and Brønsted acids, resulting in the open-shell Mn(IV)(O)(TBP8Cz(•+)):LA (LA = Zn(II), B(C6F5)3, H(+)) complexes. These Mn(IV)(O)(π-radical-cation) derivatives exhibit dramatically inhibited rates of OAT with the PAr3 substrates (k = 8.5(2) × 10(-3) - 8.7 M(-1) s(-1)), contrasting the previously observed rate increase of H-atom transfer (HAT) for Mn(IV)(O)(TBP8Cz(•+)):LA with phenols. A Hammett analysis showed that the OAT reactivity for Mn(IV)(O)(TBP8Cz(•+)):LA is influenced by the Lewis acid strength. Spectral redox titration of Mn(IV)(O)(TBP8Cz(•+)):Zn(II) gives Ered = 0.69 V vs SCE, which is nearly +700 mV above its valence tautomer Mn(V)(O)(TBP8Cz) (Ered = -0.05 V). These data suggest that the two-electron electrophilicity of the Mn(O) valence tautomers dominate OAT reactivity and do not follow the trend in one-electron redox potentials, which appear to dominate HAT reactivity. This study provides new fundamental insights regarding the relative OAT and HAT reactivity of valence tautomers such as M(V)(O)(porph) versus M(IV)(O)(porph(•+)) (M = Mn or Fe) found in heme enzymes.

Methods of selectively incorporating metals onto substrates

DOEpatents

Ernst; Richard D. , Eyring; Edward M. , Turpin; Gregory C. , Dunn; Brian C.

2008-09-30

A method for forming multi-metallic sites on a substrate is disclosed and described. A substrate including active groups such as hydroxyl can be reacted with a pretarget metal complex. The target metal attached to the active group can then be reacted with a secondary metal complex such that an oxidation-reduction (redox) reaction occurs to form a multi-metallic species. The substrate can be a highly porous material such as aerogels, xerogels, zeolites, and similar materials. Additional metal complexes can be reacted to increase catalyst loading or control co-catalyst content. The resulting compounds can be oxidized to form oxides or reduced to form metals in the ground state which are suitable for practical use.

Palladium pincer complex catalyzed stannyl and silyl transfer to propargylic substrates: synthetic scope and mechanism.

PubMed

Kjellgren, Johan; Sundén, Henrik; Szabó, Kálmán J

2005-02-16

Pincer complex catalyzed substitution of various propargylic substrates could be achieved using tin- and silicon-based dimetallic reagents to obtain propargyl- and allenylstannanes and silanes. These reactions involving chloride, mesylate, and epoxide substrates could be carried out under mild conditions, and therefore many functionalities (such as COOEt, OR, OH, NR, and NAc) are tolerated. It was shown that pincer catalysts with electron-supplying ligands, such as NCN, SCS, and SeCSe complexes, display the highest catalytic activity. The catalytic substitution of secondary propargyl chlorides and primary propargyl chlorides with electron-withdrawing substituents proceeds with high regioselectivity providing the allenyl product. Opening of the propargyl epoxides takes place with an excellent stereo- and regioselectivity to give stereodefined allenylstannanes. Silylstannanes as dimetallic reagents undergo an exclusive silyl transfer to the propargylic substrate affording allenylsilanes with high regioselectivity. According to our mechanistic studies, the key intermediate of the reaction is an organostannane (or silane)-coordinated pincer complex, which is formed from the dimetallic reagent and the corresponding pincer complex catalyst. DFT modeling studies have shown that the trimethylstannyl functionality is transferred to the propargylic substrate in a single reaction step with high allenyl selectivity. Inspection of the TS structures reveals that the trimethylstannyl group transfer is initiated by the attack of the palladium-tin sigma-bond electrons on the propargylic substrate. This is a novel mechanism in palladium chemistry, which is based on the unique topology of the pincer complex catalysts.

Total synthesis of complestatin: development of a Pd(0)-mediated indole annulation for macrocyclization.

PubMed

Shimamura, Hiroyuki; Breazzano, Steven P; Garfunkle, Joie; Kimball, F Scott; Trzupek, John D; Boger, Dale L

2010-06-09

Full details of the initial development and continued examination of a powerful intramolecular palladium(0)-mediated indole annulation for macrocyclization closure of the strained 16-membered biaryl ring system found in complestatin (1, chloropeptin II) and the definition of factors impacting its intrinsic atropodiastereoselectivity are described. Its examination and use in an alternative, second-generation total synthesis of complestatin are detailed in which the order of the macrocyclization reactions was reversed from our first-generation total synthesis. In this approach and with the ABCD biaryl ether ring system in place, the key Larock cyclization was conducted with substrate 36 (containing four phenols, five secondary amides, one carbamate, and four labile aryl chlorides) and provided the product 37 (56%) exclusively as a single atropisomer (>20:1, detection limits) possessing the natural (R)-configuration. In this instance, the complexity of the substrate and the reverse macrocyclization order did not diminish the atropodiastereoselectivity; rather, it provided an improvement over the 4:1 selectivity that was observed with the analogous substrate used to provide the isolated DEF ring system in our first-generation approach. Just as significant, the atroposelectivity represents a complete reversal of the diasteroselectivity observed with analogous macrocyclizations conducted using a Suzuki biaryl coupling.

Anticancer, antibacterial and antifungal activity of new ni (ii) and cu (ii) complexes of imidazole-phenanthroline derivatives.

PubMed

Moghadam, Mahboube Eslami; Divsalar, Adeleh; Zare, Marziye Shahraki; Gholizadeh, Roghayeh; Mahalleh, Doran; Saghatforosh, Lotfali; Sanati, Soheila

2017-11-02

Two new nickel(II) and copper(II) complexes of 2-(Furan-2-yl)-1H-Imidazo[4,5-f][1,10]Phenanthroline (FIP) and 2-(thiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline (TIP), imidazophen derivatives were synthesized. The structures of the compounds were determined by UV-visible and FT-IR spectroscopic methods and elemental analysis. The biological activities of Ni and Cu complexes, as anticancer agents, were tested against chronic myelogenous leukemia cell line, K562, at micromolar concentration. The MTT studies showed Cc 50 values are 21 and 160 µM for Cu and Ni(II) complexes, respectively; suggesting that Ni (II) complex has Cc 50 almost seven times of that obtained for cisplatin. Biological activity of the Ni(II) and Cu(II) complexes were also assayed against selective microorganisms by disc diffusion method. These results showed that the Cu(II) complex is antifungal agent but Ni(II) complex has antibacterial activity.

Synthesis, spectroscopic characterization, DNA interaction and biological activities of Mn(II), Co(II), Ni(II) and Cu(II) complexes with [(1H-1,2,4-triazole-3-ylimino)methyl]naphthalene-2-ol

NASA Astrophysics Data System (ADS)

Gaber, Mohamed; El-Wakiel, Nadia A.; El-Ghamry, Hoda; Fathalla, Shaimaa K.

2014-11-01

Manganese(II), cobalt(II), nickel(II) and copper(II) complexes of [(1H-1,2,4-triazole-3-ylimino)methyl]naphthalene-2-ol have been synthesized. The structure of complexes have been characterized by elemental analysis, molar conductance, magnetic moment measurements and spectral (IR, 1H NMR, EI-mass, UV-Vis and ESR), and thermal studies. The results showed that the chloro and nitrato Cu(II) complexes have octahedral geometry while Ni(II), Co(II) and Mn(II) complexes in addition to acetato Cu(II) complex have tetrahedral geometry. The possible structures of the metal complexes have been computed using the molecular mechanic calculations using the hyper chem. 8.03 molecular modeling program to confirm the proposed structures. The kinetic and thermodynamic parameters of the thermal decomposition steps were calculated from the TG curves. The binding modes of the complexes with DNA have been investigated by UV-Vis absorption titration. The results showed that the mode of binding of the complexes to DNA is intercalative or non-intercalative binding modes. Schiff base and its metal complexes have been screened for their in vitro antimicrobial activities against Gram positive bacteria (Staphylococcus aureus), Gram negative bacteria (Escherichia coli and Pesudomonas aeruginosa), fungi (Asperigllus flavus and Mucer) and yeast (Candida albicans and Malassezia furfur).

Heterobimetallic Complexes with MIII-(μ-OH)-MII Cores (MIII = Fe, Mn, Ga; MII = Ca, Sr, and Ba): Structural, Kinetic, and Redox Properties

PubMed Central

Park, Young Jun; Cook, Sarah A.; Sickerman, Nathaniel S.; Sano, Yohei; Ziller, Joseph W.

2013-01-01

The effects of redox-inactive metal ions on dioxygen activation were explored using a new FeII complex containing a tripodal ligand with 3 sulfonamido groups. This iron complex exhibited a faster initial rate for the reduction of O2 than its MnII analog. Increases in initial rates were also observed in the presence of group 2 metal ions for both the FeII and MnII complexes, which followed the trend NMe4+ < BaII < CaII = SrII. These studies led to the isolation of heterobimetallic complexes containing FeIII-(μ-OH)-MII cores (MII = Ca, Sr, and Ba) and one with a [SrII(OH)MnIII]+ motif. The analogous [CaII(OH)GaIII]+ complex was also prepared and its solid state molecular structure is nearly identical to that of the [CaII(OH)FeIII]+ system. Nuclear magnetic resonance studies indicated that the diamagnetic [CaII(OH)GaIII]+ complex retained its structure in solution. Electrochemical measurements on the heterobimetallic systems revealed similar one-electron reduction potentials for the [CaII(OH)FeIII]+ and [SrII(OH)FeIII]+ complexes, which were more positive than the potential observed for [BaII(OH)FeIII]+. Similar results were obtained for the heterobimetallic MnII complexes. These findings suggest that Lewis acidity is not the only factor to consider when evaluating the effects of group 2 ions on redox processes, including those within the oxygen-evolving complex of Photosystem II. PMID:24058726

A movie of the RNA polymerase nucleotide addition cycle.

PubMed

Brueckner, Florian; Ortiz, Julio; Cramer, Patrick

2009-06-01

During gene transcription, RNA polymerase (Pol) passes through repetitive cycles of adding a nucleotide to the growing mRNA chain. Here we obtained a movie of the nucleotide addition cycle by combining structural information on different functional states of the Pol II elongation complex (EC). The movie illustrates the two-step loading of the nucleoside triphosphate (NTP) substrate, closure of the active site for catalytic nucleotide incorporation, and the presumed two-step translocation of DNA and RNA, which is accompanied by coordinated conformational changes in the polymerase bridge helix and trigger loop. The movie facilitates teaching and a mechanistic analysis of transcription and can be downloaded from http://www.lmb.uni-muenchen.de/cramer/pr-materials.

Synthesis, characterization, and ligand exchange reactivity of a series of first row divalent metal 3-hydroxyflavonolate complexes.

PubMed

Grubel, Katarzyna; Rudzka, Katarzyna; Arif, Atta M; Klotz, Katie L; Halfen, Jason A; Berreau, Lisa M

2010-01-04

A series of divalent metal flavonolate complexes of the general formula [(6-Ph(2)TPA)M(3-Hfl)]X (1-5-X; X = OTf(-) or ClO(4)(-); 6-Ph(2)TPA = N,N-bis((6-phenyl-2-pyridyl)methyl)-N-((2-pyridyl)methyl)amine; M = Mn(II), Co(II), Ni(II), Cu(II), Zn(II); 3-Hfl = 3-hydroxyflavonolate) were prepared and characterized by X-ray crystallography, elemental analysis, FTIR, UV-vis, (1)H NMR or EPR, and cyclic voltammetry. All of the complexes have a bidentate coordinated flavonolate ligand. The difference in M-O distances (Delta(M-O)) involving this ligand varies through the series, with the asymmetry of flavonolate coordination increasing in the order Mn(II) approximately Ni(II) < Cu(II) < Zn(II) < Co(II). The hypsochromic shift of the absorption band I (pi-->pi*) of the coordinated flavonolate ligand in 1-5-OTf (relative to that in free anion) increases in the order Ni(II) < Mn(II) < Cu(II) < Zn(II), Co(II). Previously reported 3-Hfl complexes of divalent metals fit well with this ordering. (1)H NMR studies indicate that the 3-Hfl complexes of Co(II), Ni(II), and Zn(II) exhibit a pseudo-octahedral geometry in solution. EPR studies suggest that the Mn(II) complex 1-OTf may form binuclear structures in solution. The mononuclear Cu(II) complex 4-OTf has a distorted square pyramidal geometry. The oxidation potential of the flavonolate ligand depends on the metal ion present and/or the solution structure of the complex, with the Mn(II) complex 1-OTf exhibiting the lowest potential, followed by the pseudo-octahedral Ni(II) and Zn(II) 3-Hfl complexes, and the distorted square pyramidal Cu(II) complex 4-OTf. The Mn(II) complex [(6-Ph(2)TPA)Mn(3-Hfl)]OTf (1-OTf) is unique in the series in undergoing ligand exchange reactions in the presence of M(ClO(4))(2).6H(2)O (M = Co, Ni, Zn) in CD(3)CN to produce [(6-Ph(2)TPA)M(CD(3)CN)(n)](X)(2), [Mn(3-Hfl)(2).0.5H(2)O], and MnX(2) (X = OTf(-) or ClO(4)(-)). Under similar conditions, the 3-Hfl complexes of Co(II), Ni(II), and Cu(II) undergo flavonolate ligand exchange to produce [(6-Ph(2)TPA)M(CD(3)CN)(n)](X)(2) (M = Co, Ni, Cu; n = 1 or 2) and [Zn(3-Hfl)(2).2H(2)O]. An Fe(II) complex of 3-Hfl, [(6-Ph(2)TPA)Fe(3-Hfl)]ClO(4) (8), was isolated and characterized by elemental analysis, FTIR, UV-vis, (1)H NMR, cyclic voltammetry, and a magnetic moment measurement. This complex reacts with O(2) to produce the diiron(III) mu-oxo compound [(6-Ph(2)TPAFe(3Hfl))(2)(mu-O)](ClO(4))(2) (6).

The Legionella IcmS-IcmW protein complex is important for Dot/Icm-mediated protein translocation.

PubMed

Ninio, Shira; Zuckman-Cholon, Deborah M; Cambronne, Eric D; Roy, Craig R

2005-02-01

The intracellular pathogen Legionella pneumophila can infect and replicate within macrophages of a human host. To establish infection, Legionella require the Dot/Icm secretion system to inject protein substrates directly into the host cell cytoplasm. The mechanism by which substrate proteins are engaged and translocated by the Dot/Icm system is not well understood. Here we show that two cytosolic components of the Dot/Icm secretion machinery, the proteins IcmS and IcmW, play an important role in substrate translocation. Biochemical analysis indicates that IcmS and IcmW form a stable protein complex. In Legionella, the IcmW protein is rapidly degraded in the absence of the IcmS protein. Substrate proteins translocated into mammalian host cells by the Dot/Icm system were identified using the IcmW protein as bait in a yeast two-hybrid screen. It was determined that the IcmS-IcmW complex interacts with these substrates and plays an important role in translocation of these proteins into mammalian cells. These data are consistent with the IcmS-IcmW complex being involved in the recognition and Dot/Icm-dependent translocation of substrate proteins during Legionella infection of host cells.

Substrate-mediated delivery of gene complex nanoparticles via polydopamine coating for enhancing competitiveness of endothelial cells.

PubMed

Li, Bo-Chao; Chang, Hao; Ren, Ke-Feng; Ji, Jian

2016-11-01

Substrate-mediated delivery of functional plasmid DNA (pDNA) has been proven to be a promising strategy to promote competitiveness of endothelial cells (ECs) over smooth muscle cells (SMCs), which is beneficial to inducing fast endothelialization of implanted vascular devices. Thus, it is of great importance to develop universal approaches with simplicity and easiness to immobilize DNA complex nanoparticles on substrates. In this study, the bioinspired polydopamine (PDA) coating was employed in immobilization of DNA complex nanoparticles, which were composed of protamine (PrS) and plasmid DNA encoding with hepatocyte growth factor (HGF-pDNA) gene. We demonstrated that the DNA complex nanoparticles can be successfully immobilized onto the PDA surface. Consequently, the HGF expression of both ECs and SMCs were significantly improved when they cultured on the DNA complex nanoparticles-immobilized substrates. Furthermore, EC proliferation was specifically promoted due to bioactivity of HGF, leading to an enhancement of EC competitiveness over SMCs. Our findings demonstrated the substrate-mediated functional gene nanoparticle delivery through PDA coating as a simple and efficient approach. It may hold great potential in the field of interventional cardiovascular implants. Copyright © 2016 Elsevier B.V. All rights reserved.

Re-engineering of CYP2C9 to probe acid-base substrate selectivity.

PubMed

Tai, Guoying; Dickmann, Leslie J; Matovic, Nicholas; DeVoss, James J; Gillam, Elizabeth M J; Rettie, Allan E

2008-10-01

A common feature of many CYP2C9 ligands is their weak acidity. As revealed by crystallography, the structural basis for this behavior involves a charge-pairing interaction between an anionic moiety on the substrate and an active site R108 residue. In the present study we attempted to re-engineer CYP2C9 to better accept basic ligands by charge reversal at this key residue. We expressed and purified the R108E and R108E/D293N mutants and compared their ability with that of native CYP2C9 to interact with (S)-warfarin, diclofenac, pyrene, propranolol, and ibuprofen amine. As expected, the R108E mutant maintained all the native enzyme's pyrene 1-hydroxylation activity, but catalytic activity toward diclofenac and (S)-warfarin was abrogated. In contrast, the double mutant displayed much less selectivity in its behavior toward these control ligands. Neither of the mutants displayed significant enhancement of propranolol metabolism, and all three preparations exhibited a type II (inhibitor) rather than type I (substrate) spectrum with ibuprofen amine, although binding became progressively weaker with the single and double mutants. Collectively, these data underscore the importance of the amino acid at position 108 in the acid substrate selectivity of CYP2C9, highlight the accommodating nature of the CYP2C9 active site, and provide a cautionary note regarding facile re-engineering of these complex cytochrome P450 active sites.

Re-engineering of CYP2C9 to Probe Acid-Base Substrate Selectivity

PubMed Central

Tai, Guoying; Dickmann, Leslie J.; Matovic, Nicholas; DeVoss, James J.; Gillam, Elizabeth M. J.; Rettie, Allan E.

2009-01-01

A common feature of many CYP2C9 ligands is their weak acidity. As revealed by crystallography, the structural basis for this behavior involves a charge-pairing interaction between an anionic moiety on the substrate and an active site R108 residue. In the present study we attempted to re-engineer CYP2C9 to better accept basic ligands by charge reversal at this key residue. We expressed and purified the R108E and R108E/D293N mutants and compared their ability with that of native CYP2C9 to interact with (S)-warfarin, diclofenac, pyrene, propranolol, and ibuprofen amine. As expected, the R108E mutant maintained all the native enzyme's pyrene 1-hydroxylation activity, but catalytic activity toward diclofenac and (S)-warfarin was abrogated. In contrast, the double mutant displayed much less selectivity in its behavior toward these control ligands. Neither of the mutants displayed significant enhancement of propranolol metabolism, and all three preparations exhibited a type II (inhibitor) rather than type I (substrate) spectrum with ibuprofen amine, although binding became progressively weaker with the single and double mutants. Collectively, these data underscore the importance of the amino acid at position 108 in the acid substrate selectivity of CYP2C9, highlight the accommodating nature of the CYP2C9 active site, and provide a cautionary note regarding facile re-engineering of these complex cytochrome P450 active sites. PMID:18606741

Purification of Restriction Endonuclease EcoRII and its Co-Crystallization

NASA Technical Reports Server (NTRS)

Karpova, E. A.; Chen, L.; Meehan, E.; Pusey, M.; Rose, M. Franklin (Technical Monitor)

2000-01-01

Restriction endonuclease EcoRII (EcoRII) is a homodimeric DNA-binding protein. It belongs to the type II family of restriction-modification enzymes (subclass IIe). EcoRII recognizes the nucleotide sequence 5'-CCWGG (W=A or T) and cleaves the phosphodiester bond preceding the first cytosine. Methylation at C5 of the second cytosine inhibits cleavage. The enzyme has a unique ability to search for the presence of two substrate sites before cleavage. To the best of our knowledge no other subclass IIe restriction endonuclease has been crystallized yet, without or with a DNA-substrate. We have recently grown and characterized the crystals of this enzyme (1) Here we report on the result of co-crystallization experiments of EcoRII with an 11 b.p. oligonucleotide substrate. The dissociation constant (Kd) EcoRII: 11 b.p. was determined earlier (unpublished results). The needle-like crystals of oligonucleotide-EcoRII protein complex were obtained with this substrate by the technique of vapor diffusion hanging drops. The crystals obtained were washed and dissolved in an aliquot of 10 mM Tris-HCl buffer, pH=7.5. Running a portion of this solution on the SDS-get indicated the presence of endonuclease in the solution. A UV-spectrophotometric test of a second portion confirmed the presence of DNA. We are now working on improvement of the DNA-EcoRII protein crystals. Results obtained from these and ongoing efforts will be reported.

Mechanism of the 2,3-diphosphoglycerate-dependent phosphoglycerate mutase from rabbit muscle.

PubMed

Britton, H G; Clarke, J B

1972-11-01

1. The properties and kinetics of the 2,3-diphosphoglycerate-dependent phosphoglycerate mutases are discussed. There are at least three possible mechanisms for the reaction: (i) a phosphoenzyme (Ping Pong) mechanism; (ii) an intermolecular transfer of phosphate from 2,3-diphosphoglycerate to the substrates (sequential mechanism); (iii) an intramolecular transfer of phosphate. It is concluded that these mechanisms cannot be distinguished by conventional kinetic measurements. 2. The fluxes for the different mechanisms are calculated and it is shown that it should be possible to distinguish between the mechanisms by appropriate induced-transport tests and by comparing the fluxes of (32)P- and (14)C-labelled substrates at chemical equilibrium. 3. With (14)C-labelled substrates no induced transport was found over a wide concentration range, and with (32)P-labelled substrates co-transport occurred that was independent of concentration over a twofold range. (14)C-labelled substrates exchange at twice the rate of (32)P-labelled substrates at chemical equilibrium. The results were completely in accord with a phosphoenzyme mechanism and indicated a rate constant for the isomerization of the phosphoenzyme of not less than 4x10(6)s(-1). The intramolecular transfer of phosphate (and intermolecular transfer between two or more molecules of substrate) were completely excluded. The intermolecular transfer of phosphate from 2,3-diphosphoglycerate would have been compatible with the results only if the K(m) for 2-phosphoglycerate had been over 7.5-fold smaller than the observed value and if an isomerization of the enzyme-2,3-diphosphoglycerate complex had been the major rate-limiting step in the reaction. 4. The very rapid isomerization of the phosphoenzyme that the experiments demonstrate suggests a mechanism that does not involve a formal isomerization. According to this new scheme the enzyme is closely related mechanistically and perhaps evolutionarily to a 2,3-diphosphoglycerate diphosphatase.

Mechanism of the 2,3-diphosphoglycerate-dependent phosphoglycerate mutase from rabbit muscle

PubMed Central

Britton, H. G.; Clarke, J. B.

1972-01-01

1. The properties and kinetics of the 2,3-diphosphoglycerate-dependent phosphoglycerate mutases are discussed. There are at least three possible mechanisms for the reaction: (i) a phosphoenzyme (Ping Pong) mechanism; (ii) an intermolecular transfer of phosphate from 2,3-diphosphoglycerate to the substrates (sequential mechanism); (iii) an intramolecular transfer of phosphate. It is concluded that these mechanisms cannot be distinguished by conventional kinetic measurements. 2. The fluxes for the different mechanisms are calculated and it is shown that it should be possible to distinguish between the mechanisms by appropriate induced-transport tests and by comparing the fluxes of 32P- and 14C-labelled substrates at chemical equilibrium. 3. With 14C-labelled substrates no induced transport was found over a wide concentration range, and with 32P-labelled substrates co-transport occurred that was independent of concentration over a twofold range. 14C-labelled substrates exchange at twice the rate of 32P-labelled substrates at chemical equilibrium. The results were completely in accord with a phosphoenzyme mechanism and indicated a rate constant for the isomerization of the phosphoenzyme of not less than 4×106s−1. The intramolecular transfer of phosphate (and intermolecular transfer between two or more molecules of substrate) were completely excluded. The intermolecular transfer of phosphate from 2,3-diphosphoglycerate would have been compatible with the results only if the Km for 2-phosphoglycerate had been over 7.5-fold smaller than the observed value and if an isomerization of the enzyme-2,3-diphosphoglycerate complex had been the major rate-limiting step in the reaction. 4. The very rapid isomerization of the phosphoenzyme that the experiments demonstrate suggests a mechanism that does not involve a formal isomerization. According to this new scheme the enzyme is closely related mechanistically and perhaps evolutionarily to a 2,3-diphosphoglycerate diphosphatase. PMID:4677138

The Structure of Lombricine Kinase: Implications for Phosphagen Conformational Changes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bush, D. Jeffrey; Kirillova, Olga; Clark, Shawn A.

2012-05-29

Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309-317, which is disordered in substrate-free structures of homologs and is known from the NMR ofmore » arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His{sup 178}. Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates.« less

Cyanide as a copper and quinone-directed inhibitor of amine oxidases from pea seedlings ( Pisum sativum) and Arthrobacter globiformis: evidence for both copper coordination and cyanohydrin derivatization of the quinone cofactor.

PubMed

Shepard, Eric M; Juda, Gregory A; Ling, Ke-Qing; Sayre, Lawrence M; Dooley, David M

2004-04-01

The interactions of cyanide with two copper-containing amine oxidases (CuAOs) from pea seedlings (PSAO) and the soil bacterium Arthrobacter globiformis (AGAO) have been investigated by spectroscopic and kinetic techniques. Previously, we rationalized the effects of azide and cyanide for several CuAOs in terms of copper coordination by these exogenous ligands and their effects on the internal redox equilibrium TPQ(amr)-Cu(II) right harpoon over left harpoon TPQ(sq)-Cu(I). The mechanism of cyanide inhibition was proposed to occur through complexation to Cu(I), thereby directly competing with O(2) for reoxidation of TPQ. Although cyanide readily and reversibly reacts with quinones, no direct spectroscopic evidence for cyanohydrin derivatization of TPQ has been previously documented for CuAOs. This work describes the first direct spectroscopic evidence, using both model and enzyme systems, for cyanohydrin derivatization of TPQ. K(d) values for Cu(II)-CN(-) and Cu(I)-CN(-), as well as the K(i) for cyanide inhibition versus substrate amine, are reported for PSAO and AGAO. In spite of cyanohydrin derivatization of the TPQ cofactor in these enzymes, the uncompetitive inhibition of amine oxidation is determined to arise almost exclusively through CN(-) complexation of Cu(I).

Time-dependent 31P saturation transfer in the phosphoglucomutase reaction. Characterization of the spin system for the Cd(II) enzyme and evaluation of rate constants for the transfer process.

PubMed

Post, C B; Ray, W J; Gorenstein, D G

1989-01-24

Time-dependent 31P saturation-transfer studies were conducted with the Cd2+-activated form of muscle phosphoglucomutase to probe the origin of the 100-fold difference between its catalytic efficiency (in terms of kcat) and that of the more efficient Mg2+-activated enzyme. The present paper describes the equilibrium mixture of phosphoglucomutase and its substrate/product pair when the concentration of the Cd2+ enzyme approaches that of the substrate and how the nine-spin 31P NMR system provided by this mixture was treated. It shows that the presence of abortive complexes is not a significant factor in the reduced activity of the Cd2+ enzyme since the complex of the dephosphoenzyme and glucose 1,6-bisphosphate, which accounts for a large majority of the enzyme present at equilibrium, is catalytically competent. It also shows that rate constants for saturation transfer obtained at three different ratios of enzyme to free substrate are mutually compatible. These constants, which were measured at chemical equilibrium, can be used to provide a quantitative kinetic rationale for the reduced steady-state activity elicited by Cd2+ relative to Mg2+ [cf. Ray, W.J., Post, C.B., & Puvathingal, J.M. (1989) Biochemistry (following paper in this issue)]. They also provide minimal estimates of 350 and 150 s-1 for the rate constants describing (PO3-) transfer from the Cd2+ phosphoenzyme to the 6-position of bound glucose 1-phosphate and to the 1-position of bound glucose 6-phosphate, respectively. These minimal estimates are compared with analogous estimates for the Mg2+ and Li+ forms of the enzyme in the accompanying paper.

Malfunctioning of Chaperone-Mediated Autophagy in Parkinson's Disease: Feats, Constraints, and Flaws of Modulators.

PubMed

Tripathi, Manish Kumar; Rajput, Charul; Mishra, Saumya; Rasheed, Mohd Sami Ur; Singh, Mahendra Pratap

2018-06-11

Homeostatic regulation of class II programmed cell death/autophagy for the degradation and elimination of substandard organelles and defective proteins is decisive for the survival of dopaminergic neurons. Chaperone-mediated autophagy (CMA), one of the most highly dedicated self-sacrificing events, is accountable for the partial elimination of redundant soluble cytoplasmic proteins in Parkinson's disease (PD). CMA is characterized by the selective delivery of superfluous protein containing lysine-phenylalanine-glutamate-arginine-glutamine (KFERQ)/KFERQ-like motif to the lysosome through molecular chaperones, such as heat shock cognate-70 (Hsc-70). KFERQ/KFERQ-like motif present in the poor quality cytoplasmic substrate protein and Hsc-70 complex is recognized by a janitor protein, which is referred to as the lysosome-associated membrane protein-2A (LAMP-2A). This protein is known to facilitate an entry of substrate-chaperone complex in the lumen for hydrolytic cleavage of substrate and elimination of end-products. Impaired CMA is repeatedly blamed for an accumulation of surplus soluble proteins. However, it is still an enigma if CMA is a bonus or curse for PD. Case-control studies and cellular and animal models have deciphered the contribution of impaired CMA in PD. Current article updates the role of CMA in toxicant models and recapitulates the evidences that have highlighted a link between impaired CMA and PD. Although PD is an irreversible happening and CMA is a dual edging phenomenon, it is anticipated that fine-tuning of the latter encounters the former to a certain extent. Besides, the truth, embellishment, and propaganda regarding the issue are also emphasized in the final segment of the article.

Mutations in Kelch-like 3 and Cullin 3 cause hypertension and electrolyte abnormalities

PubMed Central

Boyden, Lynn M.; Choi, Murim; Choate, Keith A.; Nelson-Williams, Carol J.; Farhi, Anita; Toka, Hakan R.; Tikhonova, Irina R.; Bjornson, Robert; Mane, Shrikant M.; Colussi, Giacomo; Lebel, Marcel; Gordon, Richard D.; Semmekrot, Ben A.; Poujol, Alain; Välimäki, Matti J.; De Ferrari, Maria E.; Sanjad, Sami A.; Gutkin, Michael; Karet, Fiona E.; Tucci, Joseph R.; Stockigt, Jim R.; Keppler-Noreuil, Kim M.; Porter, Craig C.; Anand, Sudhir K.; Whiteford, Margo L.; Davis, Ira D.; Dewar, Stephanie B.; Bettinelli, Alberto; Fadrowski, Jeffrey J.; Belsha, Craig W.; Hunley, Tracy E.; Nelson, Raoul D.; Trachtman, Howard; Cole, Trevor R. P.; Pinsk, Maury; Bockenhauer, Detlef; Shenoy, Mohan; Vaidyanathan, Priya; Foreman, John W.; Rasoulpour, Majid; Thameem, Farook; Al-Shahrouri, Hania Z.; Radhakrishnan, Jai; Gharavi, Ali G.; Goilav, Beatrice; Lifton, Richard P.

2012-01-01

Hypertension affects one billion people and is a principal reversible risk factor for cardiovascular disease. A rare Mendelian syndrome, pseudohypoaldosteronism type II (PHAII), featuring hypertension, hyperkalemia, and metabolic acidosis, has revealed previously unrecognized physiology orchestrating the balance between renal salt reabsorption versus K+ and H+ excretion1. We used exome sequencing to identify mutations in Kelch-like 3 (KLHL3) or Cullin 3 (CUL3) in 41 PHAII kindreds. KLHL3 mutations are either recessive or dominant, while CUL3 mutations are dominant and predominantly de novo. CUL3 and BTB-Kelch proteins such as KLHL3 are components of Cullin/RING E3 ligase complexes (CRLs) that ubiquitinate substrates bound to Kelch propeller domains2–8. Dominant KLHL3 mutations are clustered in short segments within the Kelch propeller and BTB domains implicated in substrate9 and Cullin5 binding, respectively. Diverse CUL3 mutations all result in skipping of exon 9, producing an in-frame deletion. Because dominant KLHL3 and CUL3 mutations both phenocopy recessive loss-of-function KLHL3 mutations, they may abrogate ubiquitination of KLHL3 substrates. Disease features are reversed by thiazide diuretics, which inhibit the Na-Cl cotransporter (NCC) in the distal nephron of the kidney; KLHL3 and CUL3 are expressed in this location, suggesting a mechanistic link between KLHL3/CUL3 mutations, increased Na-Cl reabsorption, and disease pathogenesis. These findings demonstrate the utility of exome sequencing in disease gene identification despite combined complexities of locus heterogeneity, mixed models of transmission, and frequent de novo mutation, and establish a fundamental role for KLHL3/CUL3 in blood pressure, K+, and pH homeostasis. PMID:22266938

Mutations in the substrate binding site of human heat-shock protein 70 indicate specific interaction with HLA-DR outside the peptide binding groove

PubMed Central

Rohrer, Karin M; Haug, Markus; Schwörer, Daniela; Kalbacher, Hubert; Holzer, Ursula

2014-01-01

Heat-shock protein 70 (Hsp70)–peptide complexes are involved in MHC class I-and II-restricted antigen presentation, enabling enhanced activation of T cells. As shown previously, mammalian cytosolic Hsp70 (Hsc70) molecules interact specifically with HLA-DR molecules. This interaction might be of significance as Hsp70 molecules could transfer bound antigenic peptides in a ternary complex into the binding groove of HLA-DR molecules. The present study provides new insights into the distinct interaction of Hsp70 with HLA-DR molecules. Using a quantitative binding assay, it could be demonstrated that a point mutation of amino acids alanine 406 and valine 438 in the substrate binding pocket led to reduced peptide binding compared with the wild-type Hsp70 whereas HLA-DR binding remains unaffected. The removal of the C-terminal lid neither altered the substrate binding capacity nor the Hsp70 binding characteristics to HLA-DR. A truncated variant lacking the nucleotide binding domain showed no binding interactions with HLA-DR. Furthermore, the truncated ATPase subunit of constitutively expressed Hsc70 revealed similar binding affinities to HLA-DR compared with the complete Hsc70. Hence, it can be assumed that the Hsp70–HLA-DR interaction takes place outside the peptide binding groove and is attributed to the ATPase domain of HSP70 molecules. The Hsp70-chaperoned peptides might thereby be directly transferred into the binding groove of HLA-DR, so enabling enhanced presentation of the peptide on antigen-presenting cells and leading to an improved proliferation of responding T cells as shown previously. PMID:24428437

Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O -Methyltransferases.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernard, Steffen M.; Akey, David L.; Tripathi, Ashootosh

Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates,more » show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homolog, active site residues were identified that correlate with the 3'- or 4'- specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. Lastly, this classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.« less

Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O -Methyltransferases.

DOE PAGES

Bernard, Steffen M.; Akey, David L.; Tripathi, Ashootosh; ...

2015-02-18

Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates,more » show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homolog, active site residues were identified that correlate with the 3'- or 4'- specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. Lastly, this classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.« less

Structural characterization and antioxidant properties of Cu(II) and Ni(II) complexes derived from dicyandiamide

NASA Astrophysics Data System (ADS)

Kertmen, Seda Nur; Gonul, Ilyas; Kose, Muhammet

2018-01-01

New Cu(II) and Ni(II) complexes derived from dicyandiamide were synthesized and characterised by spectroscopic and analytical methods. Molecular structures of the complexes were determined by single crystal X-ray diffraction studies. In the complexes, the Cu(II) or Ni(II) ions are four-coordinate with a slight distorted square planar geometry. The ligands (L-nPen and L-iPen) derived from dicyandiamide formed via nucleophilic addition of alcohol solvent molecule in the presence Cu(II) or Ni(II) ions. Complexes were stabilised by intricate array of hydrogen bonding interactions. Antioxidant activity of the complexes was evaluated by DPPH radical scavenging and CUPRAC methods. The complexes exhibit antioxidant activity, however, their activities were much lower than standard antioxidants (Vitamin C and trolox).

Protein kinase A catalytic subunit primed for action: Time-lapse crystallography of Michaelis complex formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Das, Amit; Gerlits, Oksana O.; Parks, Jerry M.

The catalytic subunit of the cyclic AMP-dependent protein kinase A (PKAc) catalyzes the transfer of the γ-phosphate of bound Mg 2ATP to a serine or threonine residue of a protein substrate. Here, time-lapse X-ray crystallography was used to capture a series of complexes of PKAc with an oligopeptide substrate and unreacted Mg 2ATP, including the Michaelis complex, that reveal important geometric rearrangements in and near the active site preceding the phosphoryl transfer reaction. Contrary to the prevailing view, Mg 2+ binds first to the M1 site as a complex with ATP and is followed by Mg 2+ binding to themore » M2 site. Furthermore, the target serine hydroxyl of the peptide substrate rotates away from the active site toward the bulk solvent, which breaks the hydrogen bond with D166. In conclusion, the serine hydroxyl of the substrate rotates back toward D166 to form the Michaelis complex with the active site primed for phosphoryl transfer.« less

Protein kinase A catalytic subunit primed for action: Time-lapse crystallography of Michaelis complex formation

DOE PAGES

Das, Amit; Gerlits, Oksana O.; Parks, Jerry M.; ...

2015-11-12

The catalytic subunit of the cyclic AMP-dependent protein kinase A (PKAc) catalyzes the transfer of the γ-phosphate of bound Mg 2ATP to a serine or threonine residue of a protein substrate. Here, time-lapse X-ray crystallography was used to capture a series of complexes of PKAc with an oligopeptide substrate and unreacted Mg 2ATP, including the Michaelis complex, that reveal important geometric rearrangements in and near the active site preceding the phosphoryl transfer reaction. Contrary to the prevailing view, Mg 2+ binds first to the M1 site as a complex with ATP and is followed by Mg 2+ binding to themore » M2 site. Furthermore, the target serine hydroxyl of the peptide substrate rotates away from the active site toward the bulk solvent, which breaks the hydrogen bond with D166. In conclusion, the serine hydroxyl of the substrate rotates back toward D166 to form the Michaelis complex with the active site primed for phosphoryl transfer.« less

Analysis of splicing complexes on native gels.

PubMed

Ares, Manuel

2013-10-01

Splicing requires a complex set of ATP-dependent macromolecular associations that lead to the rearrangement of just a few covalent bonds in the pre-mRNA substrate. Seeing only the covalent bonds breaking and forming is seeing only a very small part of the process. Analysis of native splicing complexes into which the radiolabeled substrate has been assembled, but not necessarily completely reacted, has provided a good understanding of the process. This protocol describes a gel method for detecting and analyzing yeast splicing complexes formed in vitro on a radiolabeled pre-mRNA substrate. Complexes formed during the splicing reaction are quenched by dilution and addition of an excess of RNA, which is thought to strip nonspecifically bound proteins from the labeled substrate RNA. After loading on a low-percentage, low-cross-linking ratio composite agarose-acrylamide gel (in 10% glycerol), labeled bands are detected. These can be extracted and shown to contain small nuclear RNAs (snRNAs) and partly reacted pre-mRNA.

Synthesis, spectral studies and biological evaluation of 2-aminonicotinic acid metal complexes

NASA Astrophysics Data System (ADS)

Nawaz, Muhammad; Abbasi, Muhammad Waseem; Hisaindee, Soleiman; Zaki, Muhammad Javed; Abbas, Hira Fatima; Mengting, Hu; Ahmed, M. Arif

2016-05-01

We synthesized 2-aminonicotinic acid (2-ANA) complexes with metals such as Co(II), Fe(III), Ni(II), Mn(II), Zn(II), Ag(I),Cr(III), Cd(II) and Cu(II) in aqueous media. The complexes were characterized and elucidated using FT-IR, UV-Vis, a fluorescence spectrophotometer and thermo gravimetric analysis (TGA). TGA data showed that the stoichiometry of complexes was 1:2 metal/ligand except for Ag(I) and Mn(II) where the ratio was 1:1. The metal complexes showed varied antibacterial, fungicidal and nematicidal activities. The silver and zinc complexes showed highest activity against Bacillus subtilis and Bacillus licheniformis respectively. Fusarium oxysporum was highly susceptible to nickel and copper complexes whereas Macrophomina phaseolina was completely inert to the complexes. The silver and cadmium complexes were effective against the root-knot nematode Meloidogyne javanica.

Synthesis, spectroscopic and thermal studies of transition metal complexes derived from benzil and diethylenetriamine

NASA Astrophysics Data System (ADS)

Khan, Sadaf; Nami, Shahab A. A.; Siddiqi, K. S.

2007-10-01

A macrocyclic ligand, bdta (where bdta = 3,6,9,12,15,18-hexaaza-1,2,10,11-tetraphenyl-2,9,11,18-tetraenecyclododecane) has been prepared by cyclocondensation of benzil with diethylenetriamine which efficiently encapsulates transition as well as pseudo-transition metal ions leading to the formation of M(bdta)Cl 2 type complexes [where M = Mn(II), Fe(II), Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and Hg(II)]. The analytical, spectroscopic and magnetic moment data suggests an octahedral geometry for all the complexes. EPR spectra of Mn(II) and Cu(II) show considerable exchange interaction in the complex. They are non-conducting in DMSO. The TGA profile of the ligand and its complexes are identical and consists of two discreet stages. The voltammogram of Cu-complex exhibits a quasi-reversible one-electron transfer wave for Cu(II)/Cu(I) couple.

Synthesis, spectroscopic and thermal studies of transition metal complexes derived from benzil and diethylenetriamine.

PubMed

Khan, Sadaf; Nami, Shahab A A; Siddiqi, K S

2007-10-01

A macrocyclic ligand, bdta (where bdta=3,6,9,12,15,18-hexaaza-1,2,10,11-tetraphenyl-2,9,11,18-tetraenecyclododecane) has been prepared by cyclocondensation of benzil with diethylenetriamine which efficiently encapsulates transition as well as pseudo-transition metal ions leading to the formation of M(bdta)Cl2 type complexes [where M=Mn(II), Fe(II), Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and Hg(II)]. The analytical, spectroscopic and magnetic moment data suggests an octahedral geometry for all the complexes. EPR spectra of Mn(II) and Cu(II) show considerable exchange interaction in the complex. They are non-conducting in DMSO. The TGA profile of the ligand and its complexes are identical and consists of two discreet stages. The voltammogram of Cu-complex exhibits a quasi-reversible one-electron transfer wave for Cu(II)/Cu(I) couple.

Insight into the substrate specificity change caused by the Y227H mutation of α-glucosidase III from the European honeybee (Apis mellifera) through molecular dynamics simulations.

PubMed

Na Ayutthaya, Pratchaya Pramoj; Chanchao, Chanpen; Chunsrivirot, Surasak

2018-01-01

Honey from the European honeybee, Apis mellifera, is produced by α-glucosidases (HBGases) and is widely used in food, pharmaceutical, and cosmetic industries. Categorized by their substrate specificities, HBGases have three isoforms: HBGase I, II and III. Previous experimental investigations showed that wild-type HBGase III from Apis mellifera (WT) preferred sucrose to maltose as a substrate, while the Y227H mutant (MT) preferred maltose to sucrose. This mutant can potentially be used for malt hydrolysis because it can efficiently hydrolyze maltose. In this work, to elucidate important factors contributing to substrate specificity of this enzyme and gain insight into how the Y227H mutation causes substrate specificity change, WT and MT homology models were constructed, and sucrose/maltose was docked into active sites of the WT and MT. AMBER14 was employed to perform three independent molecular dynamics runs for these four complexes. Based on the relative binding free energies calculated by the MM-GBSA method, sucrose is better than maltose for WT binding, while maltose is better than sucrose for MT binding. These rankings support the experimentally observed substrate specificity that WT preferred sucrose to maltose as a substrate, while MT preferred maltose to sucrose, suggesting the importance of binding affinity for substrate specificity. We also found that the Y227H mutation caused changes in the proximities between the atoms necessary for sucrose/maltose hydrolysis that may affect enzyme efficiency in the hydrolysis of sucrose/maltose. Moreover, the per-residue binding free energy decomposition results show that Y227/H227 may be a key residue for preference binding of sucrose/maltose in the WT/MT active site. Our study provides important and novel insight into the binding of sucrose/maltose in the active site of Apis mellifera HBGase III and into how the Y227H mutation leads to the substrate specificity change at the molecular level. This knowledge could be beneficial in the design of this enzyme for increased production of desired products.

Point-of-need simultaneous electrochemical detection of lead and cadmium using low-cost stencil-printed transparency electrodes.

PubMed

Martín-Yerga, Daniel; Álvarez-Martos, Isabel; Blanco-López, M Carmen; Henry, Charles S; Fernández-Abedul, M Teresa

2017-08-15

In this work, we report a simple and yet efficient stencil-printed electrochemical platform that can be integrated into the caps of sample containers and thus, allows in-field quantification of Cd(II) and Pb(II) in river water samples. The device exploits the low-cost features of carbon (as electrode material) and paper/polyester transparency sheets (as substrate). Electrochemical analysis of the working electrodes prepared on different substrates (polyester transparency sheets, chromatographic, tracing and office papers) with hexaammineruthenium(III) showed that their electroactive area and electron transfer kinetics are highly affected by the porosity of the material. Electrodes prepared on transparency substrates showed the best electroanalytical performance for the simultaneous determination of Cd(II) and Pb(II) by square-wave anodic stripping voltammetry. Interestingly, the temperature and time at which the carbon ink was cured had significant effect on the electrochemical response, especially the capacitive current. The amount of Cd and Pb on the electrode surface can be increased about 20% by in situ electrodeposition of bismuth. The electrochemical platform showed a linear range comprised between 1 and 200 μg/L for both metals, sensitivity of analysis of 0.22 and 0.087 μA/ppb and limits of detection of 0.2 and 0.3 μg/L for Cd(II) and Pb(II), respectively. The analysis of river water samples was done directly in the container where the sample was collected, which simplifies the procedure and approaches field analysis. The developed point-of-need detection system allowed simultaneous determination of Cd(II) and Pb(II) in those samples using the standard addition method with precise and accurate results. Copyright © 2017 Elsevier B.V. All rights reserved.

N-Heterocyclic Carbene Complexes in Dehalogenation Reactions

NASA Astrophysics Data System (ADS)

Mas-Marzá, Elena; Page, Michael J.; Whittlesey, Michael K.

Catalytic dehalogenation represents an underdeveloped transformation in M-NHC chemistry with a small number of reports detailing the reactivity of Co, Ru, Ni and Pd catalysts. In situ generated nickel and palladium NHC complexes catalyse the hydrodechlorination of aryl chlorides. Lower coordinate Ni complexes are proposed to operate in the hydrodefluorination of mono- and poly-fluorinated substrates. The single example of Ru-NHC catalysed hydrodefluorination of fully and partially fluorinated aromatic substrates is characterised by an unusual regioselectivity. The highly regioselective dehydrohalogenation of relatively unreactive alkyl halide substrates is achieved with a cobalt NHC catalyst.

Ca2+-independent Activation of Ca2+/Calmodulin-dependent Protein Kinase II Bound to the C-terminal Domain of CaV2.1 Calcium Channels*

PubMed Central

Magupalli, Venkat G.; Mochida, Sumiko; Yan, Jin; Jiang, Xin; Westenbroek, Ruth E.; Nairn, Angus C.; Scheuer, Todd; Catterall, William A.

2013-01-01

Ca2+/calmodulin-dependent protein kinase II (CaMKII) forms a major component of the postsynaptic density where its functions in synaptic plasticity are well established, but its presynaptic actions are poorly defined. Here we show that CaMKII binds directly to the C-terminal domain of CaV2.1 channels. Binding is enhanced by autophosphorylation, and the kinase-channel signaling complex persists after dephosphorylation and removal of the Ca2+/CaM stimulus. Autophosphorylated CaMKII can bind the CaV2.1 channel and synapsin-1 simultaneously. CaMKII binding to CaV2.1 channels induces Ca2+-independent activity of the kinase, which phosphorylates the enzyme itself as well as the neuronal substrate synapsin-1. Facilitation and inactivation of CaV2.1 channels by binding of Ca2+/CaM mediates short term synaptic plasticity in transfected superior cervical ganglion neurons, and these regulatory effects are prevented by a competing peptide and the endogenous brain inhibitor CaMKIIN, which blocks binding of CaMKII to CaV2.1 channels. These results define the functional properties of a signaling complex of CaMKII and CaV2.1 channels in which both binding partners are persistently activated by their association, and they further suggest that this complex is important in presynaptic terminals in regulating protein phosphorylation and short term synaptic plasticity. PMID:23255606

Influence of substrate modification and C-terminal truncation on the active site structure of substrate-bound heme oxygenase from Neisseriae meningitidis; A 1H NMR study†

PubMed Central

Peng, Dungeng; Satterlee, James D.; Ma, Li-Hua; Dallas, Jerry L.; Smith, Kevin M.; Zhang, Xuhong; Sato, Michihiko; La Mar, Gerd N.

2011-01-01

Heme oxygenase, HO, from the pathogenic bacterium N. meningitidis, NmHO, which secures host iron, shares many properties with mammalian HOs, but also exhibits some key differences. The crystal structure appears more compact and the crystal-undetected C-terminus interacts with substrate in solution. The unique nature of substrate-protein, specifically pyrrole-I/II-helix-2, peripheral interactions in NmHO are probed by 2D 1H NMR to reveal unique structural features controlling substrate orientation. The thermodynamics of substrate orientational isomerism are mapped for substrates with individual vinyl → methyl → hydrogen substitutions and with enzyme C-terminal deletions. NmHO exhibits significantly stronger orientational preference, reflecting much stronger and selective pyrrole-I/II interactions with the protein matrix, than in mammalian HOs. Thus, replacing bulky vinyls with hydrogens results in a 180° rotation of substrate about the α,γ-meso axis in the active site. A "collapse" of the substrate pocket as substrate size decreases is reflected in movement of helix-2 toward the substrate as indicated by significant and selective increased NOESY cross peak intensity, increase in steric Fe-CN tilt reflected in the orientation of the major magnetic axis, and decrease in steric constraints controlling the rate of aromatic ring reorientation. The active site of NmHO appears "stressed" for native protohemin and its "collapse" upon replacing vinyls by hydrogen leads to a factor ~102 increase in substrate affinity. Interaction of the C-terminus with the active site destabilizes the crystallographic protohemin orientation by ~0.7 kcal/mol, which is consistent with optimizing the His207-Asp27 H-bond. Implications of the active site "stress" for product release are discussed. PMID:21870860

Carboxylate-assisted ruthenium-catalyzed alkyne annulations by C-H/Het-H bond functionalizations.

PubMed

Ackermann, Lutz

2014-02-18

To improve the atom- and step-economy of organic syntheses, researchers would like to capitalize upon the chemistry of otherwise inert carbon-hydrogen (C-H) bonds. During the past decade, remarkable progress in organometallic chemistry has set the stage for the development of increasingly viable metal catalysts for C-H bond activation reactions. Among these methods, oxidative C-H bond functionalizations are particularly attractive because they avoid the use of prefunctionalized starting materials. For example, oxidative annulations that involve sequential C-H and heteroatom-H bond cleavages allow for the modular assembly of regioselectively decorated heterocycles. These structures serve as key scaffolds for natural products, functional materials, crop protecting agents, and drugs. While other researchers have devised rhodium or palladium complexes for oxidative alkyne annulations, my laboratory has focused on the application of significantly less expensive, yet highly selective ruthenium complexes. This Account summarizes the evolution of versatile ruthenium(II) complexes for annulations of alkynes via C-H/N-H, C-H/O-H, or C-H/N-O bond cleavages. To achieve selective C-H bond functionalizations, we needed to understand the detailed mechanism of the crucial C-H bond metalation with ruthenium(II) complexes and particularly the importance of carboxylate assistance in this process. As a consequence, our recent efforts have resulted in widely applicable methods for the versatile preparation of differently decorated arenes and heteroarenes, providing access to among others isoquinolones, 2-pyridones, isoquinolines, indoles, pyrroles, or α-pyrones. Most of these reactions used Cu(OAc)2·H2O, which not only acted as the oxidant but also served as the essential source of acetate for the carboxylate-assisted ruthenation manifold. Notably, the ruthenium(II)-catalyzed oxidative annulations also occurred under an ambient atmosphere of air with cocatalytic amounts of Cu(OAc)2·H2O. Moreover, substrates displaying N-O bonds served as "internal oxidants" for the syntheses of isoquinolones and isoquinolines. Detailed experimental mechanistic studies have provided strong support for a catalytic cycle that relies on initial carboxylate-assisted C-H bond ruthenation, followed by coordinative insertion of the alkyne, reductive elimination, and reoxidation of the thus formed ruthenium(0) complex.

Crystal structure of the catalytic core domain of the family 6 cellobiohydrolase II, Cel6A, from Humicola insolens, at 1.92 A resolution.

PubMed

Varrot, A; Hastrup, S; Schülein, M; Davies, G J

1999-01-15

The three-dimensional structure of the catalytic core of the family 6 cellobiohydrolase II, Cel6A (CBH II), from Humicola insolens has been determined by X-ray crystallography at a resolution of 1.92 A. The structure was solved by molecular replacement using the homologous Trichoderma reesei CBH II as a search model. The H. insolens enzyme displays a high degree of structural similarity with its T. reesei equivalent. The structure features both O- (alpha-linked mannose) and N-linked glycosylation and a hexa-co-ordinate Mg2+ ion. The active-site residues are located within the enclosed tunnel that is typical for cellobiohydrolase enzymes and which may permit a processive hydrolysis of the cellulose substrate. The close structural similarity between the two enzymes implies that kinetics and chain-end specificity experiments performed on the H. insolens enzyme are likely to be applicable to the homologous T. reesei enzyme. These cast doubt on the description of cellobiohydrolases as exo-enzymes since they demonstrated that Cel6A (CBH II) shows no requirement for non-reducing chain-ends, as had been presumed. There is no crystallographic evidence in the present structure to support a mechanism involving loop opening, yet preliminary modelling experiments suggest that the active-site tunnel of Cel6A (CBH II) is too narrow to permit entry of a fluorescenyl-derivatized substrate, known to be a viable substrate for this enzyme.

Controlling the oxidation of bis-tridentate cobalt(ii) complexes having bis(2-pyridylalkyl)amines: ligand vs. metal oxidation.

PubMed

Anjana, S; Donring, S; Sanjib, P; Varghese, B; Murthy, Narasimha N

2017-08-22

Two bis-tridentate chelated cobalt(ii) complexes, which differ in the ligand structure by a methylene group, activate molecular oxygen (O 2 ), and give different oxidation products. The O 2 reaction of [Co II (pepma) 2 ] 2+ (1) with unsymmetrical 2-(2-pyridyl)-N-(2-pyridylmethyl)ethanamine (pepma) results in ligand oxidation, to the corresponding Co(ii) imine complex [Co II (pepmi) 2 ] 2+ (2). Contrastingly, the Co(ii) complex [Co II (bpma) 2 ] 2+ (3) of similar symmetrical bis(2-pyridylmethyl)amine (bpma), undergoes metal oxidation, yielding a cobalt(iii) complex, [Co III (bpma) 2 ] 2+ (4). The reversibility of the amine to imine conversion and the stability of the Co(ii) imine complex (2) are investigated. Furthermore, the solution dynamics of Co(ii) complexes are highlighted with the help of paramagnetic 1 H-NMR spectroscopy.

Syntheses, structures, and properties of imidazolate-bridged Cu(II)-Cu(II) and Cu(II)-Zn(II) dinuclear complexes of a single macrocyclic ligand with two hydroxyethyl pendants.

PubMed

Li, Dongfeng; Li, Shuan; Yang, Dexi; Yu, Jiuhong; Huang, Jin; Li, Yizhi; Tang, Wenxia

2003-09-22

The imidazolate-bridged homodinuclear Cu(II)-Cu(II) complex, [(CuimCu)L]ClO(4).0.5H(2)O (1), and heterodinuclear Cu(II)-Zn(II) complex, [(CuimZnL(-)(2H))(CuimZnL(-)(H))](ClO(4))(3) (2), of a single macrocyclic ligand with two hydroxyethyl pendants, L (L = 3,6,9,16,19,22-hexaaza-6,19-bis(2-hydroxyethyl)tricyclo[22,2,2,2(11,14)]triaconta-1,11,13,24,27,29-hexaene), have been synthesized as possible models for copper-zinc superoxide dismutase (Cu(2),Zn(2)-SOD). Their crystal structures analyzed by X-ray diffraction methods have shown that the structures of the two complexes are markedly different. Complex 1 crystallizes in the orthorhombic system, containing an imidazolate-bridged dicopper(II) [Cu-im-Cu](3+) core, in which the two copper(II) ions are pentacoordinated by virtue of an N4O environment with a Cu.Cu distance of 5.999(2) A, adopting the geometry of distorted trigonal bipyramid and tetragonal pyramid, respectively. Complex 2 crystallizes in the triclinic system, containing two similar Cu-im-Zn cores in the asymmetric unit, in which both the Cu(II) and Zn(II) ions are pentacoordinated in a distorted trigonal bipyramid geometry, with the Cu.Zn distance of 5.950(1)/5.939(1) A, respectively. Interestingly, the macrocyclic ligand with two arms possesses a chairlike (anti) conformation in complex 1, but a boatlike (syn) conformation in complex 2. Magnetic measurements and ESR spectroscopy of complex 1 have revealed the presence of an antiferromagnetic exchange interaction between the two Cu(II) ions. The ESR spectrum of the Cu(II)-Zn(II) heterodinuclear complex 2 displayed a typical signal for mononuclear trigonal bipyramidal Cu(II) complexes. From pH-dependent ESR and electronic spectroscopic studies, the imidazolate bridges in the two complexes have been found to be stable over broad pH ranges. The cyclic voltammograms of the two complexes have been investigated. Both of the two complexes can catalyze the dismutation of superoxide and show rather high activity.

Electrochemical studies of DNA interaction and antimicrobial activities of MnII, FeIII, CoII and NiII Schiff base tetraazamacrocyclic complexes

NASA Astrophysics Data System (ADS)

Kumar, Anuj; Vashistha, Vinod Kumar; Tevatia, Prashant; Singh, Randhir

2017-04-01

Tetraazamacrocyclic complexes of MnII, FeIII, CoII and NiII have been synthesized by template method. These tetraazamacrocycles have been analyzed with various techniques like molar conductance, IR, UV-vis, mass spectral and cyclic voltammetric studies. On the basis of all these studies, octahedral geometry has been assigned to these tetraazamacrocyclic complexes. The DNA binding properties of these macrocyclic complexes have been investigated by electronic absorption spectra, fluorescence spectra, cyclic voltammetric and differential pulse voltammetric studies. The cyclic voltammetric data showed that ipc and ipa were effectively decreased in the presence of calf thymus DNA, which is a strong evidence for the interaction of these macrocyclic complexes with the calf thymus DNA (ct-DNA). The heterogeneous electron transfer rate constant found in the order: KCoII > KNiII > KMnII which indicates that CoII macrocyclic complex has formed a strong intercalated intermediate. The Stern-Volmer quenching constant (KSV) and voltammetric binding constant were found in the order KSV(CoII) > KSV(NiII) > KSV(MnII) and K+(CoII) > K+(NiII) > K+(MnII) which shows that CoII macrocyclic complex exhibits the high interaction affinity towards ct-DNA by the intercalation binding. Biological studies of the macrocyclic complexes compared with the standard drug like Gentamycin, have shown antibacterial activities against E. coli, P. aeruginosa, B. cereus, S. aureus and antifungal activity against C. albicans.

Chelation, spectroscopic characterization, biological activity and crystal structure of 2,3-butanedione isonicotinylhydrazone: Determination of Zr4+ after flotation separation

NASA Astrophysics Data System (ADS)

Al-Fulaij, O. A.; Jeragh, B.; El-Sayed, A. E. M.; El-Defrawy, M. M.; El-Asmy, A. A.

2015-02-01

New metal complexes of Co(II), Ni(II) Cu(II), Zn(II), Cd(II), Pd(II) and Hg(II) with 2,3-butanedione isonicotinylhydrazone [BINH] have been prepared and investigated. Single crystal for BINH is grown and solved as orthorhombic with P 21 21 2 space group. The formula of the ligand was assigned based on the elemental analysis, mass spectra and conductivity measurements. The complexes assigned the formulae [M(BINH-H)Cl]ṡnH2O (Mdbnd Co(II), Ni(II), Cu(II), Zn(II); n = 0 or 1); [Hg(BINH-H)(H2O)2Cl]; [Cd(BINH)Cl2]ṡ2H2O and [Pd(BINH)Cl2]ṡH2O. All complexes are nonelectrolytes. BINH acts as a tridentate ligand in [M(BINH-H)Cl]ṡnH2O and [Hg(BINH-H)(H2O)2Cl] coordinating through Cdbnd Oketonic, Csbnd Oamedic and Cdbnd Nhy and as a neutral bidentate through Cdbnd Oketonic and Cdbnd Nhy in [Cd(BINH)Cl2]ṡ2H2O and [Pd(BINH)Cl2]ṡH2O; the pyridine nitrogen has no rule in coordination. The data are supported by NMR (1H and 13C) spectra. The magnetic moments and electronic spectra provide a tetrahedral structure for the Co(II), Ni(II), Cu(II), Zn(II) and Cd(II) complexes; square-planar for the Pd(II) complex and octahedral for the Hg(II) complex. The TGA of the complexes depicted the outer and inner water molecules as well as the final residue. The cobalt and cadmium complexes ended with the metal while the Cu(II), Zn(II) and Pd(II) complexes ended with complex species. [Hg(BINH-H)(H2O)2Cl] has no residue. The ligand is inactive against all tested organisms except for Bacillus thuringiensis. The Hg(II) complex is found more active than the other complexes. The flotation technique is found applicable for the separation of micro amount (10 ppm) of Zr4+ using 10 ppm of BINH and 1 × 10-5 mol L-1 of oleic acid at pH 6 with efficiency of 98% with no interferences.

Hydrophobic motif site-phosphorylated protein kinase CβII between mTORC2 and Akt regulates high glucose-induced mesangial cell hypertrophy.

PubMed

Das, Falguni; Ghosh-Choudhury, Nandini; Mariappan, Meenalakshmi M; Kasinath, Balakuntalam S; Choudhury, Goutam Ghosh

2016-04-01

PKCβII controls the pathologic features of diabetic nephropathy, including glomerular mesangial cell hypertrophy. PKCβII contains the COOH-terminal hydrophobic motif site Ser-660. Whether this hydrophobic motif phosphorylation contributes to high glucose-induced mesangial cell hypertrophy has not been determined. Here we show that, in mesangial cells, high glucose increased phosphorylation of PKCβII at Ser-660 in a phosphatidylinositol 3-kinase (PI3-kinase)-dependent manner. Using siRNAs to downregulate PKCβII, dominant negative PKCβII, and PKCβII hydrophobic motif phosphorylation-deficient mutant, we found that PKCβII regulates activation of mechanistic target of rapamycin complex 1 (mTORC1) and mesangial cell hypertrophy by high glucose. PKCβII via its phosphorylation at Ser-660 regulated phosphorylation of Akt at both catalytic loop and hydrophobic motif sites, resulting in phosphorylation and inactivation of its substrate PRAS40. Specific inhibition of mTORC2 increased mTORC1 activity and induced mesangial cell hypertrophy. In contrast, inhibition of mTORC2 decreased the phosphorylation of PKCβII and Akt, leading to inhibition of PRAS40 phosphorylation and mTORC1 activity and prevented mesangial cell hypertrophy in response to high glucose; expression of constitutively active Akt or mTORC1 restored mesangial cell hypertrophy. Moreover, constitutively active PKCβII reversed the inhibition of high glucose-stimulated Akt phosphorylation and mesangial cell hypertrophy induced by suppression of mTORC2. Finally, using renal cortexes from type 1 diabetic mice, we found that increased phosphorylation of PKCβII at Ser-660 was associated with enhanced Akt phosphorylation and mTORC1 activation. Collectively, our findings identify a signaling route connecting PI3-kinase to mTORC2 to phosphorylate PKCβII at the hydrophobic motif site necessary for Akt phosphorylation and mTORC1 activation, leading to mesangial cell hypertrophy.

Hydrophobic motif site-phosphorylated protein kinase CβII between mTORC2 and Akt regulates high glucose-induced mesangial cell hypertrophy

PubMed Central

Das, Falguni; Mariappan, Meenalakshmi M.; Kasinath, Balakuntalam S.; Choudhury, Goutam Ghosh

2016-01-01

PKCβII controls the pathologic features of diabetic nephropathy, including glomerular mesangial cell hypertrophy. PKCβII contains the COOH-terminal hydrophobic motif site Ser-660. Whether this hydrophobic motif phosphorylation contributes to high glucose-induced mesangial cell hypertrophy has not been determined. Here we show that, in mesangial cells, high glucose increased phosphorylation of PKCβII at Ser-660 in a phosphatidylinositol 3-kinase (PI3-kinase)-dependent manner. Using siRNAs to downregulate PKCβII, dominant negative PKCβII, and PKCβII hydrophobic motif phosphorylation-deficient mutant, we found that PKCβII regulates activation of mechanistic target of rapamycin complex 1 (mTORC1) and mesangial cell hypertrophy by high glucose. PKCβII via its phosphorylation at Ser-660 regulated phosphorylation of Akt at both catalytic loop and hydrophobic motif sites, resulting in phosphorylation and inactivation of its substrate PRAS40. Specific inhibition of mTORC2 increased mTORC1 activity and induced mesangial cell hypertrophy. In contrast, inhibition of mTORC2 decreased the phosphorylation of PKCβII and Akt, leading to inhibition of PRAS40 phosphorylation and mTORC1 activity and prevented mesangial cell hypertrophy in response to high glucose; expression of constitutively active Akt or mTORC1 restored mesangial cell hypertrophy. Moreover, constitutively active PKCβII reversed the inhibition of high glucose-stimulated Akt phosphorylation and mesangial cell hypertrophy induced by suppression of mTORC2. Finally, using renal cortexes from type 1 diabetic mice, we found that increased phosphorylation of PKCβII at Ser-660 was associated with enhanced Akt phosphorylation and mTORC1 activation. Collectively, our findings identify a signaling route connecting PI3-kinase to mTORC2 to phosphorylate PKCβII at the hydrophobic motif site necessary for Akt phosphorylation and mTORC1 activation, leading to mesangial cell hypertrophy. PMID:26739493

Manganese(II), iron(II), cobalt(II), and copper(II) complexes of an extended inherently chiral tris-bipyridyl cage.

PubMed

Perkins, David F; Lindoy, Leonard F; McAuley, Alexander; Meehan, George V; Turner, Peter

2006-01-17

Manganese(II), iron(II), cobalt(II), and copper(II) derivatives of two inherently chiral, Tris(bipyridyl) cages (L and L') of type [ML]-(PF(6))(2)(solvent)(n) and [FeL'](ClO(4))(2) are reported, where L is the hexa-tertiary butyl-substituted derivative of L'. These products were obtained by using the free cage and metal template procedures; the latter involved the reductive amination of the respective Tris-dialdehyde precursor complexes of iron(II), cobalt(II), or nickel(II). Electrochemical, EPR, and NMR studies have been used to probe the nature of the individual complexes. X-ray structures of the manganese(II), iron(II), and copper(II) complexes of L and the iron(II) complex of L' are presented; these are compared with the previously reported structures of the corresponding nickel(II) complex and metal-free cage (L). In each complex the metal cation occupies the cage's central cavity and is coordinated to six nitrogens from the three bipyridyl groups. The cations [MnL](2+) and [FeL](2+) are isostructural but both exhibit a different arrangement of the bound cage to that observed in the corresponding nickel(II) and copper(II) complexes. The latter have an exo-exo arrangement of the bridgehead nitrogen lone pairs, with the metal inducing a triple helical twist that extends approximately 22 A along the axial length of each complex. In contrast, [MnL](2+) and [FeL](2+) have their terminal nitrogen lone pairs directed endo, causing a significant change in the configuration of the bound ligand. In [FeL'](2+), the cage has both bridgehead nitrogen lone pairs orientated exo. Semiempirical calculations indicate that the observed endo-endo and exo-exo arrangements are of comparable energy.

Autoimmune severe hypertriglyceridemia induced by anti-apolipoprotein C-II antibody.

PubMed

Yamamoto, Hiroyasu; Tanaka, Minoru; Yoshiga, Satomi; Funahashi, Tohru; Shimomura, Iichiro; Kihara, Shinji

2014-05-01

Among type V hyperlipoproteinemias, only one-fourth of the patients have genetic defects in lipoprotein lipase (LPL) or in its associated molecules; the exact mechanism in other patients is usually unknown. The aim of the study was to report a case of severe hypertriglyceridemia induced by anti-apolipoprotein (apo) C-II autoantibody and to clarify its pathogenesis. A 29-year-old Japanese woman presented with severe persistent hypertriglyceridemia since the age of 20 years. The past history was negative for acute pancreatitis, eruptive xanthomas, or lipemia retinalis. LPL mass and activities were normal. Plasma apo C-II levels were extremely low, but no mutation was observed in APOC2. Apo C-II protein was detected in the serum by immunoprecipitation and Western blotting. Large amounts of IgG and IgM were incorporated with apo C-II protein coimmunoprecipitated by anti-apo C-II antibody. IgG, but not IgM, purified from the serum prevented interaction of apo C-II with lipid substrate and diminished LPL hydrolysis activity. We identified anti-apo C-II antibody in a myeloma-unrelated severe hypertriglyceridemic patient. In vitro analysis confirmed that the autoantibody disrupted the interaction between apo C-II and lipid substrate, suggesting the etiological role of anti-apo C-II antibody in severe hypertriglyceridemia in this patient.

Complex Formed between Intramembrane Metalloprotease SpoIVFB and Its Substrate, Pro-σK*

PubMed Central

Zhang, Yang; Halder, Sabyasachi; Kerr, Richard A.; Parrell, Daniel; Ruotolo, Brandon; Kroos, Lee

2016-01-01

Intramembrane metalloproteases (IMMPs) are conserved from bacteria to humans and control many important signaling pathways, but little is known about how IMMPs interact with their substrates. SpoIVFB is an IMMP that cleaves Pro-σK during Bacillus subtilis endospore formation. When catalytically inactive SpoIVFB was coexpressed with C-terminally truncated Pro-σK(1–126) (which can be cleaved by active SpoIVFB) in Escherichia coli, the substrate dramatically improved solubilization of the enzyme from membranes with mild detergents. Both the Pro(1–20) and σK(21–126) parts contributed to improving SpoIVFB solubilization from membranes, but only the σK part was needed to form a stable complex with SpoIVFB in a pulldown assay. The last 10 residues of SpoIVFB were required for improved solubilization from membranes by Pro-σK(1–126) and for normal interaction with the substrate. The inactive SpoIVFB·Pro-σK(1–126)-His6 complex was stable during affinity purification and gel filtration chromatography. Disulfide cross-linking of the purified complex indicated that it resembled the complex formed in vivo. Ion mobility-mass spectrometry analysis resulted in an observed mass consistent with a 4:2 SpoIVFB·Pro-σK(1–126)-His6 complex. Stepwise photobleaching of SpoIVFB fused to a fluorescent protein supported the notion that the enzyme is tetrameric during B. subtilis sporulation. The results provide the first evidence that an IMMP acts as a tetramer, give new insights into how SpoIVFB interacts with its substrate, and lay the foundation for further biochemical analysis of the enzyme·substrate complex and future structural studies. PMID:26953342

Size-matched alkyne-conjugated cyanine fluorophores to identify differences in protein glycosylation.

PubMed

Burnham-Marusich, Amanda R; Plechaty, Anna M; Berninsone, Patricia M

2014-09-01

Currently, there are few methods to detect differences in posttranslational modifications (PTMs) in a specific manner from complex mixtures. Thus, we developed an approach that combines the sensitivity and specificity of click chemistry with the resolution capabilities of 2D-DIGE. In "Click-DIGE", posttranslationally modified proteins are metabolically labeled with azido-substrate analogs, then size- and charge-matched alkyne-Cy3 or alkyne-Cy5 dyes are covalently attached to the azide of the PTM by click chemistry. The fluorescently-tagged protein samples are then multiplexed for 2DE analysis. Whereas standard DIGE labels all proteins, Click-DIGE focuses the analysis of protein differences to a targeted subset of posttranslationally modified proteins within a complex sample (i.e. specific labeling and analysis of azido glycoproteins within a cell lysate). Our data indicate that (i) Click-DIGE specifically labels azido proteins, (ii) the resulting Cy-protein conjugates are spectrally distinct, and (iii) the conjugates are size- and charge-matched at the level of 2DE. We demonstrate the utility of this approach by detecting multiple differentially expressed glycoproteins between a mutant cell line defective in UDP-galactose transport and the parental cell line. We anticipate that the diversity of azido substrates already available will enable Click-DIGE to be compatible with analysis of a wide range of PTMs. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Toward nanomolar detection by NMR through SABRE hyperpolarization.

PubMed

Eshuis, Nan; Hermkens, Niels; van Weerdenburg, Bram J A; Feiters, Martin C; Rutjes, Floris P J T; Wijmenga, Sybren S; Tessari, Marco

2014-02-19

SABRE is a nuclear spin hyperpolarization technique based on the reversible association of a substrate molecule and para-hydrogen (p-H2) to a metal complex. During the lifetime of such a complex, generally fractions of a second, the spin order of p-H2 is transferred to the nuclear spins of the substrate molecule via a transient scalar coupling network, resulting in strongly enhanced NMR signals. This technique is generally applied at relatively high concentrations (mM), in large excess of substrate with respect to metal complex. Dilution of substrate ligands below stoichiometry results in progressive decrease of signal enhancement, which precludes the direct application of SABRE to the NMR analysis of low concentration (μM) solutions. Here, we show that the efficiency of SABRE at low substrate concentrations can be restored by addition of a suitable coordinating ligand to the solution. The proposed method allowed NMR detection below 1 μM in a single scan.

Modeling liquid organic thin films on substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernacki, Bruce E.; Johnson, Timothy J.; Myers, Tanya L.

We present the rationale, methods, and results of modeling of thin film organic liquids on various substrates. These liquids may coat surfaces (substrates) either as a result of their production, dispersal via aerosols or spills. Identification of unknown coated surfaces using either reflectance or emittance spectroscopy cannot be accomplished simply through reference to reflectance signature libraries since neither the thickness of the liquid layer nor the substrate type is known beforehand and both contribute to the signature. Liquid spectral libraries offer the complex index of refraction (n,k) as a function of wavelength which by itself is useful only for thickmore » (bulk) liquid layers via computation of reflectance and transmittance coefficients using the Fresnel equations. Thin liquid layers both reflect and refract incident light in combination with reflectance from the substrate. We show modeling of various organic liquids on substrates using commercial thin film design and modeling software, as well as Monte Carlo ray tracing software to demonstrate the variety of potential signatures encountered that depend on the thickness of the liquid layer as well as the characteristics of the substrate (metal or dielectric). These substrates give rise to transflectance behavior, while many dielectric substrates have rich absorption features that provide complex signatures that combine attributes of both the liquid and the substrate. Knowledge of the complex index of refraction of both target liquids and substrates is essential in order to synthesize spectra necessary in the application of target identification algorithms.« less

IMPROVED EQUIPMENT CLEANING IN COATED AND LAMINATED SUBSTRATE MANUFACTURING FACILITIES (PHASE II)

EPA Science Inventory

The report discusses EPA efforts to identify, demonstrate, and publish pollution prevention information and opportunities for equipment cleaning for the coated and laminated substrate manufacturing industry. It summarizes initial data collected and summarized during industry obse...

Synthesis, spectral studies and biological evaluation of 2-aminonicotinic acid metal complexes.

PubMed

Nawaz, Muhammad; Abbasi, Muhammad Waseem; Hisaindee, Soleiman; Zaki, Muhammad Javed; Abbas, Hira Fatima; Mengting, Hu; Ahmed, M Arif

2016-05-15

We synthesized 2-aminonicotinic acid (2-ANA) complexes with metals such as Co(II), Fe(III), Ni(II), Mn(II), Zn(II), Ag(I),Cr(III), Cd(II) and Cu(II) in aqueous media. The complexes were characterized and elucidated using FT-IR, UV-Vis, a fluorescence spectrophotometer and thermo gravimetric analysis (TGA). TGA data showed that the stoichiometry of complexes was 1:2 metal/ligand except for Ag(I) and Mn(II) where the ratio was 1:1. The metal complexes showed varied antibacterial, fungicidal and nematicidal activities. The silver and zinc complexes showed highest activity against Bacillus subtilis and Bacillus licheniformis respectively. Fusarium oxysporum was highly susceptible to nickel and copper complexes whereas Macrophomina phaseolina was completely inert to the complexes. The silver and cadmium complexes were effective against the root-knot nematode Meloidogyne javanica. Copyright © 2016 Elsevier B.V. All rights reserved.

A novel [Mn2(μ-(C6H5)2CHCOO)2(bipy)4](bipy)(ClO4)2 complex loaded solid lipid nanoparticles: synthesis, characterization and in vitro cytotoxicity on MCF-7 breast cancer cells.

PubMed

Guney Eskiler, G; Cecener, G; Dikmen, G; Kani, I; Egeli, U; Tunca, B

2016-09-01

Manganese (Mn)-based complexes have been drawing attention due to the fact that they are more effective than other metal complexes. However, the use of Mn(II)-based complexes in medicine remains limited because of certain side effects. The aim of this study was to investigate the cytotoxic and apoptotic effects of a novel Mn(II) complex [Mn 2 (μ-(C 6 H 5 ) 2 CHCOO) 2 (bipy) 4 ](bipy)(ClO 4 ) 2 and Mn(II) complex loaded solid lipid nanoparticles (SLNs) on MCF-7 and HUVEC control cells. The average diameter of Mn(II) complex was about 1120 ± 2.43 nm, while the average particle size of Mn(II) complex-SLNs was ∼340 ± 2.27 nm. The cytotoxic effects of Mn(II) complex and Mn(II)-SLNs were 86.8 and 66.4%, respectively (p < .05). Additionally, both Mn(II) complex (39.25%) and Mn(II)-SLNs (38.05%) induced apoptosis and increased the arrest of G 0 /G 1 phase. However, Mn(II) complex exerted toxic effects on the HUVEC control cell (63.4%), whereas no toxic effects was observed when treated with Mn(II)-SLNs at 150 μM. As a consequence, SLNs might be potentially used for metal-based complexes in the treatment of cancer due to reducing size and toxic effects of metal-based complexes.

Synthesis, characterization and antimicrobial activity of some nickel, cadmium and mercury complexes of 5-methyl pyrazole-3yl-N-(2‧-methylthiophenyl) methyleneimine, (MPzOATA) ligand

NASA Astrophysics Data System (ADS)

Mandal, Susmita; Mondal, Monojit; Biswas, Jayanta Kumar; Cordes, David B.; Slawin, Alexandra M. Z.; Butcher, Ray J.; Saha, Manan; Chandra Saha, Nitis

2018-01-01

Herein, we report the syntheses and structures of Ni(II) complexes, [Ni(MPzOATA)2] (Cl) (PF6) (I), [Ni(MPzOATA)2](ClO4)2.CH3CN (II) & [Ni(MPzOATA)2](BF4)2.H2O (III); Cd(II) complex, [Cd(MPzOATA)Cl2]2 (IV) and a Hg(II) complex, [Hg(MPzOATA)Cl2] (V), of a pyrazole based 'NNS' donor ligand, 5-methylpyrazole-3yl-N-(2‧-methylthiophenyl)methyleneimine, (MPzOATA). The complexes are characterized by elemental analyses, electronic, IR, 1H- NMR (only for IV &V) spectral parameters, conductivity and fluorescence measurements. X-ray crystallographic data of the complexes reveal that the Ni(II) complexes have NiN4S2 octahedral coordination, one of them is a mixed-anion complex having Cl- and PF6- as counter anions; the Cd(II) complex is a chloro bridged binuclear complex with octahedral coordination environment around each metal centre, while the Hg(II) complex is a square pyramidal one. Among the reported complex species, the Ni(II) complexes are non-fluorescent, while the Cd(II) and Hg(II) complexes can be used as potential photoactive materials as indicated from their characteristic emission properties. The reported complexes are screened for their antimicrobial activities against some Gram positive and Gram negative microbial strains, and they are found to be potential antimicrobial agents in broad spectrum against both Gram positive and Gram negative bacteria.

Proteolytic Activity of Prostate-Specific Antigen (PSA) towards Protein Substrates and Effect of Peptides Stimulating PSA Activity

PubMed Central

Mattsson, Johanna M.; Ravela, Suvi; Hekim, Can; Jonsson, Magnus; Malm, Johan; Närvänen, Ale; Stenman, Ulf-Håkan; Koistinen, Hannu

2014-01-01

Prostate-specific antigen (PSA or kallikrein-related peptidase-3, KLK3) exerts chymotrypsin-like proteolytic activity. The main biological function of PSA is the liquefaction of the clot formed after ejaculation by cleavage of semenogelins I and II in seminal fluid. PSA also cleaves several other substrates, which may explain its putative functions in prostate cancer and its antiangiogenic activity. We compared the proteolytic efficiency of PSA towards several protein and peptide substrates and studied the effect of peptides stimulating the activity of PSA with these substrates. An endothelial cell tube formation model was used to analyze the effect of PSA-degraded protein fragments on angiogenesis. We showed that PSA degrades semenogelins I and II much more efficiently than other previously identified protein substrates, e.g., fibronectin, galectin-3 and IGFBP-3. We identified nidogen-1 as a new substrate for PSA. Peptides B2 and C4 that stimulate the activity of PSA towards small peptide substrates also enhanced the proteolytic activity of PSA towards protein substrates. Nidogen-1, galectin-3 or their fragments produced by PSA did not have any effect on endothelial cell tube formation. Although PSA cleaves several other protein substrates, in addition to semenogelins, the physiological importance of this activity remains speculative. The PSA levels in prostate are very high, but several other highly active proteases, such as hK2 and trypsin, are also expressed in the prostate and may cleave protein substrates that are weakly cleaved by PSA. PMID:25237904

Emergent behaviour in a chlorophenol-mineralising three-tiered microbial ‘food web’

PubMed Central

Wade, M.J.; Pattinson, R.W.; Parker, N.G.; Dolfing, J.

2016-01-01

Anaerobic digestion enables the water industry to treat wastewater as a resource for generating energy and recovering valuable by-products. The complexity of the anaerobic digestion process has motivated the development of complex models. However, this complexity makes it intractable to pin-point stability and emergent behaviour. Here, the widely used Anaerobic Digestion Model No. 1 (ADM1) has been reduced to its very backbone, a syntrophic two-tiered microbial ‘food chain’ and a slightly more complex three-tiered microbial ‘food web’, with their stability analysed as a function of the inflowing substrate concentration and dilution rate. Parameterised for phenol and chlorophenol degradation, steady-states were always stable and non-oscillatory. Low input concentrations of chlorophenol were sufficient to maintain chlorophenol- and phenol-degrading populations but resulted in poor conversion and a hydrogen flux that was too low to sustain hydrogenotrophic methanogens. The addition of hydrogen and phenol boosted the populations of all three organisms, resulting in the counterintuitive phenomena that (i) the phenol degraders were stimulated by adding hydrogen, even though hydrogen inhibits phenol degradation, and (ii) the dechlorinators indirectly benefitted from measures that stimulated their hydrogenotrophic competitors; both phenomena hint at emergent behaviour. PMID:26551153

Synthesis, characterization and anti-microbial activity of a novel macrocyclic ligand derived from the reaction of 2,6-pyridinedicarboxylic acid with homopiperazine and its Co(II), Ni(II), Cu(II), and Zn(II) complexes

NASA Astrophysics Data System (ADS)

Soleimani, Esmaiel

2011-05-01

The preparation of a novel macrocyclic ligand ( 1), N,N'-diethylhomopiperazinyl,2,6-pyridinedicarboxylate and its Co(II), Ni(II), Cu(II), and Zn(II) complexes are described. The ligand was prepared in EtOH from the reaction of dipotassium salt of 2,6-pyridinedicarboxylic acid with 1,2-dibromoethane in the presence of homopiperazine. Reaction of macrocyclic ligand ( 1) in EtOH with CoCl 2.6H 2O, NiCl 2.6H 2O, CuCl 2.2H 2O, and ZnCl 2·2H 2O yielded the complexes with the general formula [M(L)Cl 2] {where M = Co(II) ( 2), Ni(II) ( 3), Cu(II) ( 4), Zn ( 5), respectively}. The analysis of IR, 1H and 13C NMR spectral data of macrocyclic ligand ( 1) and its Zn(II) complex ( 5) together with their molar conductivity values, and the magnetic moments of the complexes suggest that the macrocyclic ligand ( 1) is bonded to metal(II) ions through two oxygen atoms of ester moiety and the two nitrogen atoms of homopiperazine ring. The electronic spectral data of these complexes in DMSO are in good agreement with the octahedral coordination of M(II) ions. The ligand field parameters for these complexes, i.e. splitting energy and Racah parameter were calculated to be 14,945 and 673 cm -1 for the Co(II) ( 2), 16,260 and 774 cm -1 for the Ni(II) ( 3) complexes respectively. The spliting energy of 17,262 cm -1 was obtained for the Cu(II) complex ( 4).

Synthesis, magnetic, spectral, and antimicrobial studies of Cu(II), Ni(II) Co(II), Fe(III), and UO 2(II) complexes of a new Schiff base hydrazone derived from 7-chloro-4-hydrazinoquinoline

NASA Astrophysics Data System (ADS)

El-Behery, Mostafa; El-Twigry, Haifaa

2007-01-01

A new hydrazone ligand, HL, was prepared by the reaction of 7-chloro-4-hydrazinoquinoline with o-hydroxybenzaldehyde. The ligand behaves as monoprotic bidentate. This was accounted for as the ligand contains a phenolic group and its hydrogen atom is reluctant to be replaced by a metal ion. The ligand reacted with Cu(II), Ni(II), Co(II), Fe(III), and UO 2(II) ions to yield mononuclear complexes. In the case of Fe(III) ion two complexes, mono- and binuclear complexes, were obtained in the absence and presence of LiOH, respectively. Also, mixed ligand complexes were obtained from the reaction of the metal cations Cu(II), Ni(II) and Fe(III) with the ligand (HL) and 8-hydroxyquinoline (8-OHqu) in the presence of LiOH, in the molar ratio 1:1:1:1. It is clear that 8-OHqu behaves as monoprotic bidentate ligand in such mixed ligand complexes. The ligand, HL, and its metal complexes were characterized by elemental analyses, IR, UV-vis, mass, and 1H NMR spectra, as well as magnetic moment, conductance measurements, and thermal analyses. All complexes have octahedral configurations except Cu(II) complex which has an extra square-planar geometry, while Ni(II) mixed complex has also formed a tetrahedral configuration and UO 2(II) complex which formed a favorable pentagonal biprymidial geometry. Magnetic moment of the binuclear Fe(III) complex is quite low compared to calculated value for two iron ions complex and thus shows antiferromagnetic interactions between the two adjacent ferric ions. The HL and metal complexes were tested against one stain Gram positive bacteria ( Staphylococcus aureus), Gram negative bacteria ( Escherichia coli), and fungi ( Candida albicans). The tested compounds exhibited higher antibacterial acivities.

Crystal structures of the reverse transcriptase-associated ribonuclease H domain of xenotropic murine leukemia-virus related virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Dongwen; Chung, Suhman; Miller, Maria

2012-06-19

The ribonuclease H (RNase H) domain of retroviral reverse transcriptase (RT) plays a critical role in the life cycle by degrading the RNA strands of DNA/RNA hybrids. In addition, RNase H activity is required to precisely remove the RNA primers from nascent (-) and (+) strand DNA. We report here three crystal structures of the RNase H domain of xenotropic murine leukemia virus-related virus (XMRV) RT, namely (i) the previously identified construct from which helix C was deleted, (ii) the intact domain, and (iii) the intact domain complexed with an active site {alpha}-hydroxytropolone inhibitor. Enzymatic assays showed that the intactmore » RNase H domain retained catalytic activity, whereas the variant lacking helix C was only marginally active, corroborating the importance of this helix for enzymatic activity. Modeling of the enzyme-substrate complex elucidated the essential role of helix C in binding a DNA/RNA hybrid and its likely mode of recognition. The crystal structure of the RNase H domain complexed with {beta}-thujaplicinol clearly showed that coordination by two divalent cations mediates recognition of the inhibitor.« less

Synthesis, spectral characterization, structural investigation and antimicrobial studies of mononuclear Cu(II), Ni(II), Co(II), Zn(II) and Cd(II) complexes of a new potentially hexadentate N2O4 Schiff base ligand derived from salicylaldehyde

NASA Astrophysics Data System (ADS)

Keypour, Hassan; Shayesteh, Maryam; Rezaeivala, Majid; Chalabian, Firoozeh; Elerman, Yalcin; Buyukgungor, Orhan

2013-01-01

A new potentially hexadentate N2O4 Schiff base ligand, H2L derived from condensation reaction of an aromatic diamine and salicylaldehyde, and its metal complexes were characterized by elemental analyses, IR, UV-Vis, EI-MS, 1H and 13C NMR spectra, as well as conductance measurements. It has been originated that the Schiff base ligand with Cu(II), Ni(II), Co(II), Cd(II) and Zn(II) ions form mononuclear complexes on 1:1 (metal:ligand) stoichiometry. The conductivity data confirm the non-electrolytic nature of the complexes. Also the crystal structures of the complexes [ZnL] and [CoL] have also been determined by using X-ray crystallographic technique. The Zn(II) and Co(II) complexes show a tetrahedral configuration. Electronic absorption spectra of the Cu(II) and Ni(II) complexes suggest a square-planar geometry around the central metal ion. The synthesized compounds have antibacterial activity against the three Gram-positive bacteria: Bacillus cereus, Enterococcus faecalis and Listeria monocytogenes and also against the three Gram-negative bacteria: Salmonella paraB, Citrobacter freundii and Enterobacter aerogenes. The results showed that in some cases the antibacterial activity of complexes were more than nalidixic acid and amoxicillin as standards.

C-H activation in Ir(III) and N-demethylation in Pt(II) complexes with mesoionic carbene ligands: examples of monometallic, homobimetallic and heterobimetallic complexes.

PubMed

Maity, Ramananda; Tichter, Tim; van der Meer, Margarethe; Sarkar, Biprajit

2015-11-14

Mononuclear Pt(II) and the first dinuclear Pt(II) complexes along with a cyclometalated heterobimetallic Ir(III)/Pd(II) complex bearing mesoionic carbene donor ligands are presented starting from the same bis-triazolium salt. The mononuclear Pt(II) complex possesses a free triazole moiety which is generated from the corresponding triazolium salt through an N-demethylation reaction, whereas the mononuclear Ir(III) complex features an unreacted triazolium unit.

Development of Novel DNA Cleavage Systems Based on Copper Complexes. Synthesis and Characterisation of Cu(II) Complexes of Hydroxyflavones

PubMed Central

el Amrani, F. Ben-Allal; Perelló, L.; Torres, L.

2000-01-01

Copper(II) complexes of several hydroxyflavones were prepared and characterised through their physico-chemical properties. The nuclease activity of three synthesised complexes is reported. These copper(II) complexes present more nuclease activity than the ligands and the copper(II) ion. PMID:18475969

Invariant Chain Complexes and Clusters as Platforms for MIF Signaling

PubMed Central

Lindner, Robert

2017-01-01

Invariant chain (Ii/CD74) has been identified as a surface receptor for migration inhibitory factor (MIF). Most cells that express Ii also synthesize major histocompatibility complex class II (MHC II) molecules, which depend on Ii as a chaperone and a targeting factor. The assembly of nonameric complexes consisting of one Ii trimer and three MHC II molecules (each of which is a heterodimer) has been regarded as a prerequisite for efficient delivery to the cell surface. Due to rapid endocytosis, however, only low levels of Ii-MHC II complexes are displayed on the cell surface of professional antigen presenting cells and very little free Ii trimers. The association of Ii and MHC II has been reported to block the interaction with MIF, thus questioning the role of surface Ii as a receptor for MIF on MHC II-expressing cells. Recent work offers a potential solution to this conundrum: Many Ii-complexes at the cell surface appear to be under-saturated with MHC II, leaving unoccupied Ii subunits as potential binding sites for MIF. Some of this work also sheds light on novel aspects of signal transduction by Ii-bound MIF in B-lymphocytes: membrane raft association of Ii-MHC II complexes enables MIF to target Ii-MHC II to antigen-clustered B-cell-receptors (BCR) and to foster BCR-driven signaling and intracellular trafficking. PMID:28208600

Depinning and nonequilibrium dynamic phases of particle assemblies driven over random and ordered substrates: A review

DOE PAGES

Reichhardt, Charles; Olson Reichhardt, Cynthia Jane

2016-12-20

Here, we review the depinning and nonequilibrium phases of collectively interacting particle systems driven over random or periodic substrates. This type of system is relevant to vortices in type-II superconductors, sliding charge density waves, electron crystals, colloids, stripe and pattern forming systems, and skyrmions, and could also have connections to jamming, glassy behaviors, and active matter. These systems are also ideal for exploring the broader issues of characterizing transient and steady state nonequilibrium flow phases as well as nonequilibrium phase transitions between distinct dynamical phases, analogous to phase transitions between different equilibrium states. We discuss the differences between elastic andmore » plastic depinning on random substrates and the different types of nonequilibrium phases which are associated with specific features in the velocity-force curves, fluctuation spectra, scaling relations, and local or global particle ordering. We describe how these quantities can change depending on the dimension, anisotropy, disorder strength, and the presence of hysteresis. Within the moving phase we discuss how there can be a transition from a liquid-like state to dynamically ordered moving crystal, smectic, or nematic states. Systems with periodic or quasiperiodic substrates can have multiple nonequilibrium second or first order transitions in the moving state between chaotic and coherent phases, and can exhibit hysteresis. We also discuss systems with competing repulsive and attractive interactions, which undergo dynamical transitions into stripes and other complex morphologies when driven over random substrates. Throughout this work we highlight open issues and future directions such as absorbing phase transitions, nonequilibrium work relations, inertia, the role of non-dissipative dynamics such as Magnus effects, and how these results could be extended to the broader issues of plasticity in crystals, amorphous solids, and jamming phenomena.« less

Depinning and nonequilibrium dynamic phases of particle assemblies driven over random and ordered substrates: a review

NASA Astrophysics Data System (ADS)

Reichhardt, C.; Olson Reichhardt, C. J.

2017-02-01

We review the depinning and nonequilibrium phases of collectively interacting particle systems driven over random or periodic substrates. This type of system is relevant to vortices in type-II superconductors, sliding charge density waves, electron crystals, colloids, stripe and pattern forming systems, and skyrmions, and could also have connections to jamming, glassy behaviors, and active matter. These systems are also ideal for exploring the broader issues of characterizing transient and steady state nonequilibrium flow phases as well as nonequilibrium phase transitions between distinct dynamical phases, analogous to phase transitions between different equilibrium states. We discuss the differences between elastic and plastic depinning on random substrates and the different types of nonequilibrium phases which are associated with specific features in the velocity-force curves, fluctuation spectra, scaling relations, and local or global particle ordering. We describe how these quantities can change depending on the dimension, anisotropy, disorder strength, and the presence of hysteresis. Within the moving phase we discuss how there can be a transition from a liquid-like state to dynamically ordered moving crystal, smectic, or nematic states. Systems with periodic or quasiperiodic substrates can have multiple nonequilibrium second or first order transitions in the moving state between chaotic and coherent phases, and can exhibit hysteresis. We also discuss systems with competing repulsive and attractive interactions, which undergo dynamical transitions into stripes and other complex morphologies when driven over random substrates. Throughout this work we highlight open issues and future directions such as absorbing phase transitions, nonequilibrium work relations, inertia, the role of non-dissipative dynamics such as Magnus effects, and how these results could be extended to the broader issues of plasticity in crystals, amorphous solids, and jamming phenomena.

Microbial- and thiosulfate-mediated dissolution of mercury sulfide minerals and transformation to gaseous mercury

DOE PAGES

Vázquez-Rodríguez, Adiari I.; Hansel, Colleen M.; Zhang, Tong; ...

2015-06-23

Mercury (Hg) is a toxic heavy metal that poses significant environmental and human health risks. Soils and sediments, where Hg can exist as the Hg sulfide mineral metacinnabar (β-HgS), represent major Hg reservoirs in aquatic environments. Metacinnabar has historically been considered a sink for Hg in all but severely acidic environments, and thus disregarded as a potential source of Hg back to aqueous or gaseous pools. In this study, we conducted a combination of field and laboratory incubations to identify the potential for metacinnabar as a source of dissolved Hg within near neutral pH environments and the underpinning (a)biotic mechanismsmore » at play. We show that the abundant and widespread sulfur-oxidizing bacteria of the genus Thiobacillus extensively colonized metacinnabar chips incubated within aerobic, near neutral pH creek sediments. Laboratory incubations of axenic Thiobacillus thioparus cultures led to the release of metacinnabar-hosted Hg(II) and subsequent volatilization to Hg(0). This dissolution and volatilization was greatly enhanced in the presence of thiosulfate, which served a dual role by enhancing HgS dissolution through Hg complexation and providing an additional metabolic substrate for Thiobacillus. These findings reveal a new coupled abiotic-biotic pathway for the transformation of metacinnabar-bound Hg(II) to Hg(0), while expanding the sulfide substrates available for neutrophilic chemosynthetic bacteria to Hg-laden sulfides. Lastly, they also point to mineral-hosted Hg as an underappreciated source of gaseous elemental Hg to the environment.« less

Mannostatin A, a new glycoprotein-processing inhibitor.

PubMed

Tropea, J E; Kaushal, G P; Pastuszak, I; Mitchell, M; Aoyagi, T; Molyneux, R J; Elbein, A D

1990-10-30

Mannostatin A is a metabolite produced by the microorganism Streptoverticillium verticillus and reported to be a potent competitive inhibitor of rat epididymal alpha-mannosidase. When tested against a number of other arylglycosidases, mannostatin A was inactive toward alpha- and beta-glucosidase and galactosidase as well as beta-mannosidase, but it was a potent inhibitor of jack bean, mung bean, and rat liver lysosomal alpha-mannosidases, with estimated IC50's of 70 nM, 450 nM, and 160 nM, respectively. The type of inhibition was competitive in nature. This compound also proved to be an effective competitive inhibitor of the glycoprotein-processing enzyme mannosidase II (IC50 of about 10-15 nM with p-nitrophenyl alpha-D-mannopyranoside as substrate, and about 90 nM with [3H]mannose-labeled GlcNAc-Man5GlcNAc as substrate). However, it was virtually inactive toward mannosidase I. The N-acetylated derivative of mannostatin A had no inhibitory activity. In cell culture studies, mannostatin A also proved to be a potent inhibitor of glycoprotein processing. Thus, in influenza virus infected Madin Darby canine kidney (MDCK) cells, mannostatin A blocked the normal formation of complex types of oligosaccharides on the viral glycoproteins and caused the accumulation of hybrid types of oligosaccharides. This observation is in keeping with other data which indicate that the site of action of mannostatin A is mannosidase II. Thus, mannostatin A represents the first nonalkaloidal processing inhibitor and adds to the growing list of chemical structures that can have important biological activity.

Microbial- and thiosulfate-mediated dissolution of mercury sulfide minerals and transformation to gaseous mercury

PubMed Central

Vázquez-Rodríguez, Adiari I.; Hansel, Colleen M.; Zhang, Tong; Lamborg, Carl H.; Santelli, Cara M.; Webb, Samuel M.; Brooks, Scott C.

2015-01-01

Mercury (Hg) is a toxic heavy metal that poses significant environmental and human health risks. Soils and sediments, where Hg can exist as the Hg sulfide mineral metacinnabar (β-HgS), represent major Hg reservoirs in aquatic environments. Metacinnabar has historically been considered a sink for Hg in all but severely acidic environments, and thus disregarded as a potential source of Hg back to aqueous or gaseous pools. Here, we conducted a combination of field and laboratory incubations to identify the potential for metacinnabar as a source of dissolved Hg within near neutral pH environments and the underpinning (a)biotic mechanisms at play. We show that the abundant and widespread sulfur-oxidizing bacteria of the genus Thiobacillus extensively colonized metacinnabar chips incubated within aerobic, near neutral pH creek sediments. Laboratory incubations of axenic Thiobacillus thioparus cultures led to the release of metacinnabar-hosted Hg(II) and subsequent volatilization to Hg(0). This dissolution and volatilization was greatly enhanced in the presence of thiosulfate, which served a dual role by enhancing HgS dissolution through Hg complexation and providing an additional metabolic substrate for Thiobacillus. These findings reveal a new coupled abiotic-biotic pathway for the transformation of metacinnabar-bound Hg(II) to Hg(0), while expanding the sulfide substrates available for neutrophilic chemosynthetic bacteria to Hg-laden sulfides. They also point to mineral-hosted Hg as an underappreciated source of gaseous elemental Hg to the environment. PMID:26157421

Synthesis, characterization, DFT calculations and biological studies of Mn(II), Fe(II), Co(II) and Cd(II) complexes based on a tetradentate ONNO donor Schiff base ligand

NASA Astrophysics Data System (ADS)

Abdel-Rahman, Laila H.; Ismail, Nabawia M.; Ismael, Mohamed; Abu-Dief, Ahmed M.; Ahmed, Ebtehal Abdel-Hameed

2017-04-01

This study highlights synthesis and characterization of a tetradentate ONNO Schiff base ligand namely (1, 1‧- (pyridine-2, 3-dimethyliminomethyl) naphthalene-2, 2‧-diol) and hereafter denotes as "HNDAP″ and selected metal complexes including Mn(II), Fe(II), Co(II) and Cd(II) as a central metal. HNDAP was synthesized from 1:2 M ratio condensation of 2, 3-diaminopyridine and 2- hydroxy-1-naphthaldhyde, respectively. The stoichiometric ratios of the prepared complexes were estimated using complementary techniques such as; elemental analyses (-C, H, N), FT-IR, magnetic measurements and molar conductivity. Furthermore, their physicochemical studies were carried out using thermal TGA, DTA and kinetic-thermodynamic studies along with DFT calculations. The results of elemental analyses showed that these complexes are present in a 1:1 metal-to- ligand molar ratio. Moreover, the magnetic susceptibilities values at room temperature revealed that Mn(II), Fe(II) and Co(II) complexes are paramagnetic in nature and have an octahedral (Oh) geometry. In contrast, Cd(II) is diamagnetic and stabilizes in square planar sites. The molar conductivity measurements indicated that all complexes are nonelectrolytes in dimethyl formamide. Spectral data suggested that the ligand is as tetradentate and coordinated with Co(II) ion through two phenolic OH and two azomethine nitrogen. However, for Mn(II), Fe(II) and Cd(II) complexes, the coordination occurred through two phenolic oxygen and two azomethine nitrogen with deprotonation of OH groups. The proposed chemical structures have been validated by quantum mechanics calculations. Antimicrobial activities of both the HNDAP Schiff base ligand and its metal complexes were tested against strains of Gram (-ve) E. coli and Gram (+ve) B. subtilis and S. aureus bacteria and C. albicans, A. flavus and T. rubrum fungi. All the prepared compounds showed good results of inhibition against the selected pathogenic microorganisms. The investigated HNDAP Schiff base complexes showed higher activity and stability than their corresponding HNDAP Schiff base ligand and the highest activity observed for Cd(II) complex. Moreover, the prepared Schiff base ligand and its Mn(II) and Co(II) complexes have been evaluated for their anticancer activities against two cancer cell lines namely; colon carcinoma cells (HCT-116 cell line) and hepatocellular carcinoma (Hep-G2) cell lines The interaction of Mn(II) and Co(II) complexes with calf thymus DNA (CT-DNA) was studied by absorption spectroscopic technique and viscosity measurements. Both complexes showed a successful interaction with CT-DNA via intercalation mode.

Combined experimental and theoretical study on the reactivity of compounds I and II in horseradish peroxidase biomimetics.

PubMed

Ji, Li; Franke, Alicja; Brindell, Małgorzata; Oszajca, Maria; Zahl, Achim; van Eldik, Rudi

2014-10-27

For the exploration of the intrinsic reactivity of two key active species in the catalytic cycle of horseradish peroxidase (HRP), Compound I (HRP-I) and Compound II (HRP-II), we generated in situ [Fe(IV) O(TMP(+.) )(2-MeIm)](+) and [Fe(IV) O(TMP)(2-MeIm)](0) (TMP=5,10,15,20-tetramesitylporphyrin; 2-MeIm=2-methylimidazole) as biomimetics for HRP-I and HRP-II, respectively. Their catalytic activities in epoxidation, hydrogen abstraction, and heteroatom oxidation reactions were studied in acetonitrile at -15 °C by utilizing rapid-scan UV/Vis spectroscopy. Comparison of the second-order rate constants measured for the direct reactions of the HRP-I and HRP-II mimics with the selected substrates clearly confirmed the outstanding oxidizing capability of the HRP-I mimic, which is significantly higher than that of HRP-II. The experimental study was supported by computational modeling (DFT calculations) of the oxidation mechanism of the selected substrates with the involvement of quartet and doublet HRP-I mimics ((2,4) Cpd I) and the closed-shell triplet spin HRP-II model ((3) Cpd II) as oxidizing species. The significantly lower activation barriers calculated for the oxidation systems involving (2,4) Cpd I than those found for (3) Cpd II are in line with the much higher oxidizing efficiency of the HRP-I mimic proven in the experimental part of the study. In addition, the DFT calculations show that all three reaction types catalyzed by HRP-I occur on the doublet spin surface in an effectively concerted manner, whereas these reactions may proceed in a stepwise mechanism with the HRP-II mimic as oxidant. However, the high desaturation or oxygen rebound barriers during CH bond activation processes by the HRP-II mimic predict a sufficient lifetime for the substrate radical formed through hydrogen abstraction. Thus, the theoretical calculations suggest that the dissociation of the substrate radical may be a more favorable pathway than desaturation or oxygen rebound processes. Importantly, depending on the electronic nature of the oxidizing species, that is, (2,4) Cpd I or (3) Cpd II, an interesting region-selective conversion phenomenon between sulfoxidation and H-atom abstraction was revealed in the course of the oxidation reaction of dimethylsulfide. The combined experimental and theoretical study on the elucidation of the intrinsic reactivity patterns of the HRP-I and HRP-II mimics provides a valuable tool for evaluating the particular role of the HRP active species in biological systems. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis of 2‐Alkynoates by Palladium(II)‐Catalyzed Oxidative Carbonylation of Terminal Alkynes and Alcohols

PubMed Central

Cao, Qun; Hughes, N. Louise

2016-01-01

Abstract A homogeneous PdII catalyst, utilizing a simple and inexpensive amine ligand (TMEDA), allows 2‐alkynoates to be prepared in high yields by an oxidative carbonylation of terminal alkynes and alcohols. The catalyst system overcomes many of the limitations of previous palladium carbonylation catalysts. It has an increased substrate scope, avoids large excesses of alcohol substrate and uses a desirable solvent. The catalyst employs oxygen as the terminal oxidant and can be operated under safer gas mixtures. PMID:27305489

Equilibrium vortex structures of type-II/1 superconducting films with washboard pinning landscapes

NASA Astrophysics Data System (ADS)

Wei, C. A.; Xu, X. B.; Xu, X. N.; Wang, Z. H.; Gu, M.

2018-05-01

We numerically study the equilibrium vortex structures of type-II/1 superconducting films with a periodic quasi-one-dimensional corrugated substrate. We show as a function of substrate period and pinning strength that, the vortex system displays a variety of vortex phases including arrays consisted of vortex clumps with different morphologies, ordered vortex stripes parallel and perpendicular to pinning troughs, and ordered one-dimensional vortex chains. Our simulations are helpful in understanding the structural modulations for extensive systems with both competing interactions and competing periodicities.

Free metal ion depletion by "Good's" buffers. III. N-(2-acetamido)iminodiacetic acid, 2:1 complexes with zinc(II), cobalt(II), nickel(II), and copper(II); amide deprotonation by Zn(II), Co(II), and Cu(II).

PubMed

Lance, E A; Rhodes, C W; Nakon, R

1983-09-01

Potentiometric, visible, infrared, electron spin, and nuclear magnetic resonance studies of the complexation of N-(2-acetamido)iminodiacetic acid (H2ADA) by Ca(II), Mg(II), Mn(II), Zn(II), Co(II), Ni(II), and Cu(II) are reported. Ca(II) and Mg(II) were found not to form 2:1 ADA2- to M(II) complexes, while Mn(II), Cu(II), Ni(II), Zn(II), and Co(II) did form 2:1 metal chelates at or below physiological pH values. Co(II) and Zn(II), but not Cu(II), were found to induce stepwise deprotonation of the amide groups to form [M(H-1ADA)4-(2)]. Formation (affinity) constants for the various metal complexes are reported, and the probable structures of the various metal chelates in solution are discussed on the basis of various spectral data.

The orbital ground state of the azide-substrate complex of human heme oxygenase is an indicator of distal H-bonding: implications for the enzyme mechanism.

PubMed

Ogura, Hiroshi; Evans, John P; Peng, Dungeng; Satterlee, James D; Ortiz de Montellano, Paul R; La Mar, Gerd N

2009-04-14

The active site electronic structure of the azide complex of substrate-bound human heme oxygenase 1 (hHO) has been investigated by (1)H NMR spectroscopy to shed light on the orbital/spin ground state as an indicator of the unique distal pocket environment of the enzyme. Two-dimensional (1)H NMR assignments of the substrate and substrate-contact residue signals reveal a pattern of substrate methyl contact shifts that places the lone iron pi-spin in the d(xz) orbital, rather than the d(yz) orbital found in the cyanide complex. Comparison of iron spin relaxivity, magnetic anisotropy, and magnetic susceptibilities argues for a low-spin, (d(xy))(2)(d(yz),d(xz))(3), ground state in both azide and cyanide complexes. The switch from singly occupied d(yz) for the cyanide to d(xz) for the azide complex of hHO is shown to be consistent with the orbital hole determined by the azide pi-plane in the latter complex, which is approximately 90 degrees in-plane rotated from that of the imidazole pi-plane. The induction of the altered orbital ground state in the azide relative to the cyanide hHO complex, as well as the mean low-field bias of methyl hyperfine shifts and their paramagnetic relaxivity relative to those in globins, indicates that azide exerts a stronger ligand field in hHO than in the globins, or that the distal H-bonding to azide is weaker in hHO than in globins. The Asp140 --> Ala hHO mutant that abolishes activity retains the unusual WT azide complex spin/orbital ground state. The relevance of our findings for other HO complexes and the HO mechanism is discussed.

The orbital ground state of the azide-substrate complex of human heme oxygenase is an indicator of distal H-bonding: Implications for the enzyme mechanism‡

PubMed Central

Ogura, Hiroshi; Evans, John P.; Peng, Dungeng; Satterlee, James D.; de Montellano, Paul R. Ortiz; Mar, Gerd N. La

2009-01-01

The active site electronic structure of the azide complex of substrate-bound human heme oxygenase-1, (hHO) has been investigated by 1H NMR spectroscopy to shed light on the orbital/spin ground state as an indicator of the unique distal pocket environment of the enzyme. 2D 1H NMR assignments of the substrate and substrate-contact residue signals reveal a pattern of substrate methyl contact shifts, that places the lone iron π-spin in the dxz orbital, rather than the dyz orbital found in the cyanide complex. Comparison of iron spin relaxivity, magnetic anisotropy and magnetic susceptibilities argues for a low-spin, (dxy)2(dyz,dxz)3, ground state in both azide and cyanide complexes. The switch from singly-occupied dyz for the cyanide to dxz for the azide complex of hHO is shown to be consistent with the orbital hole determined by the azide π-plane in the latter complex, which is ∼90° in-plane rotated from that of the imidazole π-plane. The induction of the altered orbital ground state in the azide relative to the cyanide hHO complex, as well as the mean low-field bias of methyl hyperfine shifts and their paramagnetic relaxivity relative to those in globins, indicate that azide exerts a stronger ligand field in hHO than in the globins, or that the distal H-bonding to azide is weaker in hHO than in globins. The Asp140 → Ala hHO mutant that abolishes activity retains the unusual WT azide complex spin/orbital ground state. The relevance of our findings for other HO complexes and the HO mechanism is discussed. PMID:19243105

Hydrogen production in single chamber microbial electrolysis cells with different complex substrates.

PubMed

Montpart, Nuria; Rago, Laura; Baeza, Juan A; Guisasola, Albert

2015-01-01

The use of synthetic wastewater containing carbon sources of different complexity (glycerol, milk and starch) was evaluated in single chamber microbial electrolysis cell (MEC) for hydrogen production. The growth of an anodic syntrophic consortium between fermentative and anode respiring bacteria was operationally enhanced and increased the opportunities of these complex substrates to be treated with this technology. During inoculation, current intensities achieved in single chamber microbial fuel cells were 50, 62.5, and 9 A m⁻³ for glycerol, milk and starch respectively. Both current intensities and coulombic efficiencies were higher than other values reported in previous works. The simultaneous degradation of the three complex substrates favored power production and COD removal. After three months in MEC operation, hydrogen production was only sustained with milk as a single substrate and with the simultaneous degradation of the three substrates. The later had the best results in terms of current intensity (150 A m⁻³), hydrogen production (0.94 m³ m⁻³ d⁻¹) and cathodic gas recovery (91%) at an applied voltage of 0.8 V. Glycerol and starch as substrates in MEC could not avoid the complete proliferation of hydrogen scavengers, even under low hydrogen retention time conditions induced by continuous nitrogen sparging.

Endomannosidase processes oligosaccharides of alpha1-antitrypsin and its naturally occurring genetic variants in the Golgi apparatus.

PubMed

Torossi, T; Fan, J-Y; Sauter-Etter, K; Roth, J; Ziak, M

2006-08-01

Endomannosidase provides an alternate glucose-trimming pathway in the Golgi apparatus. However, it is unknown if the action of endomannosidase is dependent on the conformation of the substrate. We have investigated the processing by endomannosidase of the alpha1-antitrypsin oligosaccharides and its disease-causing misfolded Z and Hong Kong variants. Oligosaccharides of wild-type and misfolded alpha1-antitrypsin expressed in castanospermine-treated hepatocytes or glucosidase II-deficient Phar 2.7 cells were selectively processed by endomannosidase and subsequently converted to complex type oligosaccharides as indicated by Endo H resistance and PNGase F sensitivity. Overexpression of endomannosidase in castanospermine-treated hepatocytes resulted in processing of all oligosaccharides of wild-type and variants of alpha1-antitrypsin. Thus, endomannosidase does not discriminate the folding state of the substrate and provides a back-up mechanism for completion of N-glycosylation of endoplasmic reticulum-escaped glucosylated glycoproteins. For exported misfolded glycoproteins, this would provide a pathway for the formation of mature oligosaccharides important for their proper trafficking and correct functioning.

Reactive Pendant Mn═O in a Synthetic Structural Model of a Proposed S4 State in the Photosynthetic Oxygen Evolving Complex.

PubMed

Vaddypally, Shivaiah; Kondaveeti, Sandeep K; Karki, Santosh; Van Vliet, Megan M; Levis, Robert J; Zdilla, Michael J

2017-04-05

The molecular mechanism of the Oxygen Evolving Center of photosystem II has been under debate for decades. One frequently cited proposal is the nucleophilic attack by water hydroxide on a pendant Mn═O moiety, though no chemical example of this reactivity at a manganese cubane cluster has been reported. We describe here the preparation, characterization, and a reactivity study of a synthetic manganese cubane cluster with a pendant manganese-oxo moiety. Reaction of this cluster with alkenes results in oxygen and hydrogen atom transfer reactions to form alcohol- and ketone-based oxygen-containing products. Nitrene transfer from core imides is negligible. The inorganic product is a cluster identical to the precursor, but with the pendant Mn═O moiety replaced by a hydrogen abstracted from the organic substrate, and is isolated in quantitative yield. 18 O and 2 H isotopic labeling studies confirm the transfer of atoms between the cluster and the organic substrate. The results suggest that the core cubane structure of this model compound remains intact, and that the pendant Mn═O moiety is preferentially reactive.

Strain-induced modification of magnetic structure and new magnetic phases in rare-earth epitaxial films

NASA Astrophysics Data System (ADS)

Dufour, C.; Dumesnil, K.; Mangin, Ph

2006-07-01

Rare earths exhibit complex magnetic phase diagrams resulting from the competition between various contributions to the magnetic energy: exchange, anisotropy and magnetostriction. The epitaxy of a rare-earth film on a substrate induces (i) a clamping to the substrate and (ii) pseudomorphic strains. Both these effects are shown to lead to modifications of the magnetic properties in (0 0 1)Dy, (0 0 1)Tb and (1 1 0)Eu films. In Dy and Tb films, spectacular variations of the Curie temperature have been evidenced. Additionally, Tb films exhibit a new large wavelength magnetic modulation. In Eu films, one of the helical magnetic domains disappears at low temperature whereas the propagation vectors of the other helices are tilted. The link between structural and magnetic properties is underlined via magnetoelastic models. Moreover, molecular beam epitaxy permits the growth of Sm in a metastable dhcp phase. The magnetic structure of dhcp Sm has been elucidated for the first time. In this review, neutron scattering is shown to be a powerful technique to reveal the magnetic structures of rare-earth films.

Ubiquitin conjugating enzyme E2-N and sequestosome-1 (p62) are components of the ubiquitination process mediated by the malin-laforin E3-ubiquitin ligase complex.

PubMed

Sánchez-Martín, Pablo; Romá-Mateo, Carlos; Viana, Rosa; Sanz, Pascual

2015-12-01

Lafora disease (LD, OMIM254780, ORPHA501) is a rare neurodegenerative form of epilepsy related to mutations in two proteins: laforin, a dual specificity phosphatase, and malin, an E3-ubiquitin ligase. Both proteins form a functional complex, where laforin recruits specific substrates to be ubiquitinated by malin. However, little is known about the mechanism driving malin-laforin mediated ubiquitination of its substrates. In this work we present evidence indicating that the malin-laforin complex interacts physically and functionally with the ubiquitin conjugating enzyme E2-N (UBE2N). This binding determines the topology of the chains that the complex is able to promote in the corresponding substrates (mainly K63-linked polyubiquitin chains). In addition, we demonstrate that the malin-laforin complex interacts with the selective autophagy adaptor sequestosome-1 (p62). Binding of p62 to the malin-laforin complex allows its recognition by LC3, a component of the autophagosomal membrane. In addition, p62 enhances the ubiquitinating activity of the malin-laforin E3-ubiquitin ligase complex. These data enrich our knowledge on the mechanism of action of the malin-laforin complex as an E3-ubiquitin ligase and reinforces the role of this complex in targeting substrates toward the autophagy pathway. Copyright © 2015 Elsevier Ltd. All rights reserved.

Theoretical investigation, biological evaluation and VEGFR2 kinase studies of metal(II) complexes derived from hydrotris(methimazolyl)borate.

PubMed

Jayakumar, S; Mahendiran, D; Srinivasan, T; Mohanraj, G; Kalilur Rahiman, A

2016-02-01

The reaction of soft tripodal scorpionate ligand, sodium hydrotris(methimazolyl)borate with M(ClO4)2·6H2O [MMn(II), Ni(II), Cu(II) or Zn(II)] in methanol leads to the cleavage of B-N bond followed by the formation of complexes of the type [M(MeimzH)4](ClO4)2·H2O (1-4), where MeimzH=methimazole. All the complexes were fully characterized by spectro-analytical techniques. The molecular structure of the zinc(II) complex (4) was determined by X-ray crystallography, which supports the observed deboronation reaction in the scorpionate ligand with tetrahedral geometry around zinc(II) ion. The electronic spectra of complexes suggested tetrahedral geometry for manganese(II) and nickel(II) complexes, and square-planar geometry for copper(II) complex. Frontier molecular orbital analysis (HOMO-LUMO) was carried out by B3LYP/6-31G(d) to understand the charge transfer occurring in the molecules. All the complexes exhibit significant antimicrobial activity against Gram (-ve) and Gram (+ve) bacterial as well as fungal strains, which are quite comparable to standard drugs streptomycin and clotrimazole. The copper(II) complex (3) showed excellent free radical scavenging activity against DPPH in all concentration with IC50 value of 30μg/mL, when compared to the other complexes. In the molecular docking studies, all the complexes showed hydrophobic, π-π and hydrogen bonding interactions with BSA. The cytotoxic activity of the complexes against human hepatocellular liver carcinoma (HepG2) cells was assessed by MTT assay, which showed exponential responses toward increasing concentration of complexes. Copyright © 2015 Elsevier B.V. All rights reserved.

Facilitated release of substrate protein from prefoldin by chaperonin.

PubMed

Zako, Tamotsu; Iizuka, Ryo; Okochi, Mina; Nomura, Tomoko; Ueno, Taro; Tadakuma, Hisashi; Yohda, Masafumi; Funatsu, Takashi

2005-07-04

Prefoldin is a chaperone that captures a protein-folding intermediate and transfers it to the group II chaperonin for correct folding. However, kinetics of interactions between prefoldin and substrate proteins have not been investigated. In this study, dissociation constants and dissociation rate constants of unfolded proteins with prefoldin were firstly measured using fluorescence microscopy. Our results suggest that binding and release of prefoldin from hyperthermophilic archaea with substrate proteins were in a dynamic equilibrium. Interestingly, the release of substrate proteins from prefoldin was facilitated when chaperonin was present, supporting a handoff mechanism of substrate proteins from prefoldin to the chaperonin.

CryoEM structures of two spliceosomal complexes: starter and dessert at the spliceosome feast.

PubMed

Nguyen, Thi Hoang Duong; Galej, Wojciech P; Fica, Sebastian M; Lin, Pei-Chun; Newman, Andrew J; Nagai, Kiyoshi

2016-02-01

The spliceosome is formed on pre-mRNA substrates from five small nuclear ribonucleoprotein particles (U1, U2, U4/U6 and U5 snRNPs), and numerous non-snRNP factors. Saccharomyces cerevisiae U4/U6.U5 tri-snRNP comprises U5 snRNA, U4/U6 snRNA duplex and approximately 30 proteins and represents a substantial part of the spliceosome before activation. Schizosaccharomyces pombe U2.U6.U5 spliceosomal complex is a post-catalytic intron lariat spliceosome containing U2 and U5 snRNPs, NTC (nineteen complex), NTC-related proteins (NTR), U6 snRNA, and an RNA intron lariat. Two recent papers describe near-complete atomic structures of these complexes based on cryoEM single-particle analysis. The U4/U6.U5 tri-snRNP structure provides crucial insight into the activation mechanism of the spliceosome. The U2.U6.U5 complex reveals the striking architecture of NTC and NTR and important features of the group II intron-like catalytic RNA core remaining after spliced mRNA is released. These two structures greatly advance our understanding of the mechanism of pre-mRNA splicing. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Synthesis, spectroscopic, biological activity and thermal characterization of ceftazidime with transition metals

NASA Astrophysics Data System (ADS)

Masoud, Mamdouh S.; Ali, Alaa E.; Elasala, Gehan S.; Kolkaila, Sherif A.

2018-03-01

Synthesis, physicochemical characterization and thermal analysis of ceftazidime complexes with transition metals (Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and Hg(II)) were discussed. It's obtained that ceftazidime act as bidentate ligand. From magnetic measurement and spectral data, octahedral structures were proposed for all complexes except for cobalt, nickel and mercury had tetrahedral structural. Hyper chemistry program confirmed binding sites of ceftazidime. Ceftazidime complexes show higher activity than ceftazidime for some strains. From TG and DTA curves the thermal decomposition mechanisms of ceftazidime and their metal complexes were suggested. The thermal decomposition of the complexes ended with the formation of metal oxides as a final product except in case of Hg complex.

Ferrocene and (arene)ruthenium(II) complexes of the natural anticancer naphthoquinone plumbagin with enhanced efficacy against resistant cancer cells and a genuine mode of action.

PubMed

Spoerlein-Guettler, Cornelia; Mahal, Katharina; Schobert, Rainer; Biersack, Bernhard

2014-09-01

A series of ferrocene and (arene)ruthenium(II) complexes attached to the naturally occurring anticancer naphthoquinones plumbagin and juglone was tested for efficacy against various cancer cell lines and for alterations in the mode of action. The plumbagin ferrocene and (p-cymene)Ru(II) conjugates 1c and 2a overcame the multi-drug drug resistance of KB-V1/Vbl cervix carcinoma cells and showed IC50 (72 h) values around 1 μM in growth inhibition assays using 3-(4,5-dimethyl-2-yl)-2,5-diphenyltetrazolium bromide (MTT). They were further investigated for their influence on the cell cycle of KB-V1/Vbl and HCT-116 colon carcinoma cells, on the generation of reactive oxygen species (ROS) by the latter cell line, for their substrate character for the P-glycoprotein drug eflux pump via the calcein-AM efflux assays, and for DNA affinity by the electrophoretic mobility shift assay (EMSA). The derivatives 1c and 2a increased the number of dead cancer cells (sub-G0/G1 fraction) in a dose- and time-dependent manner. ROS levels were significantly increased upon treatment with 1c and 2a. These compounds also showed a greater affinity to linear DNA than plumbagin. While plumbagin did not affect calcein-AM transport by P-glycoprotein the derivatives 1c and 2a exhibited a 50% or 80% inhibition of the P-glycoprotein-mediated calcein-AM efflux relative to the clinically established sensitizer verapamil. Copyright © 2014 Elsevier Inc. All rights reserved.

Studies on Some Biologically Cobalt(II), Copper(II) and Zinc(II) Complexes With ONO, NNO and SNO Donor Pyrazinoylhydrazine-Derived Ligands

PubMed Central

Praveen, Marapaka; Sherazi, Syed K. A.

1998-01-01

Biologically active complexes of Co(II), Ni(II), Cu(II) and Zn(II) with novel ONO, NNO and SNO donor pyrazinoylhydrazine-derived compounds have been prepared and characterized on the basis of analytical data and various physicochemical studies. Distorted octahedral structures for all the complexes have been proposed. The synthesized ligands and their complexes have been screened for their antibacterial activity against bacterial species Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Klebsiella pneumonae. The activity data show the metal complexes to be more active than the parent free ligands against one or more bacterial species. PMID:18475857

Organometallic ruthenium anticancer complexes inhibit human glutathione-S-transferase π.

PubMed

Lin, Yu; Huang, Yongdong; Zheng, Wei; Wang, Fuyi; Habtemariam, Abraha; Luo, Qun; Li, Xianchan; Wu, Kui; Sadler, Peter J; Xiong, Shaoxiang

2013-11-01

The organometallic ruthenium(II) anticancer complexes [(η(6)-arene)Ru(en)Cl](+) (arene = p-cymene (1), biphenyl (2) or 9,10-dihydrophenanthrene (3); en = ethylenediamine), exhibit in vitro and in vivo anticancer activities. In the present work, we show that they inhibit human glutathione-S-transferase π (GSTπ) with IC50 values of 59.4 ± 1.3, 63.2 ± 0.4 and 37.2 ± 1.1 μM, respectively. Mass spectrometry revealed that complex 1 binds to the S-donors of Cys15, Cys48 within the G-site and Cys102 at the interface of the GSTπ dimer, while complex 2 binds to Cys48 and Met92 at the dimer interface and complex 3 to Cys15, Cys48 and Met92. Moreover, the binding of complex 1 to Cys15 and Cys102, complex 2 to Cys48 and complex 3 to Cys15 induces the irreversible oxidation of the coordinated thiolates to sulfenates. Molecular modeling studies indicate that the coordination of the {(arene)Ru(en)}(2+) fragment to Cys48 blocks the hydrophilic G-site sterically, perhaps preventing substrate from proper positioning and accounting for the reduction in enzymatic activity of ruthenated GSTπ. The binding of the ruthenium arene complexes to Cys102 or Met92 disrupts the dimer interface which is an essential structural feature for the proper functioning of GSTπ, perhaps also contributing to the inhibition of GSTπ. © 2013.

Design, synthesis, spectral characterization, DNA interaction and biological activity studies of copper(II), cobalt(II) and nickel(II) complexes of 6-amino benzothiazole derivatives

NASA Astrophysics Data System (ADS)

Daravath, Sreenu; Kumar, Marri Pradeep; Rambabu, Aveli; Vamsikrishna, Narendrula; Ganji, Nirmala; Shivaraj

2017-09-01

Two novel Schiff bases, L1 = (2-benzo[d]thiazol-6-ylimino)methyl)-4,6-dichlorophenol), L2 = (1-benzo[d]thiazol-6-ylimino)methyl)-6-bromo-4-chlorophenol) and their bivalent transition metal complexes [M(L1)2] and [M(L2)2], where M = Cu(II), Co(II) and Ni(II) were synthesized and characterized by elemental analysis, NMR, IR, UV-visible, mass, magnetic moments, ESR, TGA, SEM, EDX and powder XRD. Based on the experimental data a square planar geometry around the metal ion is assigned to all the complexes (1a-2c). The interaction of synthesized metal complexes with calf thymus DNA was explored using UV-visible absorption spectra, fluorescence and viscosity measurements. The experimental evidence indicated that all the metal complexes strongly bound to CT-DNA through an intercalation mode. DNA cleavage experiments of metal(II) complexes with supercoiled pBR322 DNA have also been explored by gel electrophoresis in the presence of H2O2 as well as UV light, and it is found that the Cu(II) complexes cleaved DNA more effectively compared to Co(II), Ni(II) complexes. In addition, the ligands and their metal complexes were screened for antimicrobial activity and it is found that all the metal complexes were more potent than free ligands.

Murine Ia-associated invariant chain's processing to complex oligosaccharide forms and its dissociation from the I-Ak complex.

PubMed

Holt, G D; Swiedler, S J; Freed, J H; Hart, G W

1985-07-01

The processing of murine invariant chain (Ii) to a cell surface form bearing complex N-linked oligosaccharides has been demonstrated in the B cell lymphoma, AKTB-1b. In addition, the rate of processing of pulse-labeled Ii has been determined relative to its rate of dissociation from the alpha/beta complex of I-Ak. Ii, alpha-, and beta-chains were immunoprecipitated with anti-I-Ak or anti-Ii monoclonal antibodies. The heretofore uncharacterized complex oligosaccharide form of Ii (Ii-c) was identified in gel-purified immunoprecipitates by peptide mapping with reverse-phase HPLC. Ii-c is resistant to deglycosylation by Endo H, which is specific for high-mannose N-linkages, but can be digested with Endo F, a glycosidase capable of cleaving both complex and high-mannose N-linked oligosaccharides. Immunoprecipitation of surface iodinated cells indicates that Ii-c is expressed on the plasma membrane. Pulse-chase metabolic labeling data show that the processing of Ii to Ii-c occurs with a t1/2 of about 120 min. In contrast, the processing of both alpha- and beta-chains of I-Ak to complex forms occurs with a t1/2 of 15 to 20 min. Our data show that Ii-hm begins to dissociate rapidly from the I-Ak complex after 100 to 120 min of chase. Only a small amount (less than 5% on a per mole basis) of Ii-c was found associated with the I-Ak complexes after 300 min of continuous metabolic labeling. These results are consistent with Ii serving as a carrier for Ia antigens as they are transported to the cell surface. In addition, they suggest that the processing of Ii to Ii-c, or a late processing event of the alpha- and beta-chains, such as their sialylation, may be a possible mechanism for inducing the dissociation of Ii from the I-Ak complex.

Mitochondrial Respiration after One Session of Calf Raise Exercise in Patients with Peripheral Vascular Disease and Healthy Older Adults.

PubMed

van Schaardenburgh, Michel; Wohlwend, Martin; Rognmo, Øivind; Mattsson, Erney J R

2016-01-01

Mitochondria are essential for energy production in the muscle cell and for this they are dependent upon a sufficient supply of oxygen by the circulation. Exercise training has shown to be a potent stimulus for physiological adaptations and mitochondria play a central role. Whether changes in mitochondrial respiration are seen after exercise in patients with a reduced circulation is unknown. The aim of the study was to evaluate the time course and whether one session of calf raise exercise stimulates mitochondrial respiration in the calf muscle of patients with peripheral vascular disease. One group of patients with peripheral vascular disease (n = 11) and one group of healthy older adults (n = 11) were included. Patients performed one session of continuous calf raises followed by 5 extra repetitions after initiation of pain. Healthy older adults performed 100 continuous calf raises. Gastrocnemius muscle biopsies were collected at baseline and 15 minutes, one hour, three hours and 24 hours after one session of calf raise exercise. A multi substrate (octanoylcarnitine, malate, adp, glutamate, succinate, FCCP, rotenone) approach was used to analyze mitochondrial respiration in permeabilized fibers. Mixed-linear model for repeated measures was used for statistical analyses. Patients with peripheral vascular disease have a lower baseline respiration supported by complex I and they increase respiration supported by complex II at one hour post-exercise. Healthy older adults increase respiration supported by electron transfer flavoprotein and complex I at one hour and 24 hours post-exercise. Our results indicate a shift towards mitochondrial respiration supported by complex II as being a pathophysiological component of peripheral vascular disease. Furthermore exercise stimulates mitochondrial respiration already after one session of calf raise exercise in patients with peripheral vascular disease and healthy older adults. ClinicalTrials.gov NCT01842412.

Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria.

PubMed

Inaoka, Daniel Ken; Shiba, Tomoo; Sato, Dan; Balogun, Emmanuel Oluwadare; Sasaki, Tsuyoshi; Nagahama, Madoka; Oda, Masatsugu; Matsuoka, Shigeru; Ohmori, Junko; Honma, Teruki; Inoue, Masayuki; Kita, Kiyoshi; Harada, Shigeharu

2015-07-07

Recent studies on the respiratory chain of Ascaris suum showed that the mitochondrial NADH-fumarate reductase system composed of complex I, rhodoquinone and complex II plays an important role in the anaerobic energy metabolism of adult A. suum. The system is the major pathway of energy metabolism for adaptation to a hypoxic environment not only in parasitic organisms, but also in some types of human cancer cells. Thus, enzymes of the pathway are potential targets for chemotherapy. We found that flutolanil is an excellent inhibitor for A. suum complex II (IC50 = 0.058 μM) but less effectively inhibits homologous porcine complex II (IC50 = 45.9 μM). In order to account for the specificity of flutolanil to A. suum complex II from the standpoint of structural biology, we determined the crystal structures of A. suum and porcine complex IIs binding flutolanil and its derivative compounds. The structures clearly demonstrated key interactions responsible for its high specificity to A. suum complex II and enabled us to find analogue compounds, which surpass flutolanil in both potency and specificity to A. suum complex II. Structures of complex IIs binding these compounds will be helpful to accelerate structure-based drug design targeted for complex IIs.

Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria

PubMed Central

Inaoka, Daniel Ken; Shiba, Tomoo; Sato, Dan; Balogun, Emmanuel Oluwadare; Sasaki, Tsuyoshi; Nagahama, Madoka; Oda, Masatsugu; Matsuoka, Shigeru; Ohmori, Junko; Honma, Teruki; Inoue, Masayuki; Kita, Kiyoshi; Harada, Shigeharu

2015-01-01

Recent studies on the respiratory chain of Ascaris suum showed that the mitochondrial NADH-fumarate reductase system composed of complex I, rhodoquinone and complex II plays an important role in the anaerobic energy metabolism of adult A. suum. The system is the major pathway of energy metabolism for adaptation to a hypoxic environment not only in parasitic organisms, but also in some types of human cancer cells. Thus, enzymes of the pathway are potential targets for chemotherapy. We found that flutolanil is an excellent inhibitor for A. suum complex II (IC50 = 0.058 μM) but less effectively inhibits homologous porcine complex II (IC50 = 45.9 μM). In order to account for the specificity of flutolanil to A. suum complex II from the standpoint of structural biology, we determined the crystal structures of A. suum and porcine complex IIs binding flutolanil and its derivative compounds. The structures clearly demonstrated key interactions responsible for its high specificity to A. suum complex II and enabled us to find analogue compounds, which surpass flutolanil in both potency and specificity to A. suum complex II. Structures of complex IIs binding these compounds will be helpful to accelerate structure-based drug design targeted for complex IIs. PMID:26198225

Characterization of β-FeSi II films as a novel solar cell semiconductor

NASA Astrophysics Data System (ADS)

Fukuzawa, Yasuhiro; Ootsuka, Teruhisa; Otogawa, Naotaka; Abe, Hironori; Nakayama, Yasuhiko; Makita, Yunosuke

2006-04-01

β-FeSi II is an attractive semiconductor owing to its extremely high optical absorption coefficient (α>10 5 cm -1), and is expected to be an ideal semiconductor as a thin film solar cell. For solar cell use, to prepare high quality β-FeSi II films holding a desired Fe/Si ratio, we chose two methods; one is a molecular beam epitaxy (MBE) method in which Fe and Si were evaporated by using normal Knudsen cells, and occasionally by e-gun for Si. Another one is the facing-target sputtering (FTS) method in which deposition of β-FeSi II films is made on Si substrate that is placed out of gas plasma cloud. In both methods to obtain β-FeSi II films with a tuned Fe/Si ratio, Fe/Si super lattice was fabricated by varying Fe and Si deposition thickness. Results showed significant in- and out-diffusion of host Fe and Si atoms at the interface of Si substrates into β-FeSi II layers. It was experimentally demonstrated that this diffusion can be suppressed by the formation of template layer between the epitaxial β-FeSi II layer and the substrate. The template layer was prepared by reactive deposition epitaxy (RDE) method. By fixing the Fe/Si ratio as precisely as possible at 1/2, systematic doping experiments of acceptor (Ga and B) and donor (As) impurities into β-FeSi II were carried out. Systematical changes of electron and hole carrier concentration in these samples along variation of incorporated impurities were observed through Hall effect measurements. Residual carrier concentrations can be ascribed to not only the remaining undesired impurities contained in source materials but also to a variety of point defects mainly produced by the uncontrolled stoichiometry. A preliminary structure of n-β-FeSi II/p-Si used as a solar cell indicated a conversion efficiency of 3.7%.

Problems in aerial application. II, Effects of chlorinated hydrocarbons on substrate-linked phosphorylation.

DOT National Transportation Integrated Search

1963-03-01

In a search for an explanation of an earlier finding that dieldrin decreased the rate of methionine uptake by cardiac muscle, chickens and rats were exposed to this compound and the substrate-linked phosphorylation phenomenon was studied during the a...

Solution NMR study of environmental effects on substrate seating in human heme oxygenase: influence of polypeptide truncation, substrate modification and axial ligand.

PubMed

Zhu, Wenfeng; Li, Yiming; Wang, Jinling; Ortiz de Montellano, Paul R; La Mar, Gerd N

2006-01-01

Solution proton NMR has been used here to show that, as either the high-spin ferric, protohemin (PH) substrate complex at neutral pH, or the low-spin ferric, cyanide-inhibited PH substrate complex, the active site electronic and molecular structure of the 233- and 265-residue recombinant constructs of human heme oxygenase-1, hHO, are essentially indistinguishable. It is shown, moreover, that the equilibrium PH orientational isomerism about the alpha,gamma-meso axis is 1:1 in the water-ligated, resting-state complex, but changes to a 4:1 equilibrium ratio as the cyanide-inhibited complex, with the minor species in solution corresponding to the only one found in crystals. The introduction of significant PH orientational preference in the cyanide over the aquo complex is rationalized by the crystallographic observation for the same H2O and CN ligated complexes of rat heme oxygenase (rHO), where the steric tilt of the Fe-CN unit resulted in a approximately 1 A transition of PH into the hydrophobic interior, and stronger interaction of the vinyls with the HO matrix [M. Sugishima, H. Sakamoto, M. Noguchi, K. Fukugama, Biochemistry 42 (2003) 9898-9905]. 1H NMR spectra of the cyanide-inhibited PH complex are the most used, and most useful, for determining the distribution of orientational isomerism for PH in complexes of HO. Hence, it is imperative that the time-course of the spectra after sample preparation be considered in order to reach conclusions that relate isomeric seating of the heme with variable isomeric biliverdin products. The natural orientational isomerism of PH leads to spectral congestion that has prompted the use of a synthetic, twofold symmetric substrate, 2,4-dimethyldeuterohemin, DMDH. While the hyperfine shift pattern for non-ligated residues are very similar and are consistent with largely conserved molecular structure with the alternate substrates, the steric tilt of the Fe-CN vector towards the protein interior, as determined by the orientation of the major magnetic axes, is 2 degrees smaller for DMDH than PH, and is rationalized by the substrate translating even further into the hydrophobic interior in the cyanide complex when the bulky vinyl groups are replaced by methyl groups.

Angiotensin II-producing enzyme III from acidified serum of nephrectomized dogs.

PubMed

Haas, E; Lewis, L; Koshy, T J; Varde, A U; Renerts, L; Bagai, R C

1989-09-01

A highly active angiotensin-producing enzyme (enzyme III) was obtained from the serum of bilaterally nephrectomized dogs by acid treatment and ammonium sulfate fractionation. An inactive precursor (proenzyme III) was converted to enzyme III during prolonged storage (or by treatment with acid or with cathepsin G or by incubation at 38 degrees C as described in the following paper). Enzyme III reacted maximally at pH 7.7 and it produced up to 400 ng of angiotensin II/mL serum/h (i.e., amounts 4000 times higher than that generated by the endogenous renin present in serum after bilateral nephrectomy). Enzyme III produced angiotensin II at identical rates when either dog angiotensinogen or angiotensin I was used as substrate, but the rate was 710 times higher with synthetic tetradecapeptide renin substrate. Enzyme III is not identical to renin, cathepsin G, tonin, enzyme I, enzyme II, the calcium-dependent angiotensin I-converting enzyme, or the calcium-independent carboxy peptidase, which acts by sequential cleavage of angiotensin I. Enzyme III was inhibited by alpha-1-antitrypsin, diisopropyl fluorophosphate, and lima bean trypsin inhibitor (hence it is a serine proteinase). It was not inhibited by Captopril, Teprotide, or Enalapril. It had been reported previously that cathepsin G released from neutrophil granulocytes, by producing high local concentrations of angiotensin II, may provide a mobile means for modulating blood flow in tissue microvasculature during the inflammatory response. The present study offers a new, additional pathway, by enzyme III, for a similar rapid formation of angiotensin II from serum protein substrate or angiotensin I.

Electron transfer reactivity of the aqueous iron(IV)–oxo complex. Outer-sphere vs proton-coupled electron transfer

DOE PAGES

Bataineh, Hajem; Pestovsky, Oleg; Bakac, Andreja

2016-06-18

Here, the kinetics of oxidation of organic and inorganic reductants by aqueous iron(IV) ions, Fe IV(H 2O) 5O 2+ (hereafter Fe IV aqO 2+), are reported. The substrates examined include several water-soluble ferrocenes, hexachloroiridate(III), polypyridyl complexes M(NN) 3 2+ (M = Os, Fe and Ru; NN = phenanthroline, bipyridine and derivatives), HABTS–/ABTS 2–, phenothiazines, Co II(dmgBF 2) 2, macrocyclic nickel(II) complexes, and aqueous cerium(III). Most of the reductants were oxidized cleanly to the corresponding one-electron oxidation products, with the exception of phenothiazines which produced the corresponding oxides in a single-step reaction, and polypyridyl complexes of Fe(II) and Ru(II) that generatedmore » ligand-modified products. Fe IV aqO 2+ oxidizes even Ce(III) (E 0 in 1 M HClO 4 = 1.7 V) with a rate constant greater than 10 4 M –1 s –1. In 0.10 M aqueous HClO 4 at 25 °C, the reactions of Os(phen) 3 2+ (k = 2.5 × 10 5 M –1 s –1), IrCl 6 3– (1.6 × 10 6), ABTS 2– (4.7 × 10 7), and Fe(cp)(C 5H 4CH 2OH) (6.4 × 10 7) appear to take place by outer sphere electron transfer (OSET). The rate constants for the oxidation of Os(phen) 3 2+ and of ferrocenes remained unchanged in the acidity range 0.05 < [H+] < 0.10 M, ruling out prior protonation of Fe IV aqO 2+ and further supporting the OSET assignment. A fit to Marcus cross-relation yielded a composite parameter (log k 22 + E 0 Fe/0.059) = 17.2 ± 0.8, where k 22 and E 0 Fe are the self-exchange rate constant and reduction potential, respectively, for the Fe IV aqO 2+/Fe III aqO + couple. Comparison with literature work suggests k 22 < 10 –5 M –1 s –1 and thus E 0(Fe IV aqO 2+/Fe III aqO +) > 1.3 V. For proton-coupled electron transfer, the reduction potential is estimated at E 0 (Fe IV aqO 2+, H +/Fe III aqOH 2+) ≥ 1.95 V.« less

Polymeric Cd(II), trinuclear and mononuclear Ni(II) complexes of 5-methyl-4-phenyl-1,2,4-triazole-3-thione: Synthesis, structural characterization, thermal behaviour, fluorescence properties and antibacterial activity

NASA Astrophysics Data System (ADS)

Bharty, M. K.; Paswan, S.; Dani, R. K.; Singh, N. K.; Sharma, V. K.; Kharwar, R. N.; Butcher, R. J.

2017-02-01

Syntheses of a polymeric Cd(II) complex, [Cd(mptt)2]n (1), a trinuclear Ni(II) complex, [Ni3(μ-mptt)4(μ-H2O)2(H2O)2(ttfa)2]·3H2O (2) and a mononuclear Ni(II) complex [Ni(mptt)2(en)2] (3) have been performed using the ligand 5-methyl-4-phenyl-1,2,4-triazole-3-thione (Hmptt) and nickel(II)/cadmium(II) salts {ttfa = thenoyltrifluroacetonate). The ligand and the complexes have been characterized by various physicochemical methods in addition to their single crystal X-ray structure. The Cd centre in complex 1 adopts a distorted tetrahedral geometry with one sulfur atom and two mptt ligands provide three nitrogen atoms from three triazole units. The sulfur atom of the ligand binds covalently and overall the ligand acts as uninigative N,S/N,N bidentate moiety. The polymeric structure of complex 1 results from the N atoms of the neighboring triazole units coordinating with the Cd(II) centre. The three Ni(II) centres in the trinuclear Ni(II) complex 2 form a linear arrangement and all have six coordinated arrangements. The middle Ni(II) binds with four deprotonated triazole ring nitrogens and two water molecules form two bridges. The terminal Ni(II) centres bind through two thenoyl oxygens, two triazole nitrogens and water molecules that formed bridges with the middle Ni centre. In complex 3, the nickel(II) centre is covalently bonded through two deprotonated triazole ring nitrogens from two ligand moieties and other four sites are occupied by four nitrogens from two bidentate en ligands. Thermogravimetric analyses (TGA) of the complexes indicated for NiO as the final residue. The bioefficacy of the ligand and complexes 2 and 3 have been examined against the growth of bacteria to evaluate their anti-microbial potential. Complex 2 showed high antibacterial activity as compared to the ligand and complex 3. Complexes 1, 2 and 3 are fluorescent materials with maximum emissions at 425, 421 and 396 nm at an excitation wavelength of 323, 348 and 322 nm, respectively.

Optimization of the Yield of Lingzhi or Reishi Medicinal Mushroom, Ganoderma lucidum (Higher Basidiomycetes), Cultivated on a Sunflower Seed Hull Substrate Produced in Argentina: Effect of Olive Oil and Copper.

PubMed

Bidegain, Maximiliano A; Cubitto, Maria Amelia; Curvetto, Nestor Raul

2015-01-01

Sunflower seed hulls were used as the main component of a solid substrate for the cultivation of the lingzhi or reishi medicinal mushroom Ganoderma lucidum. This study evaluated the effects of supplementing the substrate with olive oil and copper (II) on the mushroom production (MP) parameters and fruiting body total triterpenoid content. The addition of 1.5% olive oil increased total MP by 21.7% (dry basis) in 3 flushes. Copper (60 ppm) increased the daily productivity of the first flush (MP per day) by both reducing the time needed to harvest the crop and increasing the MP. However, the MP at the second and third flushes was reduced. When both supplements were combined, the MP at the first flush was 43% higher than with control treatment. No significant change in mushroom total triterpenoid content was observed by the addition of supplements to the substrate. An increase of 145-155% in the mushroom copper content was obtained by the addition of 60 ppm copper to the substrate. It is thus recommended to use substrate formulations containing both olive oil and copper (II) and harvest just the first flush.

Direct-writing of copper-based micropatterns on polymer substrates using femtosecond laser reduction of copper (II) oxide nanoparticles

NASA Astrophysics Data System (ADS)

Mizoshiri, Mizue; Ito, Yasuaki; Sakurai, Junpei; Hata, Seiichi

2017-04-01

Copper (Cu)-based micropatterns were fabricated on polymer substrates using femtosecond laser reduction of copper (II) oxide (CuO) nanoparticles. CuO nanoparticle solution, which consisted of CuO nanoparticles, ethylene glycol as a reductant agent, and polyvinylpyrrolidone as a dispersant, was spin-coated on poly(dimethylsiloxane) (PDMS) substrates and was irradiated by focused femtosecond laser pulses to fabricate Cu-based micropatterns. When the laser pulses were raster-scanned onto the solution, CuO nanoparticles were reduced and sintered. Cu-rich and copper (I)-oxide (Cu2O)-rich micropatterns were formed at laser scanning speeds of 15 mm/s and 0.5 mm/s, respectively, and at a pulse energy of 0.54 nJ. Cu-rich electrically conductive micropatterns were obtained without significant damages on the substrates. On the other hand, Cu2O-rich micropatterns exhibited no electrical conductivity, indicating that microcracks were generated on the micropatterns by thermal expansion and shrinking of the substrates. We demonstrated a direct-writing of Cu-rich micro-temperature sensors on PDMS substrates using the foregoing laser irradiation condition. The resistance of the fabricated sensors increased with increasing temperature, which is consistent with that of Cu. This direct-writing technique is useful for fabricating Cu-polymer composite microstructures.

Effect of the type of metal on the electrical conductivity and thermal properties of metal complexes: The relation between ionic radius of metal complexes and electrical conductivity

NASA Astrophysics Data System (ADS)

Morgan, Sh. M.; El-Ghamaz, N. A.; Diab, M. A.

2018-05-01

Co(II) complexes (1-4) and Ni(II) complexes (5-8) were prepared and characterized by elemental analysis, IR spectra and thermal analysis data. Thermal decomposition of all complexes was discussed using thermogravimetric analysis. The dielectric properties and alternating current conductivity were investigated in the frequency range 0.1-100 kHz and temperature range 300-660 K. The thermal activation energies of electrical conductivity (ΔE1 and ΔE2) values for complexes were calculated and discussed. The values of ΔE1 and ΔE2 for complexes (1-8) were found to decrease with increasing the frequency. Ac electrical conductivity (σac) values increases with increasing temperatures and the values of σac for Co(II) complexes are greater than Ni(II) complexes. Co(II) complexes showed a higher conductivity than other Ni(II) complexes due to the higher crystallinity as confirmed by X-ray diffraction analysis.

The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate

DOE PAGES

Poudel, Suresh; Giannone, Richard J.; Basen, Mirko; ...

2018-03-23

Background: Caldicellulosiruptor bescii is a thermophilic cellulolytic bacterium that efficiently deconstructs lignocellulosic biomass into sugars, which subsequently can be fermented into alcohols, such as ethanol, and other products. Deconstruction of complex substrates by C. bescii involves a myriad of highly abundant, substrate-specific extracellular solute binding proteins (ESBPs) and carbohydrate-active enzymes (CAZymes) containing carbohydrate-binding modules (CBMs). Mass spectrometry-based proteomics was employed to investigate how these substrate recognition proteins and enzymes vary as a function of lignocellulosic substrates.Results:Proteomic analysis revealed several key extracellular proteins that respond specifically to either C5 or C6 mono- and polysaccharides. These include proteins of unknown functions (PUFs),more » ESBPs, and CAZymes. ESBPs that were previously shown to interact more efficiently with hemicellulose and pectin were detected in high abundance during growth on complex C5 substrates, such as switchgrass and xylan. Some proteins, such as Athe_0614 and Athe_2368, whose functions are not well defined were predicted to be involved in xylan utilization and ABC transport and were significantly more abundant in complex and C5 substrates, respectively. The proteins encoded by the entire glucan degradation locus (GDL; Athe_1857, 1859, 1860, 1865, 1867, and 1866) were highly abundant under all growth conditions, particularly when C. bescii was grown on cellobiose, switchgrass, or xylan. In contrast, the glycoside hydrolases Athe_0609 (Pullulanase) and 0610, which both possess CBM20 and a starch binding domain, appear preferential to C5/complex substrate deconstruction. Some PUFs, such as Athe_2463 and 2464, were detected as highly abundant when grown on C5 substrates (xylan and xylose), also suggesting C5-substrate specificity. In conclusion, this study reveals the protein membership of the C. bescii secretome and demonstrates its plasticity based on the complexity (mono-/disaccharides vs. polysaccharides) and type of carbon (C5 vs. C6) available to the microorganism. The presence or increased abundance of extracellular proteins as a response to specific substrates helps to further elucidate C. bescii’s utilization and conversion of lignocellulosic biomass to biofuel and other valuable products. This includes improved characterization of extracellular proteins that lack discrete functional roles and are poorly/not annotated.« less

The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poudel, Suresh; Giannone, Richard J.; Basen, Mirko

Background: Caldicellulosiruptor bescii is a thermophilic cellulolytic bacterium that efficiently deconstructs lignocellulosic biomass into sugars, which subsequently can be fermented into alcohols, such as ethanol, and other products. Deconstruction of complex substrates by C. bescii involves a myriad of highly abundant, substrate-specific extracellular solute binding proteins (ESBPs) and carbohydrate-active enzymes (CAZymes) containing carbohydrate-binding modules (CBMs). Mass spectrometry-based proteomics was employed to investigate how these substrate recognition proteins and enzymes vary as a function of lignocellulosic substrates.Results:Proteomic analysis revealed several key extracellular proteins that respond specifically to either C5 or C6 mono- and polysaccharides. These include proteins of unknown functions (PUFs),more » ESBPs, and CAZymes. ESBPs that were previously shown to interact more efficiently with hemicellulose and pectin were detected in high abundance during growth on complex C5 substrates, such as switchgrass and xylan. Some proteins, such as Athe_0614 and Athe_2368, whose functions are not well defined were predicted to be involved in xylan utilization and ABC transport and were significantly more abundant in complex and C5 substrates, respectively. The proteins encoded by the entire glucan degradation locus (GDL; Athe_1857, 1859, 1860, 1865, 1867, and 1866) were highly abundant under all growth conditions, particularly when C. bescii was grown on cellobiose, switchgrass, or xylan. In contrast, the glycoside hydrolases Athe_0609 (Pullulanase) and 0610, which both possess CBM20 and a starch binding domain, appear preferential to C5/complex substrate deconstruction. Some PUFs, such as Athe_2463 and 2464, were detected as highly abundant when grown on C5 substrates (xylan and xylose), also suggesting C5-substrate specificity. In conclusion, this study reveals the protein membership of the C. bescii secretome and demonstrates its plasticity based on the complexity (mono-/disaccharides vs. polysaccharides) and type of carbon (C5 vs. C6) available to the microorganism. The presence or increased abundance of extracellular proteins as a response to specific substrates helps to further elucidate C. bescii’s utilization and conversion of lignocellulosic biomass to biofuel and other valuable products. This includes improved characterization of extracellular proteins that lack discrete functional roles and are poorly/not annotated.« less

The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate.

PubMed

Poudel, Suresh; Giannone, Richard J; Basen, Mirko; Nookaew, Intawat; Poole, Farris L; Kelly, Robert M; Adams, Michael W W; Hettich, Robert L

2018-01-01

Caldicellulosiruptor bescii is a thermophilic cellulolytic bacterium that efficiently deconstructs lignocellulosic biomass into sugars, which subsequently can be fermented into alcohols, such as ethanol, and other products. Deconstruction of complex substrates by C. bescii involves a myriad of highly abundant, substrate-specific extracellular solute binding proteins (ESBPs) and carbohydrate-active enzymes (CAZymes) containing carbohydrate-binding modules (CBMs). Mass spectrometry-based proteomics was employed to investigate how these substrate recognition proteins and enzymes vary as a function of lignocellulosic substrates. Proteomic analysis revealed several key extracellular proteins that respond specifically to either C5 or C6 mono- and polysaccharides. These include proteins of unknown functions (PUFs), ESBPs, and CAZymes. ESBPs that were previously shown to interact more efficiently with hemicellulose and pectin were detected in high abundance during growth on complex C5 substrates, such as switchgrass and xylan. Some proteins, such as Athe_0614 and Athe_2368, whose functions are not well defined were predicted to be involved in xylan utilization and ABC transport and were significantly more abundant in complex and C5 substrates, respectively. The proteins encoded by the entire glucan degradation locus (GDL; Athe_1857, 1859, 1860, 1865, 1867, and 1866) were highly abundant under all growth conditions, particularly when C. bescii was grown on cellobiose, switchgrass, or xylan. In contrast, the glycoside hydrolases Athe_0609 (Pullulanase) and 0610, which both possess CBM20 and a starch binding domain, appear preferential to C5/complex substrate deconstruction. Some PUFs, such as Athe_2463 and 2464, were detected as highly abundant when grown on C5 substrates (xylan and xylose), also suggesting C5-substrate specificity. This study reveals the protein membership of the C. bescii secretome and demonstrates its plasticity based on the complexity (mono-/disaccharides vs. polysaccharides) and type of carbon (C5 vs. C6) available to the microorganism. The presence or increased abundance of extracellular proteins as a response to specific substrates helps to further elucidate C. bescii 's utilization and conversion of lignocellulosic biomass to biofuel and other valuable products. This includes improved characterization of extracellular proteins that lack discrete functional roles and are poorly/not annotated.

Substrate-specific regulation of ubiquitination by the anaphase-promoting complex

PubMed Central

Song, Ling

2011-01-01

By orchestrating the sequential degradation of a large number of cell cycle regulators, the ubiquitin ligase anaphase-promoting complex (APC/C) is essential for proliferation in all eukaryotes. The correct timing of APC/C-dependent substrate degradation, a critical feature of progression through mitosis, was long known to be controlled by mechanisms targeting the core APC/C-machinery. Recent experiments, however have revealed an important contribution of substrate-specific regulation of the APC/C to achieve accurate cell division. In this perspective, we describe different mechanisms of substrate-specific APC/C-regulation and discuss their importance for cell division. PMID:21191176

Synthesis, spectroscopic characterization, in-vitro antibacterial and antiproliferative activities of some metal(II) complexes of 3,4-dihydronaphthalen-1(2H)-one Schiff base

PubMed Central

Osowole, Aderoju Amoke

2012-01-01

The Schiff base, 3-hydroxy-4-{[4-(methylsulfanyl)phenyl]imino}-3,4-dihydronaphthalen-1(2H)-one, and its Mn(II), Co(II), Ni(II), Cu(II), Zn(II) and Pd(II) complexes have been synthesized and characterized by microanalysis, conductance, 1H NMR, infrared and electronic spectral measurements. The ligand exists in the ketoimine form in chloroform, and in the enolimine form in the solid state, as shown by 1H NMR and IR spectroscopies. The ligand coordinates to the metal ions in the ratio 1:1, using NO chromophores forming complexes of the type [MLNO3]H2O, with the exception of the Zn(II) and Pd(II) complexes. Electronic measurements are indicative of a four coordinate square-planar geometry for all the complexes, except for the Cu(II) and Zn(II) complexes which assume a tetrahedral geometry. None is an electrolyte in nitromethane. The ligand and the metal complexes are air-stable, but decomposed on heating at 120 °C and in the range 150-156 °C respectively. The antibacterial studies reveal that the Co(II) and the Cu(II) complexes exhibit broad-spectrum activity against Proteus mirabilis, Escherichia coli and Staphylococcus aureus with inhibitory zones range of 14.0-22.0 and 13.0-25.0 mm respectively. The antiproliferative studies show that the Zn(II) complex has the best in-vitro anticancer activity against both HT-29 (colon) carcinoma and MCF-7 (human breast) adenocarcinoma with IC50 values of 6.46 µm and 3.19 µm, which exceeds the activity of Cis-platin by 8 % and 63 % respectively. PMID:27350773

Neuroprotective Effects and Mechanisms of Curcumin-Cu(II) and -Zn(II) Complexes Systems and Their Pharmacological Implications.

PubMed

Yan, Fa-Shun; Sun, Jian-Long; Xie, Wen-Hai; Shen, Liang; Ji, Hong-Fang

2017-12-28

Alzheimer's disease (AD) is the main form of dementia and has a steadily increasing prevalence. As both oxidative stress and metal homeostasis are involved in the pathogenesis of AD, it would be interesting to develop a dual function agent, targeting the two factors. Curcumin, a natural compound isolated from the rhizome of Curcuma longa , is an antioxidant and can also chelate metal ions. Whether the complexes of curcumin with metal ions possess neuroprotective effects has not been evaluated. Therefore, the present study was designed to investigate the protective effects of the complexes of curcumin with Cu(II) or Zn(II) on hydrogen peroxide (H₂O₂)-induced injury and the underlying molecular mechanisms. The use of rat pheochromocytoma (PC12) cells, a widely used neuronal cell model system, was adopted. It was revealed that curcumin-Cu(II) complexes systems possessed enhanced O₂ ·- -scavenging activities compared to unchelated curcumin. In comparison with unchelated curcumin, the protective effects of curcumin-Cu(II) complexes systems were stronger than curcumin-Zn(II) system. Curcumin-Cu(II) or -Zn(II) complexes systems significantly enhanced the superoxide dismutase, catalase, and glutathione peroxidase activities and attenuated the increase of malondialdehyde levels and caspase-3 and caspase-9 activities, in a dose-dependent manner. The curcumin-Cu(II) complex system with a 2:1 ratio exhibited the most significant effect. Further mechanistic study demonstrated that curcumin-Cu(II) or -Zn(II) complexes systems inhibited cell apoptosis via downregulating the nuclear factor κB (NF-κB) pathway and upregulating Bcl-2/Bax pathway. In summary, the present study found that curcumin-Cu(II) or -Zn(II) complexes systems, especially the former, possess significant neuroprotective effects, which indicates the potential advantage of curcumin as a promising agent against AD and deserves further study.

Plasmonic Paper as a Novel Chem/Bio Detection Platform

NASA Astrophysics Data System (ADS)

Tian, Limei

The time varying electric field of electromagnetic (EM) radiation causes oscillation of conduction electrons of metal nanoparticles. The resonance of such oscillation, termed localized surface plasmon resonance (LSPR), falls into the visible spectral region for noble metals such as gold, silver and copper. LSPR of metal nanostructures is sensitive to numerous factors such as composition, size, shape, dielectric properties of surrounding medium, and proximity to other nanostructures (plasmon coupling). The sensitivity of LSPR to the refractive index of surrounding medium renders it an attractive platform for chemical and biological sensing. When the excitation light is in resonance with the plasmon frequency of the metal nanoparticle, it radiates a characteristic dipolar radiation causing a characteristic spatial distribution in which certain areas show higher EM field intensity, which is manifested as electromagnetic field enhancement. Surface enhanced Raman scattering (SERS) involves dramatic enhancement of the intensity of the Raman scattering from the analyte adsorbed on or in proximity to a nanostructured metal surface exhibiting such strong EM field enhancement. Both LSPR and SERS have been widely investigated for highly sensitive and label-free chemical & biological sensors. Most of the SERS/LSPR sensors demonstrated so far rely on rigid planar substrates (e.g., glass, silicon) owing to the well-established lithographic approaches, which are routinely employed for either fabrication or assembly of plasmonic nanotransducers. In many cases, their rigid nature results in low conformal contact with the sample and hence poor sample collection efficiency. We hypothesized that paper substrates are an excellent alternative to conventional rigid substrates to significantly improve the (multi-)functionality of LSPR/SERS substrates, dramatically simplify the fabrication procedures and lower the cost. The choice of paper substrates for the implementation of SERS/LSPR sensors is rationalized by numerous advantages such as (i) high specific surface area resulting in large dynamic range (ii) excellent wicking properties for rapid uptake and transport of analytes to test domains (iii) compatibility with conventional printing approaches, enabling multi-analyte plasmonic sensors (iv) significant reduction in cost (v) smaller sample volume requirement (vi) easy disposability. In this work, we have introduced novel SERS and LSPR substrates based on conventional filter paper decorated with plasmonic nanostructures, called plasmonic paper. A flexible SERS substrate based on common filter paper adsorbed with gold nanostructures allows conformal contact with real-world surfaces, enabling rapid trace detection. To realize multifunctional SERS substrates, paper substrates were cut into star-shaped structures and the fingers were differentially functionalized with polyelectrolytes that allows separation and pre-concentration of different components of a complex sample in a small surface area by taking advantage of the properties of cellulose paper and shape-enhanced capillary effect. Plasmonic paper can also serve as a novel LSPR biosensing platform by decorating the paper substrate with biofunctionalized nanostructures. Furthermore, calligraphy approach was employed to create well-isolated test domains on paper substrates using functionalized plasmonic nanostructures as ink for multiplexed chemical sensing and label-free biosensing. These plasmonic paper substrates exhibit excellent sample collection efficiency and do not require complex fabrication processes. This class of substrates is expected to have applications not only to first responders and military personal but also to several areas of medical, food analysis, and environmental research.

The facile synthesis of a chitosan Cu(II) complex by solution plasma process and evaluation of their antioxidant activities.

PubMed

Ma, Fengming; Li, Pu; Zhang, Baiqing; Wang, Zhenyu

2017-10-01

Synthesis of chitosan-Cu(II) complex by solution plasma process (SPP) irradiation was investigated. The effects of the distance between the electrodes, initial Cu(II) concentration, and initial pH on the Cu(II) adsorption capacity were evaluated. The results showed that narrower distance between the electrodes, higher initial Cu(II) concentration and higher initial pH (at pH<6) were favourable for the adsorption capacity of Cu(II). Characterization of the chitosan-Cu(II) complex by ultraviolet-visible (UV-vis), fourier transform infrared (FT-IR) and electron spin resonance (ESR) spectroscopy revealed that the main structure of chitosan was not changed after irradiation. Thermogravimetry (TG) analysis indicated that Cu(II) ions were well incorporated into the chitosan. The antioxidant activity of the chitosan-Cu(II) complex was evaluated by DPPH, ABTS, and reducing power assays. The chitosan-Cu(II) complex exhibited greater antioxidant activity than the original chitosan. Thus, SPP could be used for preparation of chitosan-Cu(II) complexes. Copyright © 2017. Published by Elsevier B.V.

Spectroscopic evaluation of Co(II), Ni(II) and Cu(II) complexes derived from thiosemicarbazone and semicarbazone

NASA Astrophysics Data System (ADS)

Chandra, Sulekh; Kumar, Anil

2007-12-01

Co(II), Ni(II) and Cu(II) complexes were synthesized with thiosemicarbazone (L 1) and semicarbazone (L 2) derived from 2-acetyl furan. These complexes were characterized by elemental analysis, molar conductance, magnetic moment, mass, IR, electronic and EPR spectral studies. The molar conductance measurement of the complexes in DMSO corresponds to non-electrolytic nature. All the complexes are of high-spin type. On the basis of different spectral studies six coordinated geometry may be assigned for all the complexes except Co(L) 2(SO 4) and Cu(L) 2(SO 4) [where L = L 1 and L 2] which are of five coordinated square pyramidal geometry.

Self-organized pattern formation at organic-inorganic interfaces during deposition: Experiment versus modeling

NASA Astrophysics Data System (ADS)

Szillat, F.; Mayr, S. G.

2011-09-01

Self-organized pattern formation during physical vapor deposition of organic materials onto rough inorganic substrates is characterized by a complex morphological evolution as a function of film thickness. We employ a combined experimental-theoretical study using atomic force microscopy and numerically solved continuum rate equations to address morphological evolution in the model system: poly(bisphenol A carbonate) on polycrystalline Cu. As the key ingredients for pattern formation, (i) curvature and interface potential driven surface diffusion, (ii) deposition noise, and (iii) interface boundary effects are identified. Good agreement of experiments and theory, fitting only the Hamaker constant and diffusivity within narrow physical parameter windows, corroborates the underlying physics and paves the way for computer-assisted interface engineering.

Synthesis, characterization and anti-microbial evaluation of Cu(II), Ni(II), Pt(II) and Pd(II) sulfonylhydrazone complexes; 2D-QSAR analysis of Ni(II) complexes of sulfonylhydrazone derivatives

NASA Astrophysics Data System (ADS)

Özbek, Neslihan; Alyar, Saliha; Alyar, Hamit; Şahin, Ertan; Karacan, Nurcan

2013-05-01

Copper(II), nickel(II), platinum(II) and palladium(II) complexes with 2-hydroxy-1-naphthaldehyde-N-methylpropanesulfonylhydrazone (nafpsmh) derived from propanesulfonic acid-1-methylhydrazide (psmh) were synthesized, their structure were identified, and antimicrobial activity of the compounds was screened against three Gram-positive and three Gram-negative bacteria. The results of antimicrobial studies indicate that Pt(II) and Pd(II) complexes showed the most activity against all bacteria. The crystal structure of 2-hydroxy-1-naphthaldehyde-N-methylpropanesulfonylhydrazone (nafpsmh) was also investigated by X-ray analysis. A series of Ni(II) sulfonyl hydrazone complexes (1-33) was synthesized and tested in vitro against Escherichia coli and Staphylococcus aureus. Their antimicrobial activities were used in the QSAR analysis. Four-parameter QSAR models revealed that nucleophilic reaction index for Ni and O atoms, and HOMO-LUMO energy gap play key roles in the antimicrobial activity.

Coexistence of group I and group II chaperonins in the archaeon Methanosarcina mazei.

PubMed

Klunker, Daniel; Haas, Bernd; Hirtreiter, Angela; Figueiredo, Luis; Naylor, Dean J; Pfeifer, Günter; Müller, Volker; Deppenmeier, Uwe; Gottschalk, Gerhard; Hartl, F Ulrich; Hayer-Hartl, Manajit

2003-08-29

Two distantly related classes of cylindrical chaperonin complexes assist in the folding of newly synthesized and stress-denatured proteins in an ATP-dependent manner. Group I chaperonins are thought to be restricted to the cytosol of bacteria and to mitochondria and chloroplasts, whereas the group II chaperonins are found in the archaeal and eukaryotic cytosol. Here we show that members of the archaeal genus Methanosarcina co-express both the complete group I (GroEL/GroES) and group II (thermosome/prefoldin) chaperonin systems in their cytosol. These mesophilic archaea have acquired between 20 and 35% of their genes by lateral gene transfer from bacteria. In Methanosarcina mazei Gö1, both chaperonins are similarly abundant and are moderately induced under heat stress. The M. mazei GroEL/GroES proteins have the structural features of their bacterial counterparts. The thermosome contains three paralogous subunits, alpha, beta, and gamma, which assemble preferentially at a molar ratio of 2:1:1. As shown in vitro, the assembly reaction is dependent on ATP/Mg2+ or ADP/Mg2+ and the regulatory role of the beta subunit. The co-existence of both chaperonin systems in the same cellular compartment suggests the Methanosarcina species as useful model systems in studying the differential substrate specificity of the group I and II chaperonins and in elucidating how newly synthesized proteins are sorted from the ribosome to the proper chaperonin for folding.

Spectroscopic and mycological studies of Co(II), Ni(II) and Cu(II) complexes with 4-aminoantipyrine derivative

NASA Astrophysics Data System (ADS)

Sharma, Amit Kumar; Chandra, Sulekh

2011-10-01

Complexes of the type [M(L)X 2], where M = Co(II), Ni(II) and Cu(II), have been synthesized with novel NO-donor Schiff's base ligand, 1,4-diformylpiperazine bis(4-imino-2,3-dimethyl-1-phenyl-3-pyrazolin-5-one) which is obtained by the acid catalyzed condensation of 1,4-diformylpiperazine with 4-aminoantipyrine. The elemental analyses, molar conductance measurements, magnetic susceptibility measurements, IR, UV, NMR, mass and EPR studies of the compounds led to the conclusion that the ligand acts as tetradentate chelate. The Schiff's base ligand forms hexacoordinated complexes having octahedral geometry for Ni(II) and tetragonal geometry for Co(II) and Cu(II) complexes. The mycological studies of the compounds were examined against the several opportunistic pathogens, i.e., Alternaria brassicae, Aspergillus niger and Fusarium oxysporum. The Cu(II) complexes were found to have most fungicidal behavior.

Synthesis, spectroscopic, fluorescence properties and biological evaluation of novel Pd(II) and Cd(II) complexes of NOON tetradentate Schiff bases.

PubMed

Ali, Omyma A M

2014-01-01

The solid complexes of Pd(II) and Cd(II) with N,N/bis(salicylaldehyde)4,5-dimethyl-1,2-phenylenediamine (H2L(1)), and N,N/bis(salicylaldehyde)4,5-dichloro-1,2-phenylenediamine (H2L(2)) have been synthesized and characterized by several techniques using elemental analysis (CHN), FT-IR, (1)H NMR, UV-Vis spectra and thermal analysis. Elemental analysis data proved 1:1 stoichiometry for the reported complexes while spectroscopic data indicated square planar and octahedral geometries for Pd(II) and Cd(II) complexes, respectively. The prepared ligands, Pd(II) and Cd(II) complexes exhibited intraligand (π-π(∗)) fluorescence and can potentially serve as photoactive materials. Thermal behavior of the complexes was studied and kinetic parameters were determined by Coats-Redfern method. Both the ligands and their complexes have been screened for antimicrobial activities. Copyright © 2013 Elsevier B.V. All rights reserved.

Structural basis of peptide recognition by the angiotensin-1 converting enzyme homologue AnCE from Drosophila melanogaster

PubMed Central

Akif, Mohd; Masuyer, Geoffrey; Bingham, Richard J; Sturrock, Edward D; Isaac, R Elwyn; Acharya, K Ravi

2012-01-01

Human somatic angiotensin-1 converting enzyme (ACE) is a zinc-dependent exopeptidase, that catalyses the conversion of the decapeptide angiotensin I to the octapeptide angiotensin II, by removing a C-terminal dipeptide. It is the principal component of the renin-angiotensin–aldosterone system that regulates blood pressure. Hence it is an important therapeutic target for the treatment of hypertension and cardiovascular disorders. Here, we report the structures of an ACE homologue from Drosophila melanogaster (AnCE; a proven structural model for the more complex human ACE) co-crystallized with mammalian peptide substrates (bradykinin, Thr6–bradykinin, angiotensin I and a snake venom peptide inhibitor, bradykinin-potentiating peptide-b). The structures determined at 2-Å resolution illustrate that both angiotensin II (the cleaved product of angiotensin I by AnCE) and bradykinin-potentiating peptide-b bind in an analogous fashion at the active site of AnCE, but also exhibit significant differences. In addition, the binding of Arg–Pro–Pro, the cleavage product of bradykinin and Thr6– bradykinin, provides additional detail of the general peptide binding in AnCE. Thus the new structures of AnCE complexes presented here improves our understanding of the binding of peptides and the mechanism by which peptides inhibit this family of enzymes. Database The atomic coordinates and structure factors for AnCE–Ang II (code 4AA1), AnCE–BPPb (code 4AA2), AnCE–BK (code 4ASQ) and AnCE–Thr6–BK (code 4ASR) complexes have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/) Structured digital abstract AnCE cleaves Ang I by enzymatic study (View interaction) Bradykinin and AnCE bind by x-ray crystallography (View interaction) BPP and AnCE bind by x-ray crystallography (View interaction) AnCE cleaves Bradykinin by enzymatic study (View interaction) Ang II and AnCE bind by x-ray crystallography (View interaction) PMID:23082758

Synthesis, characterization, antimicrobial activity and DFT studies of 2-(pyrimidin-2-ylamino)naphthalene-1,4-dione and its Mn(II), Co(II), Ni(II) and Zn(II) complexes

NASA Astrophysics Data System (ADS)

Chioma, Festus; Ekennia, Anthony C.; Ibeji, Collins U.; Okafor, Sunday N.; Onwudiwe, Damian C.; Osowole, Aderoju A.; Ujam, Oguejiofo T.

2018-07-01

A pyrimidine-based ligand, 2-(pyrimidin-2-ylamino)naphthalene-1,4-dione (L), has been synthesized by the reaction of 2-aminopyrimidine with 2-hydroxy-1,4-napthoquinone. Reaction of the ligand with Ni(II), Co(II), Mn(II) and Zn(II) acetate gave the corresponding metal complexes which were characterized by spectroscopic techniques, (infrared, electronic), elemental analysis, room-temperature magnetometry, conductance measurements and thermogravimetry-differential scanning calorimetry (TG-DSC) analyses. The room-temperature magnetic data and electronic spectral measurements of the complexes gave evidence of 4-coordinate square planar/tetrahedral geometry. The thermal analyses values obtained indicated the monohydrate complexes. The antimicrobial screening of the compounds showed mild to very good results. The Mn(II) complex showed the best result within in the range of 11.5-29 mm. The electronic, structural and spectroscopic properties of the complexes were further discussed using density functional theory. Molecular docking studies showed significant binding affinity with the drug targets and the metal complexes have potentials to be used as drugs.

SOLVENT-BASED TO WATERBASED ADHESIVE-COATED SUBSTRATE RETROFIT - VOLUME II: PROCESS OVERVIEW

EPA Science Inventory

This volume presents initial results of a study to identify the issues and barriers associated with retrofitting existing solvent-based equipment to accept waterbased adhesives as part of an EPA effort to improve equipment cleaning in the coated and laminated substrate manufactur...

Insights into the Specificity of Lysine Acetyltransferases

DOE PAGES

Tucker, Alex C.; Taylor, Keenan C.; Rank, Katherine C.; ...

2014-11-07

Reversible lysine acetylation by protein acetyltransferases is a conserved regulatory mechanism that controls diverse cellular pathways. Gcn5-related N-acetyltransferases (GNATs), named after their founding member, are found in all domains of life. GNATs are known for their role as histone acetyltransferases, but non-histone bacterial protein acetytransferases have been identified. Only structures of GNAT complexes with short histone peptide substrates are available in databases. Given the biological importance of this modification and the abundance of lysine in polypeptides, how specificity is attained for larger protein substrates is central to understanding acetyl-lysine-regulated networks. In this paper, we report the structure of a GNATmore » in complex with a globular protein substrate solved to 1.9 Å. GNAT binds the protein substrate with extensive surface interactions distinct from those reported for GNAT-peptide complexes. Finally, our data reveal determinants needed for the recognition of a protein substrate and provide insight into the specificity of GNATs.« less

Stochastic dynamics and mechanosensitivity of myosin II minifilaments

NASA Astrophysics Data System (ADS)

Albert, Philipp J.; Erdmann, Thorsten; Schwarz, Ulrich S.

2014-09-01

Tissue cells are in a state of permanent mechanical tension that is maintained mainly by myosin II minifilaments, which are bipolar assemblies of tens of myosin II molecular motors contracting actin networks and bundles. Here we introduce a stochastic model for myosin II minifilaments as two small myosin II motor ensembles engaging in a stochastic tug-of-war. Each of the two ensembles is described by the parallel cluster model that allows us to use exact stochastic simulations and at the same time to keep important molecular details of the myosin II cross-bridge cycle. Our simulation and analytical results reveal a strong dependence of myosin II minifilament dynamics on environmental stiffness that is reminiscent of the cellular response to substrate stiffness. For small stiffness, minifilaments form transient crosslinks exerting short spikes of force with negligible mean. For large stiffness, minifilaments form near permanent crosslinks exerting a mean force which hardly depends on environmental elasticity. This functional switch arises because dissociation after the power stroke is suppressed by force (catch bonding) and because ensembles can no longer perform the power stroke at large forces. Symmetric myosin II minifilaments perform a random walk with an effective diffusion constant which decreases with increasing ensemble size, as demonstrated for rigid substrates with an analytical treatment.

A Cyanobacterial Chlorophyll Synthase-HliD Complex Associates with the Ycf39 Protein and the YidC/Alb3 Insertase[W][OPEN

PubMed Central

Chidgey, Jack W.; Linhartová, Markéta; Komenda, Josef; Jackson, Philip J.; Dickman, Mark J.; Canniffe, Daniel P.; Koník, Peter; Pilný, Jan; Hunter, C. Neil; Sobotka, Roman

2014-01-01

Macromolecular membrane assemblies of chlorophyll-protein complexes efficiently harvest and trap light energy for photosynthesis. To investigate the delivery of chlorophylls to the newly synthesized photosystem apoproteins, a terminal enzyme of chlorophyll biosynthesis, chlorophyll synthase (ChlG), was tagged in the cyanobacterium Synechocystis PCC 6803 (Synechocystis) and used as bait in pull-down experiments. We retrieved an enzymatically active complex comprising ChlG and the high-light-inducible protein HliD, which associates with the Ycf39 protein, a putative assembly factor for photosystem II, and with the YidC/Alb3 insertase. 2D electrophoresis and immunoblotting also provided evidence for the presence of SecY and ribosome subunits. The isolated complex contained chlorophyll, chlorophyllide, and carotenoid pigments. Deletion of hliD elevated the level of the ChlG substrate, chlorophyllide, more than 6-fold; HliD is apparently required for assembly of FLAG-ChlG into larger complexes with other proteins such as Ycf39. These data reveal a link between chlorophyll biosynthesis and the Sec/YidC-dependent cotranslational insertion of nascent photosystem polypeptides into membranes. We expect that this close physical linkage coordinates the arrival of pigments and nascent apoproteins to produce photosynthetic pigment-protein complexes with minimal risk of accumulating phototoxic unbound chlorophylls. PMID:24681617

Synthesis, characterization, thermal and biological evaluation of Cu (II), Co (II) and Ni (II) complexes of azo dye ligand containing sulfamethaxazole moiety

NASA Astrophysics Data System (ADS)

Mallikarjuna, N. M.; Keshavayya, J.; Maliyappa, M. R.; Shoukat Ali, R. A.; Venkatesh, Talavara

2018-08-01

A novel bioactive Cu (II), Co (II) and Ni (II) complexes of the azo dye ligand (L) derived from sulfamethoxazole were synthesized. The structures of the newly synthesized compounds were characterized by elemental analysis, molar conductance, magnetic susceptibility, FTIR, UV-visible, 1H NMR, mass, thermal and powder XRD spectral techniques. Molar conductivity measurements in DMSO solution confirmed the non-electrolytic nature of the complexes. All the synthesized metal complexes were found to be monomeric and showed square planar geometry except the Co (II) complex which has six coordinate, octahedral environment. The metal complexes have exhibited potential growth inhibitory effect against tested bacterial strains as compared to the free ligand. The ligand and complexes have also shown significant antioxidant and Calf Thymus DNA cleavage activities. Further, the in silico molecular docking studies were performed to predict the possible binding sites of the ligand (L) and its metal complexes with target receptor Glu-6P.